KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features

Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of...

Full description

Saved in:

Bibliographic Details
Published in	PLoS pathogens Vol. 10; no. 1; p. e1003847
Main Authors	Arias, Carolina, Weisburd, Ben, Stern-Ginossar, Noam, Mercier, Alexandre, Madrid, Alexis S., Bellare, Priya, Holdorf, Meghan, Weissman, Jonathan S., Ganem, Don
Format	Journal Article
Language	English
Published	United States Public Library of Science 01.01.2014 Public Library of Science (PLoS)
Subjects	Architecture Biology Cell Line Deoxyribonucleic acid DNA Editing Gene expression Gene Expression Regulation, Viral - genetics Genetic aspects Genetic research Genetic transcription Genome, Viral Genomes Genomics Health aspects Herpesvirus 8, Human - genetics High-Throughput Nucleotide Sequencing Human herpesvirus 8 Humans Infections Kaposis sarcoma Messenger RNA Microbiological research Open Reading Frames Reading RNA sequencing RNA, Untranslated - genetics RNA, Viral - genetics United States
Online Access	Get full text

Cover

Loading…

Abstract	Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus.
AbstractList	Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus. Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus. Kaposi's sarcoma-associated herpesvirus (KSHV) is a cancer-causing agent in immunocompromised patients that establishes long-lasting infections in its hosts. Initially described in 1994 and extensively studied ever since, KSHV molecular biology is understood in broad outline, but many detailed questions are still to be resolved. After almost two decades, specific aspects pertaining to the organization of the KSHV genome as well as the fate of the viral transcripts during the productive stages of infection remain unexplored. Here we use a systematic genome-wide approach to investigate changes in gene and protein expression during the productive stage of infection known as the lytic cycle. We found that the viral genome has a large coding capacity, capable of generating at least 45% more products than initially anticipated by bioinformatic analyses alone, and that it uses multiple strategies to expand its coding capacity well beyond what is determined solely by the DNA sequence of its genome. We also provide an expanded and highly detailed annotation of known and new genomic features in KSHV. We have termed this new architectural and functional annotation KSHV 2.0. Our results indicate that viral genomes are more complex than anticipated, and that they are subject to tight mechanisms of regulation to ensure correct gene expression. Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus. Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus.Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus.
Audience	Academic
Author	Bellare, Priya Weisburd, Ben Mercier, Alexandre Holdorf, Meghan Madrid, Alexis S. Arias, Carolina Weissman, Jonathan S. Stern-Ginossar, Noam Ganem, Don
AuthorAffiliation	3 Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America University of North Carolina at Chapel Hill, United States of America 2 Novartis Vaccines and Diagnostics, Bioinformatics, Emeryville, California, United States of America 1 Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America
AuthorAffiliation_xml	– name: 1 Novartis Institute for Biomedical Research, Department of Infectious Diseases, Emeryville, California, United States of America – name: 2 Novartis Vaccines and Diagnostics, Bioinformatics, Emeryville, California, United States of America – name: University of North Carolina at Chapel Hill, United States of America – name: 3 Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
Author_xml	– sequence: 1 givenname: Carolina surname: Arias fullname: Arias, Carolina – sequence: 2 givenname: Ben surname: Weisburd fullname: Weisburd, Ben – sequence: 3 givenname: Noam surname: Stern-Ginossar fullname: Stern-Ginossar, Noam – sequence: 4 givenname: Alexandre surname: Mercier fullname: Mercier, Alexandre – sequence: 5 givenname: Alexis S. surname: Madrid fullname: Madrid, Alexis S. – sequence: 6 givenname: Priya surname: Bellare fullname: Bellare, Priya – sequence: 7 givenname: Meghan surname: Holdorf fullname: Holdorf, Meghan – sequence: 8 givenname: Jonathan S. surname: Weissman fullname: Weissman, Jonathan S. – sequence: 9 givenname: Don surname: Ganem fullname: Ganem, Don
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/24453964$$D View this record in MEDLINE/PubMed
BookMark	eNqVk9tu1DAQhiNURA_wBggscQFc7BLHdg69QFqt6EGtitSl3Fqz9mTrKmsHO1nBI_GWOM0WdRFCQrlINP7-P-M5HCZ71llMkpc0nVJW0A93rvcWmmnbQjelacpKXjxJDqgQbFKwgu89-t5PDkO4S1NOGc2fJfsZ54JVOT9Ifl4szr6SbJoekxmZu3Xr8RZtMBskM2tdB51xlriadLdILqB1wbwNZAFeuTVMZiE4ZaBDTc7Qtxg2xveBnKJ1ayQ3wdgVucLv3SRG0I9eC_zWo1XD0TVuEJpArtwGm1FlFAGryUlv1UBDQ04Qut5jeJ48rSOML7bvo-Tm5NOX-dnk8vPp-Xx2OVE55cWkoFrzZcogR02BYwF1XZZYpelSFSrP00pRAaIqsBKaKS10mWOlVV6LGhmr2FHyevRtGxfktspBUl6VrMqKKo_E-UhoB3ey9WYN_od0YOR9wPmVBN8Z1aAsY5F5rpTIdM5BpQAZqEyDEsuKZSCi18ft3_rlGrVC23lodkx3T6y5lSu3kayseJbRaPBua-BdLGzo5NoEhU0DFl1_n3eWV0KI4WZvRnQFMTVjaxcd1YDLGct5KTgTw-2mf6HiozF2J85gbWJ8R_B-RxCZLvZ8BX0I8nxx_R_s1S776nFpftfkYXgjcDwCyrsQPNZSmXFgY8amkTSVw6Y89FAOmyK3mxLF_A_xg_8_Zb8AIeMbTQ
CitedBy_id	crossref_primary_10_1016_j_trecan_2018_09_005 crossref_primary_10_1128_JVI_00908_17 crossref_primary_10_1371_journal_ppat_1008025 crossref_primary_10_1093_nar_gkw629 crossref_primary_10_1128_mBio_01568_20 crossref_primary_10_1371_journal_ppat_1007852 crossref_primary_10_2298_ABS230407016K crossref_primary_10_1093_gigascience_giab042 crossref_primary_10_1371_journal_ppat_1012081 crossref_primary_10_1016_j_coviro_2018_07_001 crossref_primary_10_1093_nar_gky129 crossref_primary_10_1371_journal_ppat_1007609 crossref_primary_10_1080_15476286_2017_1391442 crossref_primary_10_1101_cshperspect_a033001 crossref_primary_10_1146_annurev_virology_091919_072841 crossref_primary_10_3390_cancers12020358 crossref_primary_10_1172_JCI97053 crossref_primary_10_3390_ncrna5010006 crossref_primary_10_1016_j_micinf_2023_105268 crossref_primary_10_1128_JVI_00628_19 crossref_primary_10_1128_MCB_00399_21 crossref_primary_10_1038_s41598_019_38870_7 crossref_primary_10_1128_JVI_01300_19 crossref_primary_10_3390_ijms241914955 crossref_primary_10_3390_v12010017 crossref_primary_10_1128_JVI_02528_14 crossref_primary_10_1038_s44318_023_00019_8 crossref_primary_10_1371_journal_pone_0126439 crossref_primary_10_1371_journal_pbio_3001097 crossref_primary_10_1371_journal_ppat_1005305 crossref_primary_10_1016_j_pt_2016_03_005 crossref_primary_10_3390_v11080711 crossref_primary_10_1371_journal_ppat_1006995 crossref_primary_10_1038_s41467_023_35914_5 crossref_primary_10_1128_JVI_00274_15 crossref_primary_10_1038_s41467_021_25871_2 crossref_primary_10_3390_v12091024 crossref_primary_10_1038_s41467_023_37105_8 crossref_primary_10_1016_j_coviro_2014_04_004 crossref_primary_10_1371_journal_pone_0202513 crossref_primary_10_1038_s41592_024_02179_9 crossref_primary_10_3390_v13010118 crossref_primary_10_1128_JVI_00268_14 crossref_primary_10_7554_eLife_47261 crossref_primary_10_1016_j_isci_2023_106780 crossref_primary_10_1371_journal_ppat_1010797 crossref_primary_10_1073_pnas_1811728115 crossref_primary_10_1371_journal_ppat_1007389 crossref_primary_10_1371_journal_ppat_1010311 crossref_primary_10_3390_ncrna4040024 crossref_primary_10_3389_fmicb_2020_00850 crossref_primary_10_1128_JVI_00078_18 crossref_primary_10_1128_jvi_00565_22 crossref_primary_10_1002_jmv_70140 crossref_primary_10_1038_s41467_022_35268_4 crossref_primary_10_1002_jmv_28773 crossref_primary_10_1038_s41467_020_18718_9 crossref_primary_10_1016_j_jmb_2018_04_040 crossref_primary_10_1073_pnas_2212864120 crossref_primary_10_1080_15476286_2016_1212802 crossref_primary_10_3390_v17020177 crossref_primary_10_3389_fmicb_2020_604536 crossref_primary_10_1371_journal_ppat_1008221 crossref_primary_10_1371_journal_ppat_1008589 crossref_primary_10_1038_s41598_018_36433_w crossref_primary_10_1016_j_celrep_2020_108249 crossref_primary_10_1128_jvi_00475_23 crossref_primary_10_1111_1462_2920_12706 crossref_primary_10_1371_journal_ppat_1006844 crossref_primary_10_4236_ym_2021_52011 crossref_primary_10_29130_dubited_1212643 crossref_primary_10_3390_pathogens6030034 crossref_primary_10_1128_mBio_00823_18 crossref_primary_10_1128_JVI_00873_14 crossref_primary_10_1016_j_virusres_2019_03_024 crossref_primary_10_3389_fmicb_2022_840911 crossref_primary_10_1016_j_semcdb_2022_12_001 crossref_primary_10_1146_annurev_virology_100114_054854 crossref_primary_10_3390_v13050783 crossref_primary_10_1128_JVI_00630_19 crossref_primary_10_1146_annurev_virology_091919_065320 crossref_primary_10_1128_JVI_01342_18 crossref_primary_10_3390_pathogens6010011 crossref_primary_10_1371_journal_ppat_1005985 crossref_primary_10_1371_journal_ppat_1004652 crossref_primary_10_1038_s41467_024_54592_5 crossref_primary_10_7554_eLife_38667 crossref_primary_10_1371_journal_pone_0170914 crossref_primary_10_1080_21541248_2015_1093068 crossref_primary_10_1093_nar_gkac1190 crossref_primary_10_1371_journal_ppat_1008681 crossref_primary_10_1371_journal_ppat_1007596 crossref_primary_10_1128_JVI_02711_14 crossref_primary_10_3390_v6114165 crossref_primary_10_1371_journal_ppat_1006937 crossref_primary_10_1099_jgv_0_002053 crossref_primary_10_1002_pmic_201700255 crossref_primary_10_1128_jvi_00779_24 crossref_primary_10_1128_mBio_00071_19 crossref_primary_10_1007_s00705_018_3918_3 crossref_primary_10_1038_s41467_019_08734_9 crossref_primary_10_1128_JVI_02237_16 crossref_primary_10_1128_MRA_00851_20 crossref_primary_10_1038_s41467_020_17151_2 crossref_primary_10_1099_jgv_0_001528 crossref_primary_10_1101_gad_349276_121 crossref_primary_10_1371_journal_ppat_1007464 crossref_primary_10_1371_journal_ppat_1010992 crossref_primary_10_1146_annurev_virology_100114_054839 crossref_primary_10_3390_ijms252011268 crossref_primary_10_1128_JVI_02987_15 crossref_primary_10_1038_s44320_024_00075_0 crossref_primary_10_1128_JVI_02079_19 crossref_primary_10_1021_cr500255e crossref_primary_10_1093_nar_gkab215 crossref_primary_10_3390_v16121870 crossref_primary_10_1128_mBio_02907_21 crossref_primary_10_1016_j_gendis_2022_04_009 crossref_primary_10_1261_rna_078777_121 crossref_primary_10_3389_fmicb_2021_657036 crossref_primary_10_1128_mbio_03473_21 crossref_primary_10_3390_v15061381 crossref_primary_10_3390_v8040092 crossref_primary_10_3390_v7052542 crossref_primary_10_1093_infdis_jiy427 crossref_primary_10_1038_s41598_023_43344_y crossref_primary_10_1038_s44318_025_00398_0 crossref_primary_10_1016_j_virol_2024_110376 crossref_primary_10_1371_journal_ppat_1006482 crossref_primary_10_3390_cancers7010112 crossref_primary_10_3390_v14092010 crossref_primary_10_1038_nrm4069 crossref_primary_10_1038_s41467_024_54668_2 crossref_primary_10_1128_jvi_00179_24 crossref_primary_10_1002_jmv_29684 crossref_primary_10_7554_eLife_18311 crossref_primary_10_3390_ijms24021238 crossref_primary_10_1016_j_exppara_2020_107963 crossref_primary_10_1016_j_virusres_2015_06_012 crossref_primary_10_1126_scisignal_adg4124 crossref_primary_10_1128_jvi_01000_24 crossref_primary_10_3390_v7020604 crossref_primary_10_1371_journal_ppat_1005260 crossref_primary_10_3389_fviro_2023_1103737 crossref_primary_10_1038_s41467_025_56773_2 crossref_primary_10_3389_fmicb_2016_00151 crossref_primary_10_3390_v6124961 crossref_primary_10_7554_eLife_50960 crossref_primary_10_1146_annurev_virology_031413_085439 crossref_primary_10_1261_rna_045328_114 crossref_primary_10_1007_s40588_018_0102_1 crossref_primary_10_1016_j_virol_2022_01_005 crossref_primary_10_1007_s12250_019_00114_3 crossref_primary_10_3390_ijms20143427 crossref_primary_10_3390_v15102007 crossref_primary_10_1074_jbc_RA118_007331 crossref_primary_10_1128_JVI_00528_15 crossref_primary_10_1128_JVI_02663_14 crossref_primary_10_1128_msystems_01007_23 crossref_primary_10_3390_microorganisms10071448 crossref_primary_10_1186_s12864_016_3282_1 crossref_primary_10_1038_ncomms8126 crossref_primary_10_1016_j_celrep_2019_05_086 crossref_primary_10_1016_j_tim_2019_01_010 crossref_primary_10_1093_bfgp_elu045 crossref_primary_10_1093_ve_veac058 crossref_primary_10_1007_s00018_016_2409_5 crossref_primary_10_1111_imr_12434 crossref_primary_10_3389_fimmu_2017_00390 crossref_primary_10_1128_JVI_02063_20 crossref_primary_10_1128_JVI_00287_20 crossref_primary_10_1371_journal_ppat_1004274 crossref_primary_10_1038_s41598_017_00401_7 crossref_primary_10_1038_s41564_017_0056_8 crossref_primary_10_3389_fmicb_2017_01515 crossref_primary_10_1371_journal_ppat_1007774 crossref_primary_10_1128_JVI_00220_18 crossref_primary_10_3390_v16091418 crossref_primary_10_1186_s13059_017_1329_5 crossref_primary_10_1007_s11033_022_07268_6 crossref_primary_10_1186_s12929_020_00637_y crossref_primary_10_1128_mbio_02446_22 crossref_primary_10_1371_journal_ppat_1005473 crossref_primary_10_1016_j_semcdb_2020_06_015 crossref_primary_10_1128_JVI_01698_16 crossref_primary_10_1016_j_celrep_2020_107564 crossref_primary_10_1002_cpmc_99 crossref_primary_10_1371_journal_ppat_1011581 crossref_primary_10_1128_JVI_01858_16 crossref_primary_10_1371_journal_ppat_1009947 crossref_primary_10_3389_fmicb_2024_1484455 crossref_primary_10_3390_v12030329 crossref_primary_10_1371_journal_ppat_1005900 crossref_primary_10_1016_j_virol_2015_10_031 crossref_primary_10_1093_nar_gkx241 crossref_primary_10_1261_rna_052548_115 crossref_primary_10_1128_mBio_01633_14 crossref_primary_10_1093_plcell_koac019 crossref_primary_10_3389_fgene_2018_00259 crossref_primary_10_1093_nar_gkae540 crossref_primary_10_1128_jvi_01560_21 crossref_primary_10_3390_v12080788 crossref_primary_10_1128_JVI_03317_14 crossref_primary_10_7554_eLife_57436 crossref_primary_10_1371_journal_ppat_1012660 crossref_primary_10_3389_fmicb_2021_670542 crossref_primary_10_3389_fcimb_2021_648055 crossref_primary_10_1016_j_celrep_2019_03_063 crossref_primary_10_1007_s12250_015_3595_2 crossref_primary_10_1101_cshperspect_a032698 crossref_primary_10_1038_s41467_020_15992_5 crossref_primary_10_3390_microorganisms9061169 crossref_primary_10_7554_eLife_54037 crossref_primary_10_1371_journal_ppat_1010236 crossref_primary_10_1002_cpmc_1 crossref_primary_10_3390_v7062752 crossref_primary_10_1186_s12864_018_4604_2 crossref_primary_10_1128_mBio_03027_19 crossref_primary_10_1007_s00705_024_06021_7 crossref_primary_10_3390_v6114212 crossref_primary_10_1371_journal_ppat_1004597
Cites_doi	10.1006/viro.1998.9486 10.1016/j.virol.2004.03.049 10.1038/nmeth.1701 10.1126/science.1227919 10.1016/j.virol.2007.08.023 10.1172/JCI40567 10.1146/annurev-biochem-060208-105251 10.1126/science.274.5293.1739 10.1101/gr.7.8.768 10.1128/JVI.02374-13 10.1074/jbc.272.35.21661 10.1128/JVI.00252-12 10.1126/science.289.5484.1564 10.1073/pnas.94.2.690 10.1093/emboj/20.22.6453 10.1016/j.virusres.2012.02.010 10.1128/JVI.05497-11 10.1128/JVI.75.4.1857-1863.2001 10.2741/3322 10.1128/JVI.02705-09 10.3109/10409238.2012.714350 10.1128/JVI.69.2.1030-1036.1995 10.1038/nmeth.1923 10.1111/j.1432-1033.1977.tb11256.x 10.1371/journal.ppat.1001013 10.1101/gr.139568.112 10.1006/viro.1999.0165 10.1006/scbi.1998.0118 10.1126/science.1168978 10.1371/journal.pone.0013875 10.1006/viro.1998.9316 10.1099/vir.0.18941-0 10.1371/journal.ppat.1002339 10.1128/JVI.79.13.8493-8505.2005 10.1371/journal.ppat.1003156 10.1007/s00705-002-0813-7 10.1128/JVI.00497-09 10.1002/pmic.200300771 10.1016/S0006-291X(02)02286-6 10.1128/JVI.05988-11 10.1371/journal.ppat.1000334 10.1016/S0065-2164(09)01206-4 10.1128/JVI.76.24.12574-12583.2002 10.1128/JVI.20.3.583-588.1976 10.1128/JVI.02400-07 10.1126/science.1199478 10.1038/sj.bjc.6602938 10.1128/JVI.75.10.4843-4853.2001 10.1128/JVI.01394-06 10.1073/pnas.140129797 10.1099/0022-1317-80-3-557 10.1128/JVI.71.2.1207-1212.1997 10.1006/viro.2001.1016 10.1128/JVI.80.3.1385-1392.2006 10.1074/jbc.M111308200 10.1038/263211a0 10.1099/vir.0.81619-0 10.3389/fmicb.2012.00059 10.1083/jcb.201112145 10.1128/JVI.71.9.7030-7038.1997 10.1111/j.1469-185X.2011.00186.x 10.1073/pnas.93.25.14862 10.1016/S1097-2765(04)00091-7 10.1074/jbc.M400964200 10.1128/JVI.75.3.1487-1506.2001 10.1128/JVI.75.15.7161-7174.2001 10.1007/s11262-011-0698-1 10.1128/MCB.20.23.8635-8642.2000 10.1128/JVI.02746-12 10.1128/JVI.02119-07 10.1128/JVI.72.2.1005-1012.1998 10.1006/viro.1998.9412 10.1128/JVI.02516-08 10.1099/vir.0.80661-0 10.1128/JVI.80.6.3062-3070.2006 10.1371/journal.ppat.1002680 10.1016/j.cell.2013.06.009 10.1128/JVI.01301-09 10.1074/jbc.M110.216093 10.1073/pnas.0400541101 10.1371/journal.ppat.1003147 10.1128/JVI.71.1.839-842.1997 10.1128/JVI.73.6.4786-4793.1999 10.1038/nm0397-293 10.1128/JVI.79.2.800-811.2005 10.1128/JVI.79.8.5059-5068.2005 10.1038/nrg2026 10.1093/nar/gki251 10.1128/JVI.02726-06 10.1093/nar/gkq1251 10.1073/pnas.0810916106 10.1146/annurev.biochem.72.121801.161520 10.1128/JVI.79.20.12880-12892.2005 10.1073/pnas.93.21.11883 10.1099/0022-1317-83-1-189 10.1128/JVI.75.2.891-902.2001 10.1073/pnas.1009269107 10.3389/fmicb.2012.00165 10.1128/JVI.77.1.592-599.2003 10.1016/j.cell.2011.10.002 10.1093/nar/gkh378 10.1128/JVI.72.10.8309-8315.1998 10.1099/vir.0.041129-0 10.1074/jbc.M900025200 10.1074/jbc.273.16.9552 10.1371/journal.ppat.1000935 10.1128/JVI.71.4.3069-3076.1997 10.1038/nchembio.304 10.1128/JVI.72.6.5182-5188.1998 10.1128/JVI.79.24.15099-15106.2005 10.1126/science.7997879 10.1186/1741-7007-8-49 10.1083/jcb.201202140 10.1099/vir.0.19015-0 10.1371/journal.ppat.1003749 10.1128/JVI.01521-07 10.1038/nprot.2012.086 10.1093/gbe/evr099 10.1093/nar/gkr1192 10.1016/j.jsb.2010.10.015 10.1093/nar/9.20.5233 10.1128/JVI.75.6.2866-2878.2001 10.1128/JVI.76.23.11880-11888.2002 10.1128/JVI.00645-10 10.1128/JVI.02254-06 10.1093/bioinformatics/btp120 10.1099/0022-1317-81-8-2039 10.1038/ng1789 10.1128/JVI.01233-06 10.1007/s10529-009-9918-3 10.1128/JVI.00553-06 10.1128/JVI.00246-06 10.1186/1471-2164-12-625 10.1016/j.jviromet.2011.03.012 10.1128/JVI.74.23.10920-10929.2000 10.1128/JVI.73.7.5556-5567.1999
ContentType	Journal Article
Copyright	COPYRIGHT 2014 Public Library of Science 2014 Arias et al 2014 Arias et al 2014 Arias et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, et al. (2014) KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features. PLoS Pathog 10(1): e1003847. doi:10.1371/journal.ppat.1003847
Copyright_xml	– notice: COPYRIGHT 2014 Public Library of Science – notice: 2014 Arias et al 2014 Arias et al – notice: 2014 Arias et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, et al. (2014) KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features. PLoS Pathog 10(1): e1003847. doi:10.1371/journal.ppat.1003847
DBID	AAYXX CITATION CGR CUY CVF ECM EIF NPM ISN ISR 7X8 5PM DOA
DOI	10.1371/journal.ppat.1003847
DatabaseName	CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed Gale In Context: Canada Gale In Context: Science MEDLINE - Academic PubMed Central (Full Participant titles) View article at DOAJ
DatabaseTitle	CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic
DatabaseTitleList	MEDLINE MEDLINE - Academic
Database_xml	– sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database
DeliveryMethod	fulltext_linktorsrc
Discipline	Biology Architecture
DocumentTitleAlternate	Functional Annotation of the KSHV Genome Using NGS
EISSN	1553-7374
ExternalDocumentID	1498392796 oai_doaj_org_article_896446cc52d64ac0aa2ac2dac5b932a5 PMC3894221 A364854356 24453964 10_1371_journal_ppat_1003847
Genre	Research Support, Non-U.S. Gov't Journal Article
GeographicLocations	United States
GeographicLocations_xml	– name: United States
GrantInformation_xml	– fundername: Howard Hughes Medical Institute
GroupedDBID	--- 123 29O 2WC 53G 5VS 7X7 88E 8FE 8FH 8FI 8FJ AAFWJ AAUCC AAWOE AAYXX ABDBF ABUWG ACGFO ACIHN ACPRK ACUHS ADBBV ADRAZ AEAQA AENEX AEUYN AFKRA AFPKN AFRAH AHMBA ALMA_UNASSIGNED_HOLDINGS AOIJS B0M BAWUL BBNVY BCNDV BENPR BHPHI BPHCQ BVXVI BWKFM CCPQU CITATION CS3 DIK DU5 E3Z EAP EAS EBD EMK EMOBN ESX F5P FPL FYUFA GROUPED_DOAJ GX1 HCIFZ HMCUK HYE IAO IHR INH INR ISN ISR ITC KQ8 LK8 M1P M48 M7P MM. O5R O5S OK1 OVT P2P PGMZT PHGZM PHGZT PIMPY PQQKQ PROAC PSQYO QF4 QN7 RNS RPM SV3 TR2 TUS UKHRP WOW ~8M CGR CUY CVF ECM EIF H13 IPNFZ NPM PJZUB PPXIY PQGLB PV9 RIG RZL WOQ PMFND 7X8 5PM PUEGO - 3V. AAPBV ABPTK ADACO BBAFP M~E PQEST PQUKI PRINS
ID	FETCH-LOGICAL-c6147-71dd4b03a6ed1a4e7aff88e900bc7c6609c15a597e95d3cd5d86e9dc6f5fe3393
IEDL.DBID	M48
ISSN	1553-7374 1553-7366
IngestDate	Fri Nov 26 17:14:11 EST 2021 Wed Aug 27 01:21:14 EDT 2025 Thu Aug 21 18:42:55 EDT 2025 Fri Jul 11 10:33:22 EDT 2025 Tue Jun 17 21:42:05 EDT 2025 Tue Jun 10 20:15:39 EDT 2025 Fri Jun 27 04:33:23 EDT 2025 Fri Jun 27 04:20:16 EDT 2025 Mon Jul 21 05:54:57 EDT 2025 Tue Jul 01 01:10:10 EDT 2025 Thu Apr 24 23:09:35 EDT 2025
IsDoiOpenAccess	true
IsOpenAccess	true
IsPeerReviewed	true
IsScholarly	true
Issue	1
Language	English
License	This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. Creative Commons Attribution License
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c6147-71dd4b03a6ed1a4e7aff88e900bc7c6609c15a597e95d3cd5d86e9dc6f5fe3393
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: CA JSW DG. Performed the experiments: CA NSG ASM MH PB. Analyzed the data: CA BW AM. Contributed reagents/materials/analysis tools: AM ASM NSG. Wrote the paper: CA DG. The authors have declared that no competing interests exist.
OpenAccessLink	http://journals.scholarsportal.info/openUrl.xqy?doi=10.1371/journal.ppat.1003847
PMID	24453964
PQID	1492695559
PQPubID	23479
ParticipantIDs	plos_journals_1498392796 doaj_primary_oai_doaj_org_article_896446cc52d64ac0aa2ac2dac5b932a5 pubmedcentral_primary_oai_pubmedcentral_nih_gov_3894221 proquest_miscellaneous_1492695559 gale_infotracmisc_A364854356 gale_infotracacademiconefile_A364854356 gale_incontextgauss_ISR_A364854356 gale_incontextgauss_ISN_A364854356 pubmed_primary_24453964 crossref_citationtrail_10_1371_journal_ppat_1003847 crossref_primary_10_1371_journal_ppat_1003847
ProviderPackageCode	CITATION AAYXX
PublicationCentury	2000
PublicationDate	2014-01-00
PublicationDateYYYYMMDD	2014-01-01
PublicationDate_xml	– month: 01 year: 2014 text: 2014-01-00
PublicationDecade	2010
PublicationPlace	United States
PublicationPlace_xml	– name: United States – name: San Francisco, USA
PublicationTitle	PLoS pathogens
PublicationTitleAlternate	PLoS Pathog
PublicationYear	2014
Publisher	Public Library of Science Public Library of Science (PLoS)
Publisher_xml	– name: Public Library of Science – name: Public Library of Science (PLoS)
References	PS Moore (ref97) 1996; 274 E Kuang (ref68) 2009; 284 JS Cannon (ref117) 1999; 73 E Gottwein (ref5) 2012; 3 K Nishikura (ref48) 2010; 79 N Stern-Ginossar (ref14) 2012; 338 OR Homann (ref26) 2010; 8 M Kozak (ref54) 1981 JL Taylor (ref28) 2005; 79 FX Zhu (ref136) 2005; 79 BA Wilson (ref41) 2011; 3 R Renne (ref123) 1998; 72 BS Bowser (ref89) 2002; 76 A Grundhoff (ref60) 2001; 75 M Guttman (ref40) 2013; 154 FY Wu (ref114) 2001; 75 LV McClure (ref34) 2013; 87 V Arumugaswami (ref101) 2006; 80 LR Palam (ref83) 2011; 286 S-R Masa (ref103) 2008; 371 T Günther (ref63) 2010; 6 J Vieira (ref18) 2004; 325 MA Basrai (ref55) 1997; 7 H Gruffat (ref110) 1999; 80 SZ Gandy (ref49) 2007; 81 C Samuel (ref72) 2012; 353 FX Zhu (ref27) 1999; 73 C Trapnell (ref22) 2009; 25 V Majerciak (ref46) 2009; 14 M Bartkoski (ref32) 1976; 20 K Nealon (ref120) 2001; 75 Z Bai (ref124) 2012; 44 NK Conrad (ref44) 2009; 68 F Zhang (ref75) 2011; 39 PP Naranatt (ref108) 2002; 147 KM Vattem (ref58) 2004; 101 S Ohno (ref118) 2012; 93 E Cesarman (ref1) 1999; 9 E Kuang (ref106) 2008; 82 S Matsumura (ref112) 2005; 79 P Rimessi (ref95) 2001; 75 T Schneider-Poetsch (ref19) 2010; 6 A Sandelin (ref29) 2007; 8 PJ Desai (ref133) 2012; 86 CC Rossetto (ref39) 2012; 8 D Dittmer (ref59) 1998; 72 ST Smale (ref31) 2003; 72 Z Toth (ref64) 2010; 6 AG Hinnebusch (ref82) 1997; 272 DM Lukac (ref109) 1998; 252 J Chang (ref100) 2000; 81 EH-Y Cheng (ref98) 1997; 94 T Jaber (ref8) 2013; 87 B Langmead (ref88) 2012; 9 AS Madrid (ref53) 2012; 86 M Fresno (ref20) 1977; 72 LM Kronstad (ref57) 2013; 9 B Chandran (ref25) 1998; 249 A Unal (ref116) 1997; 71 F Neipel (ref93) 1997; 71 IP Ivanov (ref78) 2010; 107 H Li (ref111) 2002; 76 C Fritsch (ref77) 2012; 22 K Klimek-Tomczak (ref74) 2006; 94 RG Jenner (ref15) 2001; 75 T-C Yang (ref132) 2009; 31 SM Gregory (ref140) 2011; 331 N Blom (ref51) 2004; 4 M Paulose-Murphy (ref16) 2001; 75 MT Dimon (ref23) 2010; 5 Z Bai (ref35) 2013 JS May (ref122) 2005; 86 JS May (ref121) 2005; 79 S Lin (ref131) 1997; 71 B Glaunsinger (ref50) 2004; 13 G Loughran (ref79) 2012; 40 K Bourara (ref73) 2000; 289 L Wang (ref127) 2012; 86 BR Jackson (ref45) 2012; 3 DP AuCoin (ref126) 2002; 83 E Wong (ref119) 2007; 81 SR Chan (ref62) 2000; 74 DW Reid (ref69) 2012; 197 CM González (ref139) 2006; 80 A Mallela (ref47) 2012; 47 AJ Davison (ref92) 2005; 79 H Guo (ref125) 2009; 83 V Majerciak (ref61) 2006; 80 K Hiller (ref43) 2004; 32 CC Cinquina (ref137) 2000; 268 R Sun (ref33) 1996; 93 M Haque (ref102) 2006; 80 S-S Wang (ref107) 2012; 165 A David (ref70) 2012; 197 D Ganem (ref2) 2010; 120 L Coscoy (ref94) 2000; 97 E Bortz (ref129) 2007; 81 R Sarid (ref9) 1998; 72 V Majerciak (ref36) 2013; 9 DP Dittmer (ref10) 2003; 63 NT Ingolia (ref13) 2012; 7 EL Wong (ref141) 2006; 80 NT Ingolia (ref21) 2011; 147 NT Ingolia (ref12) 2009; 324 MS Hamza (ref104) 2004; 279 S Chandriani (ref6) 2010; 84 ref76 J Myoung (ref17) 2011; 174 P Carninci (ref30) 2006; 38 Y Xu (ref7) 2010; 84 G Gáspár (ref138) 2002; 297 R Santarelli (ref134) 2008; 82 W-H Tsai (ref52) 2012; 3 A Cohen (ref67) 2006; 87 B Deng (ref128) 2007; 81 S Tang (ref24) 2002; 277 A Gallo (ref71) 2012; 87 NJ Proudfoot (ref37) 1976; 263 SE Calvo (ref56) 2009; 106 JJ Russo (ref4) 1996; 93 RS Shabman (ref86) 2013; 9 W Zhong (ref38) 1997; 71 C Arias (ref66) 2009; 5 PE Pertel (ref113) 1998; 251 AJ Lincoln (ref84) 1998; 273 R Sarid (ref99) 1997; 3 C Cunningham (ref130) 2003; 84 J Cao (ref85) 1995; 69 SA Bisson (ref115) 2009; 83 S Ozgur (ref91) 2011; 174 S Koyano (ref105) 2003; 84 LR Dresang (ref11) 2011; 12 A Gaba (ref81) 2001; 20 DR Morris (ref80) 2000; 20 A Chen (ref87) 2005; 33 Y Chang (ref3) 1994 RG Nador (ref135) 2001; 287 S Covarrubias (ref65) 2011; 7 OB Spiller (ref90) 2003; 77 LM Persson (ref96) 2010; 84 TN Petersen (ref42) 2011; 8 20921384 - Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):18056-60 9573290 - J Virol. 1998 Jun;72(6):5182-8 11832484 - J Biol Chem. 2002 Apr 26;277(17):14547-56 12651739 - Annu Rev Biochem. 2003;72:449-79 20532208 - PLoS Pathog. 2010;6(6):e1000935 10091993 - J Gen Virol. 1999 Mar;80 ( Pt 3):557-61 11160684 - J Virol. 2001 Feb;75(4):1857-63 24155407 - J Virol. 2014 Jan;88(1):377-92 17963810 - Virology. 2008 Feb 5;371(1):14-31 15246263 - Virology. 2004 Aug 1;325(2):225-40 15023341 - Mol Cell. 2004 Mar 12;13(5):713-23 22563327 - Front Microbiol. 2012 May 03;3:165 9444993 - J Virol. 1998 Feb;72(2):1005-12 17913828 - J Virol. 2007 Dec;81(24):13544-51 22879431 - Genome Res. 2012 Nov;22(11):2208-18 17020939 - J Virol. 2006 Dec;80(24):11968-81 16645617 - Nat Genet. 2006 Jun;38(6):626-35 23382680 - PLoS Pathog. 2013 Jan;9(1):e1003147 319998 - Eur J Biochem. 1977 Jan;72(2):323-30 9268289 - J Biol Chem. 1997 Aug 29;272(35):21661-4 16415016 - J Virol. 2006 Feb;80(3):1385-92 23810193 - Cell. 2013 Jul 3;154(1):240-51 10364304 - J Virol. 1999 Jul;73(7):5556-67 8985427 - J Virol. 1997 Jan;71(1):839-42 9837804 - Virology. 1998 Nov 25;251(2):402-13 23302891 - J Virol. 2013 Mar;87(6):3461-70 16306581 - J Virol. 2005 Dec;79(24):15099-106 11707416 - EMBO J. 2001 Nov 15;20(22):6453-63 11435597 - J Virol. 2001 Aug;75(15):7161-74 9878608 - Virology. 1998 Dec 20;252(2):304-12 12111412 - Arch Virol. 2002 Jul;147(7):1349-70 22090138 - J Virol. 2012 Feb;86(3):1348-57 21959131 - Nat Methods. 2011;8(10):785-6 186635 - J Virol. 1976 Dec;20(3):583-8 23382684 - PLoS Pathog. 2013 Jan;9(1):e1003156 8876232 - Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11883-8 19142585 - Biotechnol Lett. 2009 May;31(5):629-37 20409324 - BMC Biol. 2010;8:49 16404425 - Br J Cancer. 2006 Feb 27;94(4):586-92 22363332 - Front Microbiol. 2012 Feb 20;3:59 20661424 - PLoS Pathog. 2010;6(7):e1001013 16973577 - J Virol. 2006 Oct;80(19):9730-40 16528027 - J Gen Virol. 2006 Apr;87(Pt 4):795-802 7997879 - Science. 1994 Dec 16;266(5192):1865-9 10900043 - J Gen Virol. 2000 Aug;81(Pt 8):2039-47 20534856 - J Virol. 2010 Aug;84(16):7934-42 24244170 - PLoS Pathog. 2013;9(11):e1003749 10343068 - Semin Cancer Biol. 1999 Jun;9(3):165-74 10233939 - J Virol. 1999 Jun;73(6):4786-93 17634243 - J Virol. 2007 Sep;81(18):10137-50 19300492 - PLoS Pathog. 2009 Mar;5(3):e1000334 21227927 - Nucleic Acids Res. 2011 Apr;39(8):3128-40 11222712 - J Virol. 2001 Mar;75(6):2866-78 20192758 - Annu Rev Biochem. 2010;79:321-49 22156057 - Nucleic Acids Res. 2012 Apr;40(7):2898-906 9055856 - Nat Med. 1997 Mar;3(3):293-8 21285359 - J Biol Chem. 2011 Apr 1;286(13):10939-49 9733875 - J Virol. 1998 Oct;72(10):8309-15 19906914 - J Virol. 2010 Feb;84(3):1334-47 19372376 - Proc Natl Acad Sci U S A. 2009 May 5;106(18):7507-12 15613308 - J Virol. 2005 Jan;79(2):800-11 22180077 - Virus Genes. 2012 Apr;44(2):225-36 22371709 - Front Microbiol. 2012 Feb 22;3:60 22013050 - J Virol. 2012 Jan;86(1):594-8 12771416 - J Gen Virol. 2003 Jun;84(Pt 6):1471-83 15174133 - Proteomics. 2004 Jun;4(6):1633-49 15247271 - J Biol Chem. 2004 Sep 10;279(37):38325-30 21682836 - Biol Rev Camb Philos Soc. 2012 Feb;87(1):95-110 22046136 - PLoS Pathog. 2011 Oct;7(10):e1002339 20118940 - Nat Chem Biol. 2010 Mar;6(3):209-217 9060668 - J Virol. 1997 Apr;71(4):3069-76 21948395 - Genome Biol Evol. 2011;3:1245-52 7301588 - Nucleic Acids Res. 1981 Oct 24;9(20):5233-52 22366521 - Virus Res. 2012 May;165(2):157-69 822353 - Nature. 1976 Sep 16;263(5574):211-4 16188990 - J Virol. 2005 Oct;79(20):12880-92 22472439 - J Cell Biol. 2012 Apr 2;197(1):45-57 18305046 - J Virol. 2008 May;82(9):4562-72 10683342 - Virology. 2000 Mar 1;268(1):201-17 9012846 - Proc Natl Acad Sci U S A. 1997 Jan 21;94(2):690-4 21047556 - J Struct Biol. 2011 Apr;174(1):37-43 11152521 - J Virol. 2001 Feb;75(3):1487-506 11073965 - Mol Cell Biol. 2000 Dec;20(23):8635-42 8995643 - J Virol. 1997 Feb;71(2):1207-12 21419799 - J Virol Methods. 2011 Jun;174(1-2):12-21 8939871 - Science. 1996 Dec 6;274(5293):1739-44 12438583 - J Virol. 2002 Dec;76(24):12574-83 12414930 - J Virol. 2002 Dec;76(23):11880-8 12727810 - Cancer Res. 2003 May 1;63(9):2010-5 9267801 - Genome Res. 1997 Aug;7(8):768-71 21252346 - Science. 2011 Jan 21;331(6015):330-4 15795291 - J Virol. 2005 Apr;79(8):5059-68 17392360 - J Virol. 2007 Jun;81(12):6761-4 19279093 - J Virol. 2009 May;83(10):5056-66 12477863 - J Virol. 2003 Jan;77(1):592-9 10968794 - Science. 2000 Sep 1;289(5484):1564-6 15215414 - Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W375-9 12771417 - J Gen Virol. 2003 Jun;84(Pt 6):1485-91 20364091 - J Clin Invest. 2010 Apr;120(4):939-49 12359216 - Biochem Biophys Res Commun. 2002 Oct 4;297(4):756-9 21809195 - Curr Top Microbiol Immunol. 2012;353:163-95 10859362 - Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):8051-6 15784886 - J Gen Virol. 2005 Apr;86(Pt 4):919-28 17215290 - J Virol. 2007 Apr;81(7):3640-4 21079731 - PLoS One. 2010;5(11):e13875 11134302 - J Virol. 2001 Jan;75(2):891-902 16809309 - J Virol. 2006 Jul;80(14):7037-51 22674989 - J Virol. 2012 Aug;86(16):8693-704 19273144 - Front Biosci (Landmark Ed). 2009;14:1516-28 22589717 - PLoS Pathog. 2012;8(5):e1002680 22472436 - J Cell Biol. 2012 Apr 2;197(1):7-9 22388286 - Nat Methods. 2012 Apr;9(4):357-9 19426857 - Adv Appl Microbiol. 2009;68:241-61 22258865 - J Gen Virol. 2012 May;93(Pt 5):1076-80 22185355 - BMC Genomics. 2011;12:625 22988838 - Crit Rev Biochem Mol Biol. 2012 Nov-Dec;47(6):493-501 9261433 - J Virol. 1997 Sep;71(9):7030-8 22056041 - Cell. 2011 Nov 11;147(4):789-802 9545285 - J Biol Chem. 1998 Apr 17;273(16):9552-60 24067953 - J Virol. 2013 Dec;87(23):12838-49 15277680 - Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11269-74 17486122 - Nat Rev Genet. 2007 Jun;8(6):424-36 20357088 - J Virol. 2010 Jun;84(11):5465-75 22836135 - Nat Protoc. 2012 Aug;7(8):1534-50 19304659 - J Biol Chem. 2009 May 15;284(20):13958-68 9740785 - Virology. 1998 Sep 15;249(1):140-9 11312356 - J Virol. 2001 May;75(10):4843-53 19656880 - J Virol. 2009 Oct;83(20):10582-95 23180859 - Science. 2012 Nov 23;338(6110):1088-93 18057234 - J Virol. 2008 Feb;82(4):1838-50 19289445 - Bioinformatics. 2009 May 1;25(9):1105-11 15956592 - J Virol. 2005 Jul;79(13):8493-505 19213877 - Science. 2009 Apr 10;324(5924):218-23 16501115 - J Virol. 2006 Mar;80(6):3062-70 11069986 - J Virol. 2000 Dec;74(23):10920-9 7815480 - J Virol. 1995 Feb;69(2):1030-6 11752716 - J Gen Virol. 2002 Jan;83(Pt 1):189-93 8962146 - Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14862-7 11504542 - Virology. 2001 Aug 15;287(1):62-70 15731337 - Nucleic Acids Res. 2005;33(4):1169-81
References_xml	– volume: 252 start-page: 304 year: 1998 ident: ref109 article-title: Reactivation of Kaposi's sarcoma-associated herpesvirus infection from latency by expression of the ORF 50 transactivator, a homolog of the EBV R protein publication-title: Virology doi: 10.1006/viro.1998.9486 – volume: 325 start-page: 225 year: 2004 ident: ref18 article-title: Use of the red fluorescent protein as a marker of Kaposi's sarcoma-associated herpesvirus lytic gene expression publication-title: Virology doi: 10.1016/j.virol.2004.03.049 – volume: 8 start-page: 785 year: 2011 ident: ref42 article-title: SignalP 4.0: discriminating signal peptides from transmembrane regions publication-title: Nature methods doi: 10.1038/nmeth.1701 – volume: 338 start-page: 1088 year: 2012 ident: ref14 article-title: Decoding human cytomegalovirus publication-title: Science (New York, NY) doi: 10.1126/science.1227919 – volume: 371 start-page: 14 year: 2008 ident: ref103 article-title: Transcriptional regulation of the open reading frame 35 encoded by Kaposi's sarcoma-associated herpesvirus publication-title: Virology doi: 10.1016/j.virol.2007.08.023 – volume: 120 start-page: 939 year: 2010 ident: ref2 article-title: KSHV and the pathogenesis of Kaposi sarcoma: listening to human biology and medicine publication-title: The Journal of clinical investigation doi: 10.1172/JCI40567 – volume: 79 start-page: 321 year: 2010 ident: ref48 article-title: Functions and regulation of RNA editing by ADAR deaminases publication-title: Annual review of biochemistry doi: 10.1146/annurev-biochem-060208-105251 – volume: 274 start-page: 1739 year: 1996 ident: ref97 article-title: Molecular Mimicry of Human Cytokine and Cytokine Response Pathway Genes by KSHV publication-title: Science doi: 10.1126/science.274.5293.1739 – volume: 7 start-page: 768 year: 1997 ident: ref55 article-title: Small Open Reading Frames: Beautiful Needles in the Haystack publication-title: Genome Res doi: 10.1101/gr.7.8.768 – ident: ref76 – volume: 87 start-page: 12838 year: 2013 ident: ref34 article-title: Comprehensive Mapping and Analysis of Kaposi's Sarcoma-Associated Herpesvirus 3′ UTRs Identify Differential Posttranscriptional Control of Gene Expression in Lytic versus Latent Infection publication-title: Journal of virology doi: 10.1128/JVI.02374-13 – volume: 272 start-page: 21661 year: 1997 ident: ref82 article-title: Translational Regulation of Yeast GCN4. A window on factors that control initiator-tRNA binding to the ribosome publication-title: Journal of Biological Chemistry doi: 10.1074/jbc.272.35.21661 – volume: 86 start-page: 8693 year: 2012 ident: ref53 article-title: Kaposi's sarcoma-associated herpesvirus ORF54/dUTPase downregulates a ligand for the NK activating receptor NKp44 publication-title: Journal of virology doi: 10.1128/JVI.00252-12 – volume: 289 start-page: 1564 year: 2000 ident: ref73 article-title: Generation of G-to-A and C-to-U Changes in HIV-1 Transcripts by RNA Editing publication-title: Science doi: 10.1126/science.289.5484.1564 – volume: 94 start-page: 690 year: 1997 ident: ref98 article-title: A Bcl-2 homolog encoded by Kaposi sarcoma-associated virus, human herpesvirus 8, inhibits apoptosis but does not heterodimerize with Bax or Bak publication-title: Proceedings of the National Academy of Sciences doi: 10.1073/pnas.94.2.690 – volume: 20 start-page: 6453 year: 2001 ident: ref81 article-title: Physical evidence for distinct mechanisms of translational control by upstream open reading frames publication-title: The EMBO journal doi: 10.1093/emboj/20.22.6453 – volume: 165 start-page: 157 year: 2012 ident: ref107 article-title: Positive and negative regulation in the promoter of the ORF46 gene of Kaposi's sarcoma-associated herpesvirus publication-title: Virus research doi: 10.1016/j.virusres.2012.02.010 – volume: 353 start-page: 163 year: 2012 ident: ref72 article-title: ADARs: viruses and innate immunity publication-title: Current Topics in Microbiology and Immunology – volume: 86 start-page: 1348 year: 2012 ident: ref127 article-title: Distinct domains in ORF52 tegument protein mediate essential functions in murine gammaherpesvirus 68 virion tegumentation and secondary envelopment publication-title: Journal of virology doi: 10.1128/JVI.05497-11 – volume: 75 start-page: 1857 year: 2001 ident: ref60 article-title: Mechanisms governing expression of the v-FLIP gene of Kaposi's sarcoma-associated herpesvirus publication-title: Journal of virology doi: 10.1128/JVI.75.4.1857-1863.2001 – volume: 14 start-page: 1516 year: 2009 ident: ref46 article-title: Kaposi's sarcoma-associated herpesvirus ORF57 in viral RNA processing publication-title: Frontiers in Bioscience doi: 10.2741/3322 – volume: 84 start-page: 5465 year: 2010 ident: ref7 article-title: Making sense of antisense: seemingly noncoding RNAs antisense to the master regulator of Kaposi's sarcoma-associated herpesvirus lytic replication do not regulate that transcript but serve as mRNAs encoding small peptides publication-title: Journal of virology doi: 10.1128/JVI.02705-09 – volume: 47 start-page: 493 year: 2012 ident: ref47 article-title: A-to-I editing of protein coding and noncoding RNAs publication-title: Critical reviews in biochemistry and molecular biology doi: 10.3109/10409238.2012.714350 – volume: 69 start-page: 1030 year: 1995 ident: ref85 article-title: Translational inhibition by a human cytomegalovirus upstream open reading frame despite inefficient utilization of its AUG codon publication-title: J Virol doi: 10.1128/JVI.69.2.1030-1036.1995 – volume: 9 start-page: 357 year: 2012 ident: ref88 article-title: Fast gapped-read alignment with Bowtie 2 publication-title: Nature methods doi: 10.1038/nmeth.1923 – volume: 72 start-page: 323 year: 1977 ident: ref20 article-title: Inhibition of Translation in Eukaryotic Systems by Harringtonine publication-title: European Journal of Biochemistry doi: 10.1111/j.1432-1033.1977.tb11256.x – volume: 6 start-page: e1001013 year: 2010 ident: ref64 article-title: Epigenetic analysis of KSHV latent and lytic genomes publication-title: PLoS pathogens doi: 10.1371/journal.ppat.1001013 – volume: 22 start-page: 2208 year: 2012 ident: ref77 article-title: Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting publication-title: Genome research doi: 10.1101/gr.139568.112 – volume: 268 start-page: 201 year: 2000 ident: ref137 article-title: Dihydrofolate reductase from Kaposi's sarcoma-associated herpesvirus publication-title: Virology doi: 10.1006/viro.1999.0165 – volume: 9 start-page: 165 year: 1999 ident: ref1 article-title: The role of Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) in lymphoproliferative diseases publication-title: Seminars in cancer biology doi: 10.1006/scbi.1998.0118 – volume: 324 start-page: 218 year: 2009 ident: ref12 article-title: Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling publication-title: Science (New York, NY) doi: 10.1126/science.1168978 – volume: 5 start-page: e13875 year: 2010 ident: ref23 article-title: HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data publication-title: PloS one doi: 10.1371/journal.pone.0013875 – volume: 249 start-page: 140 year: 1998 ident: ref25 article-title: Human herpesvirus-8 ORF K8.1 gene encodes immunogenic glycoproteins generated by spliced transcripts publication-title: Virology doi: 10.1006/viro.1998.9316 – volume: 84 start-page: 1485 year: 2003 ident: ref105 article-title: Glycoproteins M and N of human herpesvirus 8 form a complex and inhibit cell fusion publication-title: Journal of General Virology doi: 10.1099/vir.0.18941-0 – volume: 7 start-page: e1002339 year: 2011 ident: ref65 article-title: Coordinated destruction of cellular messages in translation complexes by the gammaherpesvirus host shutoff factor and the mammalian exonuclease Xrn1 publication-title: PLoS pathogens doi: 10.1371/journal.ppat.1002339 – volume: 79 start-page: 8493 year: 2005 ident: ref112 article-title: Activation of the Kaposi's sarcoma-associated herpesvirus major latency locus by the lytic switch protein RTA (ORF50) publication-title: Journal of virology doi: 10.1128/JVI.79.13.8493-8505.2005 – volume: 9 start-page: e1003156 year: 2013 ident: ref57 article-title: Dual short upstream open reading frames control translation of a herpesviral polycistronic mRNA publication-title: PLoS pathogens doi: 10.1371/journal.ppat.1003156 – volume: 147 start-page: 1349 year: 2002 ident: ref108 article-title: Characterization of gamma2-human herpesvirus-8 glycoproteins gH and gL publication-title: Archives of virology doi: 10.1007/s00705-002-0813-7 – volume: 83 start-page: 10582 year: 2009 ident: ref125 article-title: Open reading frame 33 of a gammaherpesvirus encodes a tegument protein essential for virion morphogenesis and egress publication-title: Journal of virology doi: 10.1128/JVI.00497-09 – volume: 4 start-page: 1633 year: 2004 ident: ref51 article-title: Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence publication-title: Proteomics doi: 10.1002/pmic.200300771 – volume: 297 start-page: 756 year: 2002 ident: ref138 article-title: Gammaherpesviruses encode functional dihydrofolate reductase activity publication-title: Biochemical and Biophysical Research Communications doi: 10.1016/S0006-291X(02)02286-6 – volume: 86 start-page: 594 year: 2012 ident: ref133 article-title: Reconstitution of the Kaposi's sarcoma-associated herpesvirus nuclear egress complex and formation of nuclear membrane vesicles by coexpression of ORF67 and ORF69 gene products publication-title: Journal of virology doi: 10.1128/JVI.05988-11 – volume: 5 start-page: e1000334 year: 2009 ident: ref66 article-title: Activation of host translational control pathways by a viral developmental switch publication-title: PLoS pathogens doi: 10.1371/journal.ppat.1000334 – volume: 68 start-page: 241 year: 2009 ident: ref44 article-title: Posttranscriptional gene regulation in Kaposi's sarcoma-associated herpesvirus publication-title: Advances in applied microbiology doi: 10.1016/S0065-2164(09)01206-4 – volume: 76 start-page: 12574 year: 2002 ident: ref89 article-title: Transcriptional Regulation of the K1 Gene Product of Kaposi's Sarcoma-Associated Herpesvirus publication-title: Journal of Virology doi: 10.1128/JVI.76.24.12574-12583.2002 – volume: 20 start-page: 583 year: 1976 ident: ref32 article-title: RNA synthesis in cells infected with herpes simplex virus. XIII. Differences in the methylation patterns of viral RNA during the reproductive cycle publication-title: Journal of Virology doi: 10.1128/JVI.20.3.583-588.1976 – volume: 82 start-page: 4562 year: 2008 ident: ref134 article-title: Identification and characterization of the product encoded by ORF69 of Kaposi's sarcoma-associated herpesvirus publication-title: Journal of virology doi: 10.1128/JVI.02400-07 – volume: 331 start-page: 330 year: 2011 ident: ref140 article-title: Discovery of a viral NLR homolog that inhibits the inflammasome publication-title: Science (New York, NY) doi: 10.1126/science.1199478 – volume: 94 start-page: 586 year: 2006 ident: ref74 article-title: Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa publication-title: British journal of cancer doi: 10.1038/sj.bjc.6602938 – volume: 75 start-page: 4843 year: 2001 ident: ref16 article-title: Transcription program of human herpesvirus 8 (kaposi's sarcoma-associated herpesvirus) publication-title: Journal of virology doi: 10.1128/JVI.75.10.4843-4853.2001 – volume: 80 start-page: 11968 year: 2006 ident: ref61 article-title: Gene structure and expression of Kaposi's sarcoma-associated herpesvirus ORF56, ORF57, ORF58, and ORF59 publication-title: Journal of virology doi: 10.1128/JVI.01394-06 – volume: 97 start-page: 8051 year: 2000 ident: ref94 article-title: Kaposi's sarcoma-associated herpesvirus encodes two proteins that block cell surface display of MHC class I chains by enhancing their endocytosis publication-title: Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.140129797 – volume: 80 start-page: 557 year: 1999 ident: ref110 article-title: Kaposi's sarcoma-associated herpesvirus (human herpesvirus-8) encodes a homologue of the Epstein-Barr virus bZip protein EB1 publication-title: J Gen Virol doi: 10.1099/0022-1317-80-3-557 – volume: 71 start-page: 1207 year: 1997 ident: ref38 article-title: Characterization of ribonucleoprotein complexes containing an abundant polyadenylated nuclear RNA encoded by Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8) publication-title: J Virol doi: 10.1128/JVI.71.2.1207-1212.1997 – volume: 287 start-page: 62 year: 2001 ident: ref135 article-title: Expression of Kaposi's sarcoma-associated herpesvirus G protein-coupled receptor monocistronic and bicistronic transcripts in primary effusion lymphomas publication-title: Virology doi: 10.1006/viro.2001.1016 – volume: 80 start-page: 1385 year: 2006 ident: ref141 article-title: Transcriptional regulation of the Kaposi's sarcoma-associated herpesvirus K15 gene publication-title: Journal of virology doi: 10.1128/JVI.80.3.1385-1392.2006 – volume: 277 start-page: 14547 year: 2002 ident: ref24 article-title: Kaposi's sarcoma-associated herpesvirus K8 exon 3 contains three 5′-splice sites and harbors a K8.1 transcription start site publication-title: The Journal of biological chemistry doi: 10.1074/jbc.M111308200 – volume: 263 start-page: 211 year: 1976 ident: ref37 article-title: 3′ Non-coding region sequences in eukaryotic messenger RNA publication-title: Nature doi: 10.1038/263211a0 – volume: 87 start-page: 795 year: 2006 ident: ref67 article-title: An essential role of ERK signalling in TPA-induced reactivation of Kaposi's sarcoma-associated herpesvirus publication-title: The Journal of general virology doi: 10.1099/vir.0.81619-0 – volume: 3 start-page: 59 year: 2012 ident: ref45 article-title: The Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein and Its Multiple Roles in mRNA Biogenesis publication-title: Frontiers in microbiology doi: 10.3389/fmicb.2012.00059 – volume: 197 start-page: 45 year: 2012 ident: ref70 article-title: Nuclear translation visualized by ribosome-bound nascent chain puromycylation publication-title: The Journal of cell biology doi: 10.1083/jcb.201112145 – volume: 71 start-page: 7030 year: 1997 ident: ref116 article-title: The protease and the assembly protein of Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8) publication-title: J Virol doi: 10.1128/JVI.71.9.7030-7038.1997 – volume: 87 start-page: 95 year: 2012 ident: ref71 article-title: ADARs: allies or enemies? The importance of A-to-I RNA editing in human disease: from cancer to HIV-1 publication-title: Biological reviews of the Cambridge Philosophical Society doi: 10.1111/j.1469-185X.2011.00186.x – volume: 93 start-page: 14862 year: 1996 ident: ref4 article-title: Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8) publication-title: Proceedings of the National Academy of Sciences doi: 10.1073/pnas.93.25.14862 – volume: 13 start-page: 713 year: 2004 ident: ref50 article-title: Lytic KSHV Infection Inhibits Host Gene Expression by Accelerating Global mRNA Turnover publication-title: Molecular Cell doi: 10.1016/S1097-2765(04)00091-7 – volume: 279 start-page: 38325 year: 2004 ident: ref104 article-title: ORF36 protein kinase of Kaposi's sarcoma herpesvirus activates the c-Jun N-terminal kinase signaling pathway publication-title: The Journal of biological chemistry doi: 10.1074/jbc.M400964200 – volume: 75 start-page: 1487 year: 2001 ident: ref114 article-title: Origin-independent assembly of Kaposi's sarcoma-associated herpesvirus DNA replication compartments in transient cotransfection assays and association with the ORF-K8 protein and cellular PML publication-title: Journal of virology doi: 10.1128/JVI.75.3.1487-1506.2001 – volume: 75 start-page: 7161 year: 2001 ident: ref95 article-title: Transcription pattern of human herpesvirus 8 open reading frame K3 in primary effusion lymphoma and Kaposi's sarcoma publication-title: Journal of virology doi: 10.1128/JVI.75.15.7161-7174.2001 – volume: 44 start-page: 225 year: 2012 ident: ref124 article-title: A cluster of transcripts encoded by KSHV ORF30–33 gene locus publication-title: Virus genes doi: 10.1007/s11262-011-0698-1 – volume: 20 start-page: 8635 year: 2000 ident: ref80 article-title: Upstream Open Reading Frames as Regulators of mRNA Translation publication-title: Molecular and Cellular Biology doi: 10.1128/MCB.20.23.8635-8642.2000 – volume: 87 start-page: 3461 year: 2013 ident: ref8 article-title: A virally encoded small peptide regulates RTA stability and facilitates Kaposi's sarcoma-associated herpesvirus lytic replication publication-title: Journal of virology doi: 10.1128/JVI.02746-12 – volume: 82 start-page: 1838 year: 2008 ident: ref106 article-title: Activation of p90 ribosomal S6 kinase by ORF45 of Kaposi's sarcoma-associated herpesvirus and its role in viral lytic replication publication-title: Journal of virology doi: 10.1128/JVI.02119-07 – volume: 72 start-page: 1005 year: 1998 ident: ref9 article-title: Transcription Mapping of the Kaposi's Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Genome in a Body Cavity-Based Lymphoma Cell Line (BC-1) publication-title: J Virol doi: 10.1128/JVI.72.2.1005-1012.1998 – volume: 251 start-page: 402 year: 1998 ident: ref113 article-title: Human herpesvirus-8 glycoprotein B interacts with Epstein-Barr virus (EBV) glycoprotein 110 but fails to complement the infectivity of EBV mutants publication-title: Virology doi: 10.1006/viro.1998.9412 – volume: 83 start-page: 5056 year: 2009 ident: ref115 article-title: A Kaposi's Sarcoma-Associated Herpesvirus Protein That Forms Inhibitory Complexes with Type I Interferon Receptor Subunits, Jak and STAT Proteins, and Blocks Interferon-Mediated Signal Transduction publication-title: Journal of Virology doi: 10.1128/JVI.02516-08 – volume: 86 start-page: 919 year: 2005 ident: ref122 article-title: Murine gammaherpesvirus-68 ORF28 encodes a non-essential virion glycoprotein publication-title: The Journal of general virology doi: 10.1099/vir.0.80661-0 – volume: 80 start-page: 3062 year: 2006 ident: ref139 article-title: Identification and characterization of the Orf49 protein of Kaposi's sarcoma-associated herpesvirus publication-title: Journal of virology doi: 10.1128/JVI.80.6.3062-3070.2006 – volume: 8 start-page: e1002680 year: 2012 ident: ref39 article-title: KSHV PAN RNA associates with demethylases UTX and JMJD3 to activate lytic replication through a physical interaction with the virus genome publication-title: PLoS pathogens doi: 10.1371/journal.ppat.1002680 – volume: 154 start-page: 240 year: 2013 ident: ref40 article-title: Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins publication-title: Cell doi: 10.1016/j.cell.2013.06.009 – volume: 84 start-page: 1334 year: 2010 ident: ref96 article-title: Wide-scale use of Notch signaling factor CSL/RBP-Jkappa in RTA-mediated activation of Kaposi's sarcoma-associated herpesvirus lytic genes publication-title: Journal of virology doi: 10.1128/JVI.01301-09 – volume: 286 start-page: 10939 year: 2011 ident: ref83 article-title: Phosphorylation of eIF2 facilitates ribosomal bypass of an inhibitory upstream ORF to enhance CHOP translation publication-title: The Journal of biological chemistry doi: 10.1074/jbc.M110.216093 – volume: 101 start-page: 11269 year: 2004 ident: ref58 article-title: Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells publication-title: Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.0400541101 – volume: 9 start-page: e1003147 year: 2013 ident: ref86 article-title: An upstream open reading frame modulates ebola virus polymerase translation and virus replication publication-title: PLoS pathogens doi: 10.1371/journal.ppat.1003147 – volume: 71 start-page: 839 year: 1997 ident: ref93 article-title: Human herpesvirus 8 encodes a homolog of interleukin-6 publication-title: Journal of virology doi: 10.1128/JVI.71.1.839-842.1997 – volume: 73 start-page: 4786 year: 1999 ident: ref117 article-title: Human Herpesvirus 8-Encoded Thymidine Kinase and Phosphotransferase Homologues Confer Sensitivity to Ganciclovir publication-title: J Virol doi: 10.1128/JVI.73.6.4786-4793.1999 – volume: 3 start-page: 293 year: 1997 ident: ref99 article-title: Kaposi's sarcoma-associated herpesvirus encodes a functional Bcl-2 homologue publication-title: Nature Medicine doi: 10.1038/nm0397-293 – volume: 79 start-page: 800 year: 2005 ident: ref136 article-title: Virion proteins of Kaposi's sarcoma-associated herpesvirus publication-title: Journal of virology doi: 10.1128/JVI.79.2.800-811.2005 – volume: 79 start-page: 5059 year: 2005 ident: ref121 article-title: The murine gammaherpesvirus 68 ORF27 gene product contributes to intercellular viral spread publication-title: Journal of virology doi: 10.1128/JVI.79.8.5059-5068.2005 – volume: 8 start-page: 424 year: 2007 ident: ref29 article-title: Mammalian RNA polymerase II core promoters: insights from genome-wide studies publication-title: Nature reviews Genetics doi: 10.1038/nrg2026 – volume: 33 start-page: 1169 year: 2005 ident: ref87 article-title: Translation of the first upstream ORF in the hepatitis B virus pregenomic RNA modulates translation at the core and polymerase initiation codons publication-title: Nucleic acids research doi: 10.1093/nar/gki251 – volume: 81 start-page: 6761 year: 2007 ident: ref119 article-title: Murine gammaherpesvirus 68 open reading frame 24 is required for late gene expression after DNA replication publication-title: Journal of virology doi: 10.1128/JVI.02726-06 – volume: 39 start-page: 3128 year: 2011 ident: ref75 article-title: An upstream ORF with non-AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA publication-title: Nucleic acids research doi: 10.1093/nar/gkq1251 – volume: 106 start-page: 7507 year: 2009 ident: ref56 article-title: Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans publication-title: Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.0810916106 – volume: 72 start-page: 449 year: 2003 ident: ref31 article-title: The RNA polymerase II core promoter publication-title: Annual review of biochemistry doi: 10.1146/annurev.biochem.72.121801.161520 – volume: 79 start-page: 12880 year: 2005 ident: ref92 article-title: New genes from old: redeployment of dUTPase by herpesviruses publication-title: Journal of virology doi: 10.1128/JVI.79.20.12880-12892.2005 – volume: 93 start-page: 11883 year: 1996 ident: ref33 article-title: Polyadenylated nuclear RNA encoded by Kaposi sarcoma-associated herpesvirus publication-title: PNAS doi: 10.1073/pnas.93.21.11883 – volume: 83 start-page: 189 year: 2002 ident: ref126 article-title: The human herpesvirus-8 (Kaposi's sarcoma-associated herpesvirus) ORF 40/41 region encodes two distinct transcripts publication-title: J Gen Virol doi: 10.1099/0022-1317-83-1-189 – volume: 75 start-page: 891 year: 2001 ident: ref15 article-title: Kaposi's sarcoma-associated herpesvirus latent and lytic gene expression as revealed by DNA arrays publication-title: Journal of virology doi: 10.1128/JVI.75.2.891-902.2001 – volume: 107 start-page: 18056 year: 2010 ident: ref78 article-title: Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1) publication-title: Proceedings of the National Academy of Sciences doi: 10.1073/pnas.1009269107 – volume: 3 start-page: 165 year: 2012 ident: ref5 article-title: Kaposi's Sarcoma-Associated Herpesvirus microRNAs publication-title: Frontiers in microbiology doi: 10.3389/fmicb.2012.00165 – volume: 77 start-page: 592 year: 2003 ident: ref90 article-title: Complement Regulation by Kaposi's Sarcoma-Associated Herpesvirus ORF4 Protein publication-title: Journal of Virology doi: 10.1128/JVI.77.1.592-599.2003 – volume: 147 start-page: 789 issue: 4 year: 2011 ident: ref21 article-title: Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes publication-title: Cell doi: 10.1016/j.cell.2011.10.002 – volume: 32 start-page: 375 year: 2004 ident: ref43 article-title: PrediSi: prediction of signal peptides and their cleavage positions publication-title: Nucleic Acids Research doi: 10.1093/nar/gkh378 – volume: 72 start-page: 8309 year: 1998 ident: ref59 article-title: A Cluster of Latently Expressed Genes in Kaposi's Sarcoma-Associated Herpesvirus publication-title: J Virol doi: 10.1128/JVI.72.10.8309-8315.1998 – volume: 93 start-page: 1076 year: 2012 ident: ref118 article-title: ORF23 of murine gammaherpesvirus 68 is non-essential for in vitro and in vivo infection publication-title: The Journal of general virology doi: 10.1099/vir.0.041129-0 – volume: 284 start-page: 13958 year: 2009 ident: ref68 article-title: Mechanism of sustained activation of ribosomal S6 kinase (RSK) and ERK by kaposi sarcoma-associated herpesvirus ORF45: multiprotein complexes retain active phosphorylated ERK AND RSK and protect them from dephosphorylation publication-title: The Journal of biological chemistry doi: 10.1074/jbc.M900025200 – volume: 273 start-page: 9552 year: 1998 ident: ref84 article-title: Inhibition of CCAAT/Enhancer-binding Protein alpha and beta Translation by Upstream Open Reading Frames publication-title: Journal of Biological Chemistry doi: 10.1074/jbc.273.16.9552 – volume: 63 start-page: 2010 year: 2003 ident: ref10 article-title: Transcription Profile of Kaposi's Sarcoma-associated Herpesvirus in Primary Kaposi's Sarcoma Lesions as Determined by Real-Time PCR Arrays publication-title: Cancer Res – volume: 6 start-page: e1000935 year: 2010 ident: ref63 article-title: The epigenetic landscape of latent Kaposi sarcoma-associated herpesvirus genomes publication-title: PLoS pathogens doi: 10.1371/journal.ppat.1000935 – volume: 71 start-page: 3069 year: 1997 ident: ref131 article-title: Identification, expression, and immunogenicity of Kaposi's sarcoma- associated herpesvirus-encoded small viral capsid antigen publication-title: J Virol doi: 10.1128/JVI.71.4.3069-3076.1997 – volume: 6 start-page: 209 year: 2010 ident: ref19 article-title: Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin publication-title: Nature chemical biology doi: 10.1038/nchembio.304 – volume: 72 start-page: 5182 year: 1998 ident: ref123 article-title: Limited Transmission of Kaposi's Sarcoma-Associated Herpesvirus in Cultured Cells publication-title: J Virol doi: 10.1128/JVI.72.6.5182-5188.1998 – volume: 79 start-page: 15099 year: 2005 ident: ref28 article-title: Transcriptional analysis of latent and inducible Kaposi's sarcoma-associated herpesvirus transcripts in the K4 to K7 region publication-title: Journal of virology doi: 10.1128/JVI.79.24.15099-15106.2005 – start-page: 1865 year: 1994 ident: ref3 article-title: Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma publication-title: Science (New York, NY) doi: 10.1126/science.7997879 – volume: 8 start-page: 49 year: 2010 ident: ref26 article-title: MochiView: versatile software for genome browsing and DNA motif analysis publication-title: BMC biology doi: 10.1186/1741-7007-8-49 – volume: 197 start-page: 7 year: 2012 ident: ref69 article-title: The enduring enigma of nuclear translation publication-title: The Journal of cell biology doi: 10.1083/jcb.201202140 – volume: 84 start-page: 1471 year: 2003 ident: ref130 article-title: Transcription mapping of human herpesvirus 8 genes encoding viral interferon regulatory factors publication-title: Journal of General Virology doi: 10.1099/vir.0.19015-0 – volume: 9 start-page: e1003749 year: 2013 ident: ref36 article-title: A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection publication-title: PLoS pathogens doi: 10.1371/journal.ppat.1003749 – volume: 81 start-page: 13544 year: 2007 ident: ref49 article-title: RNA editing of the human herpesvirus 8 kaposin transcript eliminates its transforming activity and is induced during lytic replication publication-title: Journal of virology doi: 10.1128/JVI.01521-07 – year: 2013 ident: ref35 article-title: Genome-wide mapping and screening of KSHV 3′ UTRs identify bicistronic and polycistronic viral transcripts as frequent targets of KSHV microRNAs publication-title: Journal of virology – volume: 7 start-page: 1534 year: 2012 ident: ref13 article-title: The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments publication-title: Nature protocols doi: 10.1038/nprot.2012.086 – volume: 3 start-page: 1245 year: 2011 ident: ref41 article-title: Putatively Noncoding Transcripts Show Extensive Association with Ribosomes publication-title: Genome biology and evolution doi: 10.1093/gbe/evr099 – volume: 40 start-page: 2898 year: 2012 ident: ref79 article-title: Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5 publication-title: Nucleic acids research doi: 10.1093/nar/gkr1192 – volume: 174 start-page: 37 year: 2011 ident: ref91 article-title: The Kaposi's sarcoma-associated herpesvirus ORF6 DNA binding protein forms long DNA-free helical protein filaments publication-title: Journal of structural biology doi: 10.1016/j.jsb.2010.10.015 – start-page: 5233 year: 1981 ident: ref54 article-title: Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes publication-title: Nucleic acids research doi: 10.1093/nar/9.20.5233 – volume: 75 start-page: 2866 year: 2001 ident: ref120 article-title: Lytic replication of Kaposi's sarcoma-associated herpesvirus results in the formation of multiple capsid species: isolation and molecular characterization of A, B, and C capsids from a gammaherpesvirus publication-title: Journal of virology doi: 10.1128/JVI.75.6.2866-2878.2001 – volume: 76 start-page: 11880 year: 2002 ident: ref111 article-title: The Kaposi's Sarcoma-Associated Herpesvirus K12 Transcript from a Primary Effusion Lymphoma Contains Complex Repeat Elements, Is Spliced, and Initiates from a Novel Promoter publication-title: Journal of Virology doi: 10.1128/JVI.76.23.11880-11888.2002 – volume: 84 start-page: 7934 year: 2010 ident: ref6 article-title: The lytic transcriptome of Kaposi's sarcoma-associated herpesvirus reveals extensive transcription of noncoding regions, including regions antisense to important genes publication-title: Journal of virology doi: 10.1128/JVI.00645-10 – volume: 3 start-page: 60 year: 2012 ident: ref52 article-title: Ser-634 and Ser-636 of Kaposi's Sarcoma-Associated Herpesvirus RTA are Involved in Transactivation and are Potential Cdk9 Phosphorylation Sites publication-title: Frontiers in microbiology – volume: 81 start-page: 3640 year: 2007 ident: ref128 article-title: Direct visualization of the putative portal in the Kaposi's sarcoma-associated herpesvirus capsid by cryoelectron tomography publication-title: Journal of virology doi: 10.1128/JVI.02254-06 – volume: 25 start-page: 1105 year: 2009 ident: ref22 article-title: TopHat: discovering splice junctions with RNA-Seq publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btp120 – volume: 81 start-page: 2039 year: 2000 ident: ref100 article-title: On the control of late gene expression in Kaposi's sarcoma-associated herpesvirus (human herpesvirus-8) publication-title: J Gen Virol doi: 10.1099/0022-1317-81-8-2039 – volume: 38 start-page: 626 year: 2006 ident: ref30 article-title: Genome-wide analysis of mammalian promoter architecture and evolution publication-title: Nature genetics doi: 10.1038/ng1789 – volume: 81 start-page: 10137 year: 2007 ident: ref129 article-title: Murine gammaherpesvirus 68 ORF52 encodes a tegument protein required for virion morphogenesis in the cytoplasm publication-title: Journal of virology doi: 10.1128/JVI.01233-06 – volume: 31 start-page: 629 year: 2009 ident: ref132 article-title: Recombinant ORF66 and ORFK12 antigens for the detection of human herpesvirus 8 antibodies in HIV-positive and -negative patients publication-title: Biotechnology letters doi: 10.1007/s10529-009-9918-3 – volume: 80 start-page: 7037 year: 2006 ident: ref102 article-title: Genetic organization and hypoxic activation of the Kaposi's sarcoma-associated herpesvirus ORF34–37 gene cluster publication-title: Journal of virology doi: 10.1128/JVI.00553-06 – volume: 80 start-page: 9730 year: 2006 ident: ref101 article-title: ORF18 is a transfactor that is essential for late gene transcription of a gammaherpesvirus publication-title: Journal of virology doi: 10.1128/JVI.00246-06 – volume: 12 start-page: 625 year: 2011 ident: ref11 article-title: Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes publication-title: BMC genomics doi: 10.1186/1471-2164-12-625 – volume: 174 start-page: 12 year: 2011 ident: ref17 article-title: Generation of a doxycycline-inducible KSHV producer cell line of endothelial origin: maintenance of tight latency with efficient reactivation upon induction publication-title: Journal of virological methods doi: 10.1016/j.jviromet.2011.03.012 – volume: 74 start-page: 10920 year: 2000 ident: ref62 article-title: Characterization of Human Herpesvirus 8 ORF59 Protein (PF-8) and Mapping of the Processivity and Viral DNA Polymerase-Interacting Domains publication-title: Journal of Virology doi: 10.1128/JVI.74.23.10920-10929.2000 – volume: 73 start-page: 5556 year: 1999 ident: ref27 article-title: Identification of the Immediate-Early Transcripts of Kaposi's Sarcoma-Associated Herpesvirus publication-title: Journal of virology doi: 10.1128/JVI.73.7.5556-5567.1999 – reference: 23382680 - PLoS Pathog. 2013 Jan;9(1):e1003147 – reference: 16404425 - Br J Cancer. 2006 Feb 27;94(4):586-92 – reference: 16501115 - J Virol. 2006 Mar;80(6):3062-70 – reference: 21285359 - J Biol Chem. 2011 Apr 1;286(13):10939-49 – reference: 21227927 - Nucleic Acids Res. 2011 Apr;39(8):3128-40 – reference: 21047556 - J Struct Biol. 2011 Apr;174(1):37-43 – reference: 319998 - Eur J Biochem. 1977 Jan;72(2):323-30 – reference: 22589717 - PLoS Pathog. 2012;8(5):e1002680 – reference: 15613308 - J Virol. 2005 Jan;79(2):800-11 – reference: 22090138 - J Virol. 2012 Feb;86(3):1348-57 – reference: 19426857 - Adv Appl Microbiol. 2009;68:241-61 – reference: 20534856 - J Virol. 2010 Aug;84(16):7934-42 – reference: 21959131 - Nat Methods. 2011;8(10):785-6 – reference: 16528027 - J Gen Virol. 2006 Apr;87(Pt 4):795-802 – reference: 16645617 - Nat Genet. 2006 Jun;38(6):626-35 – reference: 22563327 - Front Microbiol. 2012 May 03;3:165 – reference: 17215290 - J Virol. 2007 Apr;81(7):3640-4 – reference: 15956592 - J Virol. 2005 Jul;79(13):8493-505 – reference: 9740785 - Virology. 1998 Sep 15;249(1):140-9 – reference: 17963810 - Virology. 2008 Feb 5;371(1):14-31 – reference: 17486122 - Nat Rev Genet. 2007 Jun;8(6):424-36 – reference: 11160684 - J Virol. 2001 Feb;75(4):1857-63 – reference: 9444993 - J Virol. 1998 Feb;72(2):1005-12 – reference: 9733875 - J Virol. 1998 Oct;72(10):8309-15 – reference: 11222712 - J Virol. 2001 Mar;75(6):2866-78 – reference: 9261433 - J Virol. 1997 Sep;71(9):7030-8 – reference: 15023341 - Mol Cell. 2004 Mar 12;13(5):713-23 – reference: 9837804 - Virology. 1998 Nov 25;251(2):402-13 – reference: 20661424 - PLoS Pathog. 2010;6(7):e1001013 – reference: 21809195 - Curr Top Microbiol Immunol. 2012;353:163-95 – reference: 12414930 - J Virol. 2002 Dec;76(23):11880-8 – reference: 22988838 - Crit Rev Biochem Mol Biol. 2012 Nov-Dec;47(6):493-501 – reference: 17913828 - J Virol. 2007 Dec;81(24):13544-51 – reference: 10683342 - Virology. 2000 Mar 1;268(1):201-17 – reference: 12477863 - J Virol. 2003 Jan;77(1):592-9 – reference: 10364304 - J Virol. 1999 Jul;73(7):5556-67 – reference: 7997879 - Science. 1994 Dec 16;266(5192):1865-9 – reference: 9267801 - Genome Res. 1997 Aug;7(8):768-71 – reference: 12651739 - Annu Rev Biochem. 2003;72:449-79 – reference: 12771417 - J Gen Virol. 2003 Jun;84(Pt 6):1485-91 – reference: 9573290 - J Virol. 1998 Jun;72(6):5182-8 – reference: 21079731 - PLoS One. 2010;5(11):e13875 – reference: 23810193 - Cell. 2013 Jul 3;154(1):240-51 – reference: 15247271 - J Biol Chem. 2004 Sep 10;279(37):38325-30 – reference: 21419799 - J Virol Methods. 2011 Jun;174(1-2):12-21 – reference: 11832484 - J Biol Chem. 2002 Apr 26;277(17):14547-56 – reference: 12727810 - Cancer Res. 2003 May 1;63(9):2010-5 – reference: 12359216 - Biochem Biophys Res Commun. 2002 Oct 4;297(4):756-9 – reference: 20357088 - J Virol. 2010 Jun;84(11):5465-75 – reference: 11752716 - J Gen Virol. 2002 Jan;83(Pt 1):189-93 – reference: 20921384 - Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):18056-60 – reference: 19273144 - Front Biosci (Landmark Ed). 2009;14:1516-28 – reference: 19213877 - Science. 2009 Apr 10;324(5924):218-23 – reference: 20118940 - Nat Chem Biol. 2010 Mar;6(3):209-217 – reference: 11435597 - J Virol. 2001 Aug;75(15):7161-74 – reference: 9545285 - J Biol Chem. 1998 Apr 17;273(16):9552-60 – reference: 10343068 - Semin Cancer Biol. 1999 Jun;9(3):165-74 – reference: 22366521 - Virus Res. 2012 May;165(2):157-69 – reference: 15795291 - J Virol. 2005 Apr;79(8):5059-68 – reference: 22013050 - J Virol. 2012 Jan;86(1):594-8 – reference: 23382684 - PLoS Pathog. 2013 Jan;9(1):e1003156 – reference: 15246263 - Virology. 2004 Aug 1;325(2):225-40 – reference: 19372376 - Proc Natl Acad Sci U S A. 2009 May 5;106(18):7507-12 – reference: 19289445 - Bioinformatics. 2009 May 1;25(9):1105-11 – reference: 22674989 - J Virol. 2012 Aug;86(16):8693-704 – reference: 24155407 - J Virol. 2014 Jan;88(1):377-92 – reference: 22879431 - Genome Res. 2012 Nov;22(11):2208-18 – reference: 22156057 - Nucleic Acids Res. 2012 Apr;40(7):2898-906 – reference: 8985427 - J Virol. 1997 Jan;71(1):839-42 – reference: 12111412 - Arch Virol. 2002 Jul;147(7):1349-70 – reference: 9012846 - Proc Natl Acad Sci U S A. 1997 Jan 21;94(2):690-4 – reference: 22472439 - J Cell Biol. 2012 Apr 2;197(1):45-57 – reference: 8876232 - Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11883-8 – reference: 21682836 - Biol Rev Camb Philos Soc. 2012 Feb;87(1):95-110 – reference: 822353 - Nature. 1976 Sep 16;263(5574):211-4 – reference: 24244170 - PLoS Pathog. 2013;9(11):e1003749 – reference: 186635 - J Virol. 1976 Dec;20(3):583-8 – reference: 20532208 - PLoS Pathog. 2010;6(6):e1000935 – reference: 8995643 - J Virol. 1997 Feb;71(2):1207-12 – reference: 22836135 - Nat Protoc. 2012 Aug;7(8):1534-50 – reference: 21948395 - Genome Biol Evol. 2011;3:1245-52 – reference: 11073965 - Mol Cell Biol. 2000 Dec;20(23):8635-42 – reference: 16973577 - J Virol. 2006 Oct;80(19):9730-40 – reference: 15174133 - Proteomics. 2004 Jun;4(6):1633-49 – reference: 20192758 - Annu Rev Biochem. 2010;79:321-49 – reference: 21252346 - Science. 2011 Jan 21;331(6015):330-4 – reference: 24067953 - J Virol. 2013 Dec;87(23):12838-49 – reference: 7815480 - J Virol. 1995 Feb;69(2):1030-6 – reference: 17020939 - J Virol. 2006 Dec;80(24):11968-81 – reference: 11504542 - Virology. 2001 Aug 15;287(1):62-70 – reference: 19656880 - J Virol. 2009 Oct;83(20):10582-95 – reference: 11152521 - J Virol. 2001 Feb;75(3):1487-506 – reference: 22046136 - PLoS Pathog. 2011 Oct;7(10):e1002339 – reference: 15277680 - Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11269-74 – reference: 16415016 - J Virol. 2006 Feb;80(3):1385-92 – reference: 23180859 - Science. 2012 Nov 23;338(6110):1088-93 – reference: 22363332 - Front Microbiol. 2012 Feb 20;3:59 – reference: 22056041 - Cell. 2011 Nov 11;147(4):789-802 – reference: 10859362 - Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):8051-6 – reference: 17634243 - J Virol. 2007 Sep;81(18):10137-50 – reference: 10233939 - J Virol. 1999 Jun;73(6):4786-93 – reference: 16809309 - J Virol. 2006 Jul;80(14):7037-51 – reference: 17392360 - J Virol. 2007 Jun;81(12):6761-4 – reference: 15215414 - Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W375-9 – reference: 20409324 - BMC Biol. 2010;8:49 – reference: 22185355 - BMC Genomics. 2011;12:625 – reference: 23302891 - J Virol. 2013 Mar;87(6):3461-70 – reference: 20364091 - J Clin Invest. 2010 Apr;120(4):939-49 – reference: 22371709 - Front Microbiol. 2012 Feb 22;3:60 – reference: 10968794 - Science. 2000 Sep 1;289(5484):1564-6 – reference: 22258865 - J Gen Virol. 2012 May;93(Pt 5):1076-80 – reference: 16188990 - J Virol. 2005 Oct;79(20):12880-92 – reference: 11069986 - J Virol. 2000 Dec;74(23):10920-9 – reference: 7301588 - Nucleic Acids Res. 1981 Oct 24;9(20):5233-52 – reference: 11707416 - EMBO J. 2001 Nov 15;20(22):6453-63 – reference: 11134302 - J Virol. 2001 Jan;75(2):891-902 – reference: 12438583 - J Virol. 2002 Dec;76(24):12574-83 – reference: 18057234 - J Virol. 2008 Feb;82(4):1838-50 – reference: 19279093 - J Virol. 2009 May;83(10):5056-66 – reference: 15784886 - J Gen Virol. 2005 Apr;86(Pt 4):919-28 – reference: 9060668 - J Virol. 1997 Apr;71(4):3069-76 – reference: 19906914 - J Virol. 2010 Feb;84(3):1334-47 – reference: 22472436 - J Cell Biol. 2012 Apr 2;197(1):7-9 – reference: 11312356 - J Virol. 2001 May;75(10):4843-53 – reference: 8962146 - Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14862-7 – reference: 19142585 - Biotechnol Lett. 2009 May;31(5):629-37 – reference: 12771416 - J Gen Virol. 2003 Jun;84(Pt 6):1471-83 – reference: 9878608 - Virology. 1998 Dec 20;252(2):304-12 – reference: 10900043 - J Gen Virol. 2000 Aug;81(Pt 8):2039-47 – reference: 19300492 - PLoS Pathog. 2009 Mar;5(3):e1000334 – reference: 15731337 - Nucleic Acids Res. 2005;33(4):1169-81 – reference: 9055856 - Nat Med. 1997 Mar;3(3):293-8 – reference: 10091993 - J Gen Virol. 1999 Mar;80 ( Pt 3):557-61 – reference: 19304659 - J Biol Chem. 2009 May 15;284(20):13958-68 – reference: 8939871 - Science. 1996 Dec 6;274(5293):1739-44 – reference: 22388286 - Nat Methods. 2012 Apr;9(4):357-9 – reference: 22180077 - Virus Genes. 2012 Apr;44(2):225-36 – reference: 16306581 - J Virol. 2005 Dec;79(24):15099-106 – reference: 9268289 - J Biol Chem. 1997 Aug 29;272(35):21661-4 – reference: 18305046 - J Virol. 2008 May;82(9):4562-72
SSID	ssj0041316
Score	2.543028
Snippet	Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic... Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic...
SourceID	plos doaj pubmedcentral proquest gale pubmed crossref
SourceType	Open Website Open Access Repository Aggregation Database Index Database Enrichment Source
StartPage	e1003847
SubjectTerms	Architecture Biology Cell Line Deoxyribonucleic acid DNA Editing Gene expression Gene Expression Regulation, Viral - genetics Genetic aspects Genetic research Genetic transcription Genome, Viral Genomes Genomics Health aspects Herpesvirus 8, Human - genetics High-Throughput Nucleotide Sequencing Human herpesvirus 8 Humans Infections Kaposis sarcoma Messenger RNA Microbiological research Open Reading Frames Reading RNA sequencing RNA, Untranslated - genetics RNA, Viral - genetics
SummonAdditionalLinks	– databaseName: View article at DOAJ dbid: DOA link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV3db9MwELdQJSReEN_rGMggpD1lS-KPxHsbiKkwsQfG0N6ii-10lbqkatZJ_En8l7uL06pBoL3wGp8b-e7q-51z_h1jHzxk3tDVLZcrFUnhZWQgx1SlrNDiJeA8Ou_4dqYnF_LrpbrcavVFNWGBHjgo7jA3GLG1tSp1WoKNAVKwqQOrSoQe0LGXYsxbJ1NhD8aduWt6Sk1xokxo3V-aE1ly2NvoYLEAoo-ORU6tVbaCUsfdv9mhR4t50_4Nfv5ZRbkVlk6esMc9nuTHYR1P2QNfP2MPQ4fJX8_Z79PzyU-eHsRHHDiVjy_9VShZ51DXTfgOz5uKIw7kp0AlXPstb9H7m2uIoLeddxxNu_Dt7Wy5ajnxul57TiXzU15T6jztyKu73-prs2mI2KHQu3nd3Pp5mDWz-F7HKZqGQ0he-Y5atH3BLk4-__g0ifruDJHFkJ5FWeKcLGMB2rsEpM-gqvLcmzgubWa1jo1NFGC-4o1ywjrlcu2Ns7pSlRfCiJdsVDe132E8LhNKQ62QvpSgE8hjE_sK4YRUAkozZmJtnsL21OXUQWNedN_jMkxhgrYLMmrRG3XMos2sRaDuuEf-I1l-I0vE290DdMeid8fiPnccs_fkNwVRa9RUuzOFVdsWX87PimOhZa4Qnup_Cn0fCO33QlWDi7XQ35dAlRFl10BybyCJG4QdDO-QD6_X3GK2ZwgWZwaH3q39uqBZVHBX-2bVyaTaKMw3x-xV8PONYhARKoF6GLNs8A8YaG44Us-uOupyhMcyTZPd_6Hq1-wRolcZzsP22OhmufJvECHelG-7zeAOL39n-g priority: 102 providerName: Directory of Open Access Journals
Title	KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features
URI	https://www.ncbi.nlm.nih.gov/pubmed/24453964 https://www.proquest.com/docview/1492695559 https://pubmed.ncbi.nlm.nih.gov/PMC3894221 https://doaj.org/article/896446cc52d64ac0aa2ac2dac5b932a5 http://dx.doi.org/10.1371/journal.ppat.1003847
Volume	10
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
link	http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwhV1ta9swEBZtymAMxta9NFsXtDHoJwe_SLI1GCMdzbKVhpEsI9-MLMltILUzuwnrT9q_3MmyQz0a9tW6M_bpdPecdLpD6L0Woebm6paKKHVIoInDRQShSpLCjCcC-Mx-x8WYjWbk25zO91DTs7UWYHlvaGf6Sc2KZf_3r9tPsOA_Vl0bQq9h6q9WwhSEdgOwuPvoAHxTaHoaXJDtuQJYbI_VF-h2cbYcVFXHf2utO6tlXt4HRf_NqLzjooZP0OMaW-KBVYanaE9nh-jR4M5RwSF6YJtP3j5Df86no5_Y77sf8AAbs1DoK5vNjgdZltsjepynGCAiPhcmu-ukxFNYGPm1cJpp1QqPdLHS5WZRrEv8RWf5tcZVIgIem6ja1rWu3jW1adtmaKI3gFBLPM43emm5FhKLTOEhOFq7P4kNPIWPLp-j2fDsx-eRUzducCR4-9AJPaVI4gaCaeUJokORplGkuesmMpSMuVx6VEAoozlVgVRURUxzJVlKUx0EPHiBOlme6SOE3cQzEaoMiE6IYJ6IXO7qFJAGoYFIeBcFzWzFsq5qbpprLOPqqC6E6MYKPzZzHNdz3EXOlmtlq3r8h_7UKMKW1tTkrh7kxWVcL_E44oAtmZTUV4wI6QrhC-krIWkCIFnQLnpn1Cg2VTcyk9ZzKdZlGX-djuNBwEhEAbmynUSTFtFJTZTm8LNS1FcpQGSmmleL8rhFCbZDtoaPjEo3_1xCIMgNYg45DL1t1Dw2XCYXL9P5uqLxGacQinbRS6v2W8EAWKQByKGLwtaCaEmuPZItrqqq5oCcie97r3Z_0mv0EOAqsRtgx6hzU6z1G4CEN0kP7YfzsIcOTs_G3ye9amOlV638vxPGZ3g
linkProvider	Scholars Portal
openUrl	ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=KSHV+2.0%3A+A+Comprehensive+Annotation+of+the+Kaposi%27s+Sarcoma-Associated+Herpesvirus+Genome+Using+Next-Generation+Sequencing+Reveals+Novel+Genomic+and+Functional+Features&rft.jtitle=PLoS+pathogens&rft.au=Arias%2C+Carolina&rft.au=Weisburd%2C+Ben&rft.au=Stern-Ginossar%2C+Noam&rft.au=Mercier%2C+Alexandre&rft.date=2014-01-01&rft.pub=Public+Library+of+Science&rft.eissn=1553-7374&rft.volume=10&rft.issue=1&rft_id=info:doi/10.1371%2Fjournal.ppat.1003847&rft.externalDocID=1498392796
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1553-7374&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1553-7374&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1553-7374&client=summon