Genome-Wide Analysis of Histone Modifications： H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica
While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by...
Saved in:
| Published in | Molecular plant Vol. 6; no. 5; pp. 1463 - 1472 |
|---|---|
| Main Authors | , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Elsevier Inc
01.09.2013
Cell Press Oxford University Press |
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing （ChlP-Seq）, to investigate the genome-wide distribution of four histone modifications： di and trimethylation of H3K4 （H3K4me2 and H3K4me3） and acylation of H3K9 and H3K27 （H3K9ac and H3K27ac） in Oryza sativa L. japonica. By analyz- ing published DNase-Seq data, this study explored DNase-Hypersensitive （DH） sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites （TSSs） of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites. |
|---|---|
| AbstractList | SUMMARY H3K4me2/3, H3K9ac, and H3K27ac investigated by ChIP-Seq showed enrichment in generic regions and transcription start sites, and associated with active transcription in rice. They were used to discover unannotated genes and to predict transcription factor binding sites together with DNase-Seq data. While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions--a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites. [PUBLICATION ABSTRACT] While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions—a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites.H3K4me2/3, H3K9ac, and H3K27ac investigated by ChIP-Seq showed enrichment in generic regions and transcription start sites, and associated with active transcription in rice. They were used to discover unannotated genes and to predict transcription factor binding sites together with DNase-Seq data. While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions—a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites. H3K4me2/3, H3K9ac, and H3K27ac investigated by ChIP-Seq showed enrichment in generic regions and transcription start sites, and associated with active transcription in rice. They were used to discover unannotated genes and to predict transcription factor binding sites together with DNase-Seq data. While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites. While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites.While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites. H3K4me2/3, H3K9ac, and H3K27ac investigated by ChIP-Seq showed enrichment in generic regions and transcription start sites, and associated with active transcription in rice. They were used to discover unannotated genes and to predict transcription factor binding sites together with DNase-Seq data. While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions—a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites. While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing （ChlP-Seq）, to investigate the genome-wide distribution of four histone modifications： di and trimethylation of H3K4 （H3K4me2 and H3K4me3） and acylation of H3K9 and H3K27 （H3K9ac and H3K27ac） in Oryza sativa L. japonica. By analyz- ing published DNase-Seq data, this study explored DNase-Hypersensitive （DH） sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites （TSSs） of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites. |
| Author | Zhou Du Hui Li Qiang Wei Xin Zhao Chunchao Wang Qilin Zhu Xin Yi Wenying Xua X. Shirley Liu Weiwei Jin Zhen Su |
| AuthorAffiliation | State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize, Ministry of Agriculture, China Agricultura University, Beijing 100193, China Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Ave, Boston, MA 02215, USA These authors contributed equally to the article. Present address： Department of Bioinformatics, School of Life Sciences andTechnology, Tongji University, 1239 Siping Road, Shanghai 200092, China |
| Author_xml | – sequence: 1 givenname: Zhou surname: Du fullname: Du, Zhou organization: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China – sequence: 2 givenname: Hui surname: Li fullname: Li, Hui organization: National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize, Ministry of Agriculture, China Agricultural University, Beijing 100193, China – sequence: 3 givenname: Qiang surname: Wei fullname: Wei, Qiang organization: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China – sequence: 4 givenname: Xin surname: Zhao fullname: Zhao, Xin organization: National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize, Ministry of Agriculture, China Agricultural University, Beijing 100193, China – sequence: 5 givenname: Chunchao surname: Wang fullname: Wang, Chunchao organization: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China – sequence: 6 givenname: Qilin surname: Zhu fullname: Zhu, Qilin organization: National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize, Ministry of Agriculture, China Agricultural University, Beijing 100193, China – sequence: 7 givenname: Xin surname: Yi fullname: Yi, Xin organization: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China – sequence: 8 givenname: Wenying surname: Xu fullname: Xu, Wenying organization: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China – sequence: 9 givenname: X. Shirley surname: Liu fullname: Liu, X. Shirley email: xsliu@jimmy.harvard.edu organization: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Ave, Boston, MA 02215, USA – sequence: 10 givenname: Weiwei surname: Jin fullname: Jin, Weiwei email: weiweijin@cau.edu.cn organization: National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize, Ministry of Agriculture, China Agricultural University, Beijing 100193, China – sequence: 11 givenname: Zhen surname: Su fullname: Su, Zhen email: zhensu@cau.edu.cn organization: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23355544$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFks1uEzEUhUeoiP7AghdARmxA6jT-Hc9sKlUVNEBQNyCWlmPfSV3N2FN7Eik8Cs_CO_EKuElaQVWJlY_k75x77XsPiz0fPBTFS4JPCG7YpB8mKY2Y1E-KAyIFLZu6kntZV5KXFAu6XxymdI1xheuKPSv2KWNCCM4PingBPvRQfncW0JnX3Tq5hEKLpi6NuQr6EqxrndGjCz79_vUTTdln3gM93gm2EY02x0h7e6up1AY5jy7j-odGKTtXGs1O0Cc9BJ-TnhdPW90leLE7j4pvH95_PZ-Ws8uLj-dns9IITMeSW2CY15RKyTmTTFhGeNNiWrFW1rUhgGUD8waEaGtKJG4rWmMLlNkW5tiyo-J0mzss5z1YA36MulNDdL2OaxW0U__eeHelFmGlWM0pYTwHvN0FxHCzhDSq3iUDXac9hGVSFGPMSENx_V-UcMYlp1VNM_rmAXodljH_fKYExlQIvKn96u_m77u-m1wGJlvAxJBShFYZN26mlN_iOkWwut0N1Q9quxvZ8e6B4y70MZZtWcgDWjmIKhkH3oB1EcyobHCPul7vKlwFv7hxfnFfgue1zK1T9geNQ9UC |
| CitedBy_id | crossref_primary_10_1093_nar_gkx919 crossref_primary_10_1038_s41467_022_28453_y crossref_primary_10_1186_s13020_021_00502_6 crossref_primary_10_1016_j_anireprosci_2014_03_012 crossref_primary_10_3390_genes10050355 crossref_primary_10_1093_nar_gky209 crossref_primary_10_3390_agronomy13020519 crossref_primary_10_1007_s11738_020_3015_6 crossref_primary_10_1186_s12870_024_05318_8 crossref_primary_10_1038_s41477_019_0589_3 crossref_primary_10_1002_pmic_201700036 crossref_primary_10_1371_journal_pgen_1008764 crossref_primary_10_1104_pp_15_00934 crossref_primary_10_1080_15592294_2015_1104446 crossref_primary_10_1186_s13072_017_0132_6 crossref_primary_10_1101_gr_220079_116 crossref_primary_10_1111_pce_13660 crossref_primary_10_7717_peerj_10811 crossref_primary_10_1007_s00299_024_03160_8 crossref_primary_10_1186_s12864_019_5609_1 crossref_primary_10_1007_s13765_016_0236_x crossref_primary_10_1016_j_bbagrm_2016_06_006 crossref_primary_10_1093_hr_uhae259 crossref_primary_10_1007_s12038_013_9388_6 crossref_primary_10_1016_j_molp_2022_03_009 crossref_primary_10_3390_ijms232112918 crossref_primary_10_3390_ijms24119349 crossref_primary_10_18632_oncotarget_6867 crossref_primary_10_1007_s11033_020_06013_1 crossref_primary_10_1093_jxb_erab072 crossref_primary_10_1016_j_molp_2016_05_013 crossref_primary_10_1038_s41467_018_05829_7 crossref_primary_10_1016_j_csbj_2021_12_027 crossref_primary_10_1080_07391102_2014_1003198 crossref_primary_10_1093_jxb_erw119 crossref_primary_10_1016_j_plaphy_2014_11_012 crossref_primary_10_3389_fphys_2014_00211 crossref_primary_10_1038_s41598_017_09680_6 crossref_primary_10_1093_nar_gku1162 crossref_primary_10_3390_plants12152852 crossref_primary_10_3390_plants5030037 crossref_primary_10_1111_tpj_70040 crossref_primary_10_1007_s11103_017_0636_2 crossref_primary_10_1074_jbc_M114_579292 crossref_primary_10_1111_jipb_12871 crossref_primary_10_1186_s12864_022_09070_x crossref_primary_10_1007_s11103_023_01375_z crossref_primary_10_3389_fpls_2014_00803 crossref_primary_10_1093_hr_uhae328 crossref_primary_10_1093_jxb_erac155 crossref_primary_10_1093_pcp_pcae121 crossref_primary_10_2139_ssrn_4102874 crossref_primary_10_1016_j_plantsci_2019_03_009 crossref_primary_10_1038_s41467_019_09513_2 crossref_primary_10_1007_s00425_015_2405_2 crossref_primary_10_1093_nsr_nww042 crossref_primary_10_1111_plb_13057 crossref_primary_10_1021_acs_jafc_0c07035 crossref_primary_10_1186_s12284_019_0342_6 crossref_primary_10_1007_s11103_015_0358_2 crossref_primary_10_1111_mpp_13037 crossref_primary_10_3390_ijms232415950 crossref_primary_10_3389_fgene_2019_00306 crossref_primary_10_1016_j_ygeno_2022_110433 crossref_primary_10_3389_fgene_2020_00766 crossref_primary_10_1093_nar_gky025 crossref_primary_10_1016_j_molp_2020_12_020 crossref_primary_10_1021_acs_jafc_2c08863 crossref_primary_10_1016_j_ygeno_2015_05_005 crossref_primary_10_1007_s00122_019_03518_7 crossref_primary_10_1074_mcp_RA118_000640 crossref_primary_10_1016_j_plantsci_2018_04_010 crossref_primary_10_1093_plphys_kiae229 crossref_primary_10_1186_s12864_019_6038_x crossref_primary_10_1186_s13072_019_0285_6 crossref_primary_10_3390_plants13152079 crossref_primary_10_3389_fpls_2015_00846 crossref_primary_10_1016_j_csbj_2021_04_068 crossref_primary_10_1038_srep08635 crossref_primary_10_1093_plcell_koaa027 crossref_primary_10_1134_S2079086423020093 crossref_primary_10_1007_s11103_020_00985_1 crossref_primary_10_1038_s41467_020_16457_5 crossref_primary_10_31857_S0042132423010106 crossref_primary_10_1016_j_bbrc_2018_04_048 crossref_primary_10_1038_s41467_024_53300_7 crossref_primary_10_1051_jbio_2017004 crossref_primary_10_3390_plants10040706 crossref_primary_10_1016_j_pbi_2020_08_007 crossref_primary_10_1093_bfgp_ely004 crossref_primary_10_1186_s13059_017_1273_4 crossref_primary_10_3389_fpls_2018_01228 crossref_primary_10_1111_nph_15897 crossref_primary_10_3389_fgene_2022_949027 crossref_primary_10_1016_j_molp_2018_01_007 crossref_primary_10_1007_s13205_020_02331_0 |
| Cites_doi | 10.1186/gb-2009-10-6-r62 10.1038/nrg2522 10.1007/s00412-011-0315-z 10.1023/A:1022567625228 10.1093/nar/gkl976 10.1186/1471-2164-12-134 10.1101/gr.116467.110 10.1038/nrg2270 10.1101/gr.229102 10.1093/bioinformatics/btp479 10.1016/j.gde.2009.02.001 10.1101/gr.121541.111 10.1046/j.1365-313X.2002.01294.x 10.1002/j.1460-2075.1993.tb06025.x 10.1073/pnas.1016071107 10.1105/tpc.110.080481 10.1101/gr.131342.111 10.1023/A:1006423324025 10.1038/nbt.1621 10.1038/ng.154 10.1105/tpc.107.056879 10.1016/j.cell.2007.05.009 10.1093/bioinformatics/btp324 10.1038/nature05915 10.1186/gb-2011-12-8-r83 10.1186/gb-2008-9-9-r137 10.1105/tpc.109.066845 10.1101/gr.5509507 10.1038/nrg2905 10.1105/tpc.109.072041 10.1046/j.1365-313X.2003.01971.x 10.1101/gr.112623.110 10.1093/genetics/163.3.1221 10.1016/j.pbi.2007.07.013 10.1007/s10142-012-0263-6 10.1186/1471-2229-10-238 10.1093/nar/gkg108 |
| ContentType | Journal Article |
| Copyright | 2013 The Authors. All rights reserved. The Author 2013. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS. The Author 2013. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS. 2013 |
| Copyright_xml | – notice: 2013 The Authors. All rights reserved. – notice: The Author 2013. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS. – notice: The Author 2013. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS. 2013 |
| DBID | 2RA 92L CQIGP W94 WU4 ~WA 6I. AAFTH AAYXX CITATION CGR CUY CVF ECM EIF NPM K9. 7X8 7S9 L.6 5PM |
| DOI | 10.1093/mp/sst018 |
| DatabaseName | 维普_期刊 中文科技期刊数据库-CALIS站点 中文科技期刊数据库-7.0平台 中文科技期刊数据库-自然科学 中文科技期刊数据库-自然科学-生物科学 中文科技期刊数据库- 镜像站点 ScienceDirect Open Access Titles Elsevier:ScienceDirect:Open Access CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Health & Medical Complete (Alumni) MEDLINE - Academic AGRICOLA AGRICOLA - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) ProQuest Health & Medical Complete (Alumni) MEDLINE - Academic AGRICOLA AGRICOLA - Academic |
| DatabaseTitleList | ProQuest Health & Medical Complete (Alumni) AGRICOLA MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 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: 2 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 | Botany |
| DocumentTitleAlternate | Genome-Wide Analysis of Histone Modifications： H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica |
| EISSN | 1752-9867 |
| EndPage | 1472 |
| ExternalDocumentID | PMC3842134 3223572271 23355544 10_1093_mp_sst018 S1674205214602203 47523352 |
| Genre | Research Support, Non-U.S. Gov't Journal Article Research Support, N.I.H., Extramural |
| GrantInformation_xml | – fundername: NIGMS NIH HHS grantid: GM99409 – fundername: NIGMS NIH HHS grantid: R01 GM099409 |
| GroupedDBID | --- --M .2P .I3 0R~ 123 1RT 2RA 2WC 4.4 457 53G 6I. 7-5 70D 8P~ 92L AABVA AACTN AAEDT AAEDW AAFTH AAIAV AAIKJ AAIYJ AAKOC AALRI AAOAW AATLK AAVLN AAXUO ABFNM ABGRD ABJNI ABMAC ABNKS ABVKL ABXDB ABYKQ ABZBJ ACDAQ ACGFS ACPRK ACRLP ADBBV ADEYI ADEZE ADFTL ADOCK ADZTZ AEBSH AEGPL AEKER AENEX AEXQZ AFKWA AFRAH AFTJW AFXIZ AGHFR AGKEF AGUBO AHMBA AHXPO AIEXJ AIJHB AIKHN AITUG AJBFU AJOXV AKHUL ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ AXJTR BKOJK BLXMC CKLRP CQIGP CS3 CW9 CZ4 DU5 E3Z EBS EDH EE~ EFJIC EFLBG EJD ESX F5P F9B FDB FIRID FYGXN GBLVA H5~ HW0 HZ~ IOX IXB KOM M-Z M41 M49 N9A NCXOZ NU- O0~ O9- OAUVE OK1 OVD P2P PQQKQ Q1. RCE RD5 ROL RW1 RXO SPCBC SSA SSZ T5K TEORI TR2 W8F W94 WU4 X7H ~91 ~G- ~WA AAHBH AAMRU AAQFI AATTM AAXKI AAYWO AAYXX ACVFH ADCNI ADVLN AEIPS AEUPX AFPUW AGCQF AGRNS AIGII AIIUN AKBMS AKRWK AKYEP ANKPU APXCP BNPGV CITATION H13 SSH TGP CGR CUY CVF ECM EFKBS EIF NPM K9. 7X8 7S9 L.6 5PM |
| ID | FETCH-LOGICAL-c502t-4de30482277443735d3149f0263f788c1e079eb9e55f82170f6280de23dfeb0d3 |
| IEDL.DBID | IXB |
| ISSN | 1674-2052 1752-9867 |
| IngestDate | Thu Aug 21 14:12:56 EDT 2025 Fri Jul 11 15:15:58 EDT 2025 Thu Jul 10 17:23:05 EDT 2025 Wed Aug 13 08:20:29 EDT 2025 Mon Jul 21 06:03:26 EDT 2025 Thu Apr 24 23:06:58 EDT 2025 Tue Jul 01 01:40:44 EDT 2025 Fri Feb 23 02:27:16 EST 2024 Wed Feb 14 10:39:38 EST 2024 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 5 |
| Keywords | genomics chromatin structure and remodeling rice gene regulation epigenetics bioinformatics |
| Language | English |
| License | http://www.elsevier.com/open-access/userlicense/1.0 https://www.elsevier.com/tdm/userlicense/1.0 |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c502t-4de30482277443735d3149f0263f788c1e079eb9e55f82170f6280de23dfeb0d3 |
| Notes | 31-2013/Q While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing （ChlP-Seq）, to investigate the genome-wide distribution of four histone modifications： di and trimethylation of H3K4 （H3K4me2 and H3K4me3） and acylation of H3K9 and H3K27 （H3K9ac and H3K27ac） in Oryza sativa L. japonica. By analyz- ing published DNase-Seq data, this study explored DNase-Hypersensitive （DH） sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites （TSSs） of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites. bioinformatics; chromatin structure and remodeling; epigenetics; gene regulation; genomics; rice. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
| OpenAccessLink | https://www.sciencedirect.com/science/article/pii/S1674205214602203 |
| PMID | 23355544 |
| PQID | 1500255034 |
| PQPubID | 135333 |
| PageCount | 10 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_3842134 proquest_miscellaneous_2000319208 proquest_miscellaneous_1434742682 proquest_journals_1500255034 pubmed_primary_23355544 crossref_citationtrail_10_1093_mp_sst018 crossref_primary_10_1093_mp_sst018 elsevier_sciencedirect_doi_10_1093_mp_sst018 chongqing_primary_47523352 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2013-09-01 |
| PublicationDateYYYYMMDD | 2013-09-01 |
| PublicationDate_xml | – month: 09 year: 2013 text: 2013-09-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England – name: Cambridge – name: UK |
| PublicationTitle | Molecular plant |
| PublicationTitleAlternate | Molecular Plant |
| PublicationYear | 2013 |
| Publisher | Elsevier Inc Cell Press Oxford University Press |
| Publisher_xml | – name: Elsevier Inc – name: Cell Press – name: Oxford University Press |
| References | Zhang, Bernatavichute, Cokus, Pellegrini, Jacobsen (bib37) 2009; 10 Ha, Ng, Li (bib6) 2011; 21 Zhang, Wu, Schnable, Zeng, Freeling, Crawford, Jiang (bib36) 2011; 22 Jiang, Pugh (bib12) 2009; 10 Wang, Zang, Rosenfeld, Schones, Barski, Cuddapah, Cui, Roh, Peng, Zhang (bib35) 2008; 40 Berger (bib3) 2007; 447 Jang, Chung, Hemmes, Jung, Chua (bib11) 2011; 23 Creyghton, Cheng, Welstead, Kooistra, Carey, Steine, Hanna, Lodato, Frampton, Sharp (bib5) 2010; 107 Li, Wang, He, Ma, Su, He, Stolc, Tongprasit, Jin, Jiang (bib18) 2008; 20 Nagaki, Talbert, Zhong, Dawe, Henikoff, Jiang (bib22) 2003; 163 Shin, Liu, Manrai, Liu (bib28) 2009; 25 Li (bib17) 2009; 25 Zhang, Liu, Meyer, Eeckhoute, Johnson, Bernstein, Nusbaum, Myers, Brown, Li (bib38) 2008; 9 Wang, He, Liu, Cheng, Talbert, Jin (bib33) 2011; 120 Wang, Schones, Zhao (bib34) 2009; 19 Ouyang, Zhu, Hamilton, Lin, Campbell, Childs, Thibaud-Nissen, Malek, Lee, Zheng (bib23) 2007; 35 Kosugi, Ohashi (bib16) 2002; 30 Johannesson, Wang, Engström (bib13) 2001; 45 Song, Zhang, Grasfeder, Boyle, Giresi, Lee, Sheffield, Gräf, Huss, Keefe (bib30) 2011; 21 Meister, Williams, Monfared (bib21) 2004; 37 Barski, Cuddapah, Cui, Roh, Schones, Wang, Wei, Chepelev, Zhao (bib2) 2007; 129 Johannesson, Wang, Hanson (bib14) 2003; 51 Charron, He, Elling, Deng (bib4) 2009; 21 Zhou, Goren, Bernstein (bib39) 2010; 12 Pfluger, Wagner (bib24) 2007; 10 Itoh, Tanaka, Barrero, Yamasaki, Fujii, Hilton, Antonio, Aono, Apweiler, Bruskiewich (bib10) 2007; 17 Liu, Ortiz, Taing, Meyer, Lee, Zhang, Shin, Wong, Ma, Lei (bib19) 2011; 12 Shin, Li, Gao, Baldwin, Li (bib29) 2012; 12 Sessa, Morelli, Ruberti (bib27) 1993; 12 Ho, Bishop, Karchenko, Negre, White, Park (bib9) 2011; 12 Kent, Sugnet, Furey, Roskin, Pringle, Zahler, Haussler (bib15) 2002; 12 Schones, Zhao (bib26) 2008; 9 He, Zhu, Elling, Chen, Wang, Guo, Liang, He, Zhang, Chen (bib7) 2010; 22 Heintzman, Stuart, Hon, Fu, Ching, Hawkins, Barrera, Van Calcar, Qu, Ching (bib8) 2007; 39 Matys, Fricke, Geffers (bib20) 2003; 31 Trapnell, Williams, Pertea, Mortazavi, Kwan, van Baren, Salzberg, Wold, Pachter (bib31) 2010; 28 Aoyama, Dong, Wu, Carabelli (bib1) 1995; 7 Pique-Regi, Degner, Pai, Gaffney, Gilad, Pritchard (bib25) 2011; 21 van Dijk, Ding, Malkaram, Riethoven, Liu, Yang, Laczko, Chen, Xia, Ladunga (bib32) 2010; 10 Shin (10.1093/mp/sst018_bib28) 2009; 25 Shin (10.1093/mp/sst018_bib29) 2012; 12 Zhang (10.1093/mp/sst018_bib38) 2008; 9 Ho (10.1093/mp/sst018_bib9) 2011; 12 Zhou (10.1093/mp/sst018_bib39) 2010; 12 Sessa (10.1093/mp/sst018_bib27) 1993; 12 Barski (10.1093/mp/sst018_bib2) 2007; 129 van Dijk (10.1093/mp/sst018_bib32) 2010; 10 Kent (10.1093/mp/sst018_bib15) 2002; 12 Kosugi (10.1093/mp/sst018_bib16) 2002; 30 Li (10.1093/mp/sst018_bib17) 2009; 25 Meister (10.1093/mp/sst018_bib21) 2004; 37 Song (10.1093/mp/sst018_bib30) 2011; 21 Wang (10.1093/mp/sst018_bib33) 2011; 120 Pfluger (10.1093/mp/sst018_bib24) 2007; 10 Zhang (10.1093/mp/sst018_bib37) 2009; 10 Wang (10.1093/mp/sst018_bib34) 2009; 19 Itoh (10.1093/mp/sst018_bib10) 2007; 17 Johannesson (10.1093/mp/sst018_bib14) 2003; 51 Ouyang (10.1093/mp/sst018_bib23) 2007; 35 Berger (10.1093/mp/sst018_bib3) 2007; 447 Heintzman (10.1093/mp/sst018_bib8) 2007; 39 Jang (10.1093/mp/sst018_bib11) 2011; 23 Matys (10.1093/mp/sst018_bib20) 2003; 31 Wang (10.1093/mp/sst018_bib35) 2008; 40 Zhang (10.1093/mp/sst018_bib36) 2011; 22 Jiang (10.1093/mp/sst018_bib12) 2009; 10 Schones (10.1093/mp/sst018_bib26) 2008; 9 Liu (10.1093/mp/sst018_bib19) 2011; 12 Trapnell (10.1093/mp/sst018_bib31) 2010; 28 Pique-Regi (10.1093/mp/sst018_bib25) 2011; 21 Charron (10.1093/mp/sst018_bib4) 2009; 21 Nagaki (10.1093/mp/sst018_bib22) 2003; 163 Creyghton (10.1093/mp/sst018_bib5) 2010; 107 Li (10.1093/mp/sst018_bib18) 2008; 20 Aoyama (10.1093/mp/sst018_bib1) 1995; 7 Johannesson (10.1093/mp/sst018_bib13) 2001; 45 He (10.1093/mp/sst018_bib7) 2010; 22 Ha (10.1093/mp/sst018_bib6) 2011; 21 17145706 - Nucleic Acids Res. 2007 Jan;35(Database issue):D883-7 19451168 - Bioinformatics. 2009 Jul 15;25(14):1754-60 21859476 - Genome Biol. 2011;12(8):R83 21394438 - Chromosoma. 2011 Aug;120(4):353-65 21317377 - Plant Cell. 2011 Feb;23(2):459-70 12678559 - Plant Mol Biol. 2003 Mar;51(5):719-29 14731261 - Plant J. 2004 Feb;37(3):426-38 20086188 - Plant Cell. 2010 Jan;22(1):17-33 21324879 - Genome Res. 2011 Apr;21(4):590-8 8535134 - Plant Cell. 1995 Nov;7(11):1773-85 19299119 - Curr Opin Genet Dev. 2009 Apr;19(2):127-34 20008096 - Plant Cell. 2009 Dec;21(12):3732-48 12000681 - Plant J. 2002 May;30(3):337-48 21106759 - Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6 12045153 - Genome Res. 2002 Jun;12(6):996-1006 17210932 - Genome Res. 2007 Feb;17(2):175-83 17522673 - Nature. 2007 May 24;447(7143):407-12 21356108 - BMC Genomics. 2011;12:134 22110044 - Genome Res. 2012 Jan;22(1):151-62 11247607 - Plant Mol Biol. 2001 Jan;45(1):63-73 19508735 - Genome Biol. 2009;10(6):R62 18250624 - Nat Rev Genet. 2008 Mar;9(3):179-91 19689956 - Bioinformatics. 2009 Oct 1;25(19):2605-6 17277777 - Nat Genet. 2007 Mar;39(3):311-8 17512414 - Cell. 2007 May 18;129(4):823-37 18552846 - Nat Genet. 2008 Jul;40(7):897-903 18798982 - Genome Biol. 2008;9(9):R137 18263775 - Plant Cell. 2008 Feb;20(2):259-76 21750106 - Genome Res. 2011 Oct;21(10):1757-67 20436464 - Nat Biotechnol. 2010 May;28(5):511-5 21050490 - BMC Plant Biol. 2010;10:238 17884714 - Curr Opin Plant Biol. 2007 Dec;10(6):645-52 19204718 - Nat Rev Genet. 2009 Mar;10(3):161-72 22249597 - Funct Integr Genomics. 2012 Mar;12(1):119-30 21116306 - Nat Rev Genet. 2011 Jan;12(1):7-18 8253077 - EMBO J. 1993 Sep;12(9):3507-17 12663558 - Genetics. 2003 Mar;163(3):1221-5 12520026 - Nucleic Acids Res. 2003 Jan 1;31(1):374-8 21106904 - Genome Res. 2011 Mar;21(3):447-55 |
| References_xml | – volume: 31 start-page: 374 year: 2003 end-page: 378 ident: bib20 article-title: TRANSFAC®: transcriptional regulation, from patterns to profiles publication-title: Nucleic Acids Res – volume: 9 start-page: R137 year: 2008 ident: bib38 article-title: Model-based analysis of ChIP-Seq (MACS) publication-title: Genome Biol – volume: 21 start-page: 590 year: 2011 end-page: 598 ident: bib6 article-title: Coordinated histone modifications are associated with gene expression variation within and between species publication-title: Genome Res – volume: 9 start-page: 179 year: 2008 end-page: 191 ident: bib26 article-title: Genome-wide approaches to studying chromatin modifications publication-title: Nat. Rev. Genet – volume: 129 start-page: 823 year: 2007 end-page: 837 ident: bib2 article-title: High-resolution profiling of histone methylations in the human genome publication-title: Cell – volume: 17 start-page: 175 year: 2007 end-page: 183 ident: bib10 article-title: Curated genome annotation of publication-title: Genome Res – volume: 30 start-page: 337 year: 2002 end-page: 348 ident: bib16 article-title: DNA binding and dimerization specificity and potential targets for the TCP protein family publication-title: Plant J – volume: 37 start-page: 426 year: 2004 end-page: 438 ident: bib21 article-title: Definition and interactions of a positive regulatory element of the publication-title: Plant J – volume: 19 start-page: 127 year: 2009 end-page: 134 ident: bib34 article-title: Characterization of human epigenomes publication-title: Curr. Opin. Genet. Dev – volume: 107 start-page: 21931 year: 2010 end-page: 21936 ident: bib5 article-title: Histone H3K27ac separates active from poised enhancers and predicts developmental state publication-title: Proc. Natl Acad. Sci. U S A – volume: 12 start-page: 134 year: 2011 ident: bib9 article-title: ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis publication-title: BMC Genomics – volume: 20 start-page: 259 year: 2008 end-page: 276 ident: bib18 article-title: High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression publication-title: Plant Cell – volume: 447 start-page: 407 year: 2007 end-page: 412 ident: bib3 article-title: The complex language of chromatin regulation during transcription publication-title: Nature – volume: 22 start-page: 17 year: 2010 end-page: 33 ident: bib7 article-title: Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids publication-title: Plant Cell – volume: 12 start-page: 7 year: 2010 end-page: 18 ident: bib39 article-title: Charting histone modifications and the functional organization of mammalian genomes publication-title: Nat. Rev. Genet – volume: 28 start-page: 511 year: 2010 end-page: 515 ident: bib31 article-title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation publication-title: Nat. Biotechnol – volume: 10 start-page: 238 year: 2010 ident: bib32 article-title: Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in publication-title: BMC Plant Biol – volume: 7 start-page: 1773 year: 1995 end-page: 1785 ident: bib1 article-title: Ectopic expression of the publication-title: Plant Cell – volume: 21 start-page: 3732 year: 2009 end-page: 3748 ident: bib4 article-title: Dynamic landscapes of four histone modifications during deetiolation in publication-title: Plant Cell – volume: 21 start-page: 1757 year: 2011 end-page: 1767 ident: bib30 article-title: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity publication-title: Genome Res – volume: 12 start-page: 3507 year: 1993 end-page: 3517 ident: bib27 article-title: The Athb-1 and –2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities publication-title: EMBO J – volume: 163 start-page: 1221 year: 2003 end-page: 1225 ident: bib22 article-title: Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of publication-title: Genetics – volume: 10 start-page: 161 year: 2009 end-page: 172 ident: bib12 article-title: Nucleosome positioning and gene regulation: advances through genomics publication-title: Nat. Rev. Genet – volume: 22 start-page: 151 year: 2011 end-page: 162 ident: bib36 article-title: High-resolution mapping of open chromatin in the rice genome publication-title: Genome Res – volume: 35 start-page: D883 year: 2007 end-page: D887 ident: bib23 article-title: The TIGR Rice Genome Annotation Resource: improvements and new features publication-title: Nucleic Acids Res – volume: 10 start-page: R62 year: 2009 ident: bib37 article-title: Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in publication-title: Genome Biol – volume: 12 start-page: R83 year: 2011 ident: bib19 article-title: Cistrome: an integrative platform for transcriptional regulation studies publication-title: Genome Biol – volume: 12 start-page: 996 year: 2002 end-page: 1006 ident: bib15 article-title: The human genome browser at UCSC publication-title: Genome Res – volume: 39 start-page: 311 year: 2007 end-page: 318 ident: bib8 article-title: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome publication-title: Nature – volume: 25 start-page: 2605 year: 2009 end-page: 2606 ident: bib28 article-title: CEAS: publication-title: Bioinformatics – volume: 12 start-page: 119 year: 2012 end-page: 130 ident: bib29 article-title: Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells publication-title: Funct. Integr. Genomics – volume: 23 start-page: 459 year: 2011 end-page: 470 ident: bib11 article-title: Rapid and reversible light-mediated chromatin modifications of publication-title: Plant Cell – volume: 120 start-page: 353 year: 2011 end-page: 365 ident: bib33 article-title: Characterization of CENH3 proteins and centromere-associated DNA sequences in diploid and allotetraploid Brassica species publication-title: Chromosoma – volume: 10 start-page: 645 year: 2007 end-page: 652 ident: bib24 article-title: Histone modifications and dynamic regulation of genome accessibility in plants publication-title: Curr. Opin. Plant Biol – volume: 45 start-page: 63 year: 2001 end-page: 73 ident: bib13 article-title: DNA-binding and dimerization preferences of publication-title: Plant Mol. Biol – volume: 51 start-page: 719 year: 2003 end-page: 729 ident: bib14 article-title: The publication-title: Plant Mol. Biol – volume: 25 start-page: 1754 year: 2009 end-page: 1760 ident: bib17 article-title: Fast and accurate short read alignment with Burrows–Wheeler transform publication-title: Bioinformatics – volume: 40 start-page: 897 year: 2008 end-page: 903 ident: bib35 article-title: Combinatorial patterns of histone acetylations and methylations in the human genome publication-title: Nat. Genet – volume: 21 start-page: 447 year: 2011 end-page: 455 ident: bib25 article-title: Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data publication-title: Genome Res – volume: 39 start-page: 311 year: 2007 ident: 10.1093/mp/sst018_bib8 article-title: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome publication-title: Nature – volume: 10 start-page: R62 year: 2009 ident: 10.1093/mp/sst018_bib37 article-title: Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana publication-title: Genome Biol doi: 10.1186/gb-2009-10-6-r62 – volume: 10 start-page: 161 year: 2009 ident: 10.1093/mp/sst018_bib12 article-title: Nucleosome positioning and gene regulation: advances through genomics publication-title: Nat. Rev. Genet doi: 10.1038/nrg2522 – volume: 120 start-page: 353 year: 2011 ident: 10.1093/mp/sst018_bib33 article-title: Characterization of CENH3 proteins and centromere-associated DNA sequences in diploid and allotetraploid Brassica species publication-title: Chromosoma doi: 10.1007/s00412-011-0315-z – volume: 51 start-page: 719 year: 2003 ident: 10.1093/mp/sst018_bib14 article-title: The Arabidopsis thaliana homeobox gene ATHB5 is a potential regulator of abscisic acid responsiveness in developing seedlings publication-title: Plant Mol. Biol doi: 10.1023/A:1022567625228 – volume: 35 start-page: D883 year: 2007 ident: 10.1093/mp/sst018_bib23 article-title: The TIGR Rice Genome Annotation Resource: improvements and new features publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl976 – volume: 12 start-page: 134 year: 2011 ident: 10.1093/mp/sst018_bib9 article-title: ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis publication-title: BMC Genomics doi: 10.1186/1471-2164-12-134 – volume: 21 start-page: 590 year: 2011 ident: 10.1093/mp/sst018_bib6 article-title: Coordinated histone modifications are associated with gene expression variation within and between species publication-title: Genome Res doi: 10.1101/gr.116467.110 – volume: 9 start-page: 179 year: 2008 ident: 10.1093/mp/sst018_bib26 article-title: Genome-wide approaches to studying chromatin modifications publication-title: Nat. Rev. Genet doi: 10.1038/nrg2270 – volume: 12 start-page: 996 year: 2002 ident: 10.1093/mp/sst018_bib15 article-title: The human genome browser at UCSC publication-title: Genome Res doi: 10.1101/gr.229102 – volume: 25 start-page: 2605 year: 2009 ident: 10.1093/mp/sst018_bib28 article-title: CEAS: cis-regulatory element annotation system publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp479 – volume: 19 start-page: 127 year: 2009 ident: 10.1093/mp/sst018_bib34 article-title: Characterization of human epigenomes publication-title: Curr. Opin. Genet. Dev doi: 10.1016/j.gde.2009.02.001 – volume: 21 start-page: 1757 year: 2011 ident: 10.1093/mp/sst018_bib30 article-title: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity publication-title: Genome Res doi: 10.1101/gr.121541.111 – volume: 30 start-page: 337 year: 2002 ident: 10.1093/mp/sst018_bib16 article-title: DNA binding and dimerization specificity and potential targets for the TCP protein family publication-title: Plant J doi: 10.1046/j.1365-313X.2002.01294.x – volume: 12 start-page: 3507 year: 1993 ident: 10.1093/mp/sst018_bib27 article-title: The Athb-1 and –2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities publication-title: EMBO J doi: 10.1002/j.1460-2075.1993.tb06025.x – volume: 107 start-page: 21931 year: 2010 ident: 10.1093/mp/sst018_bib5 article-title: Histone H3K27ac separates active from poised enhancers and predicts developmental state publication-title: Proc. Natl Acad. Sci. U S A doi: 10.1073/pnas.1016071107 – volume: 23 start-page: 459 year: 2011 ident: 10.1093/mp/sst018_bib11 article-title: Rapid and reversible light-mediated chromatin modifications of Arabidopsis phytochrome A locus publication-title: Plant Cell doi: 10.1105/tpc.110.080481 – volume: 22 start-page: 151 year: 2011 ident: 10.1093/mp/sst018_bib36 article-title: High-resolution mapping of open chromatin in the rice genome publication-title: Genome Res doi: 10.1101/gr.131342.111 – volume: 45 start-page: 63 year: 2001 ident: 10.1093/mp/sst018_bib13 article-title: DNA-binding and dimerization preferences of Arabidopsis homeodomain–leucine zipper transcription factors in vitro publication-title: Plant Mol. Biol doi: 10.1023/A:1006423324025 – volume: 28 start-page: 511 year: 2010 ident: 10.1093/mp/sst018_bib31 article-title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation publication-title: Nat. Biotechnol doi: 10.1038/nbt.1621 – volume: 40 start-page: 897 year: 2008 ident: 10.1093/mp/sst018_bib35 article-title: Combinatorial patterns of histone acetylations and methylations in the human genome publication-title: Nat. Genet doi: 10.1038/ng.154 – volume: 20 start-page: 259 year: 2008 ident: 10.1093/mp/sst018_bib18 article-title: High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression publication-title: Plant Cell doi: 10.1105/tpc.107.056879 – volume: 129 start-page: 823 year: 2007 ident: 10.1093/mp/sst018_bib2 article-title: High-resolution profiling of histone methylations in the human genome publication-title: Cell doi: 10.1016/j.cell.2007.05.009 – volume: 25 start-page: 1754 year: 2009 ident: 10.1093/mp/sst018_bib17 article-title: Fast and accurate short read alignment with Burrows–Wheeler transform publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp324 – volume: 447 start-page: 407 year: 2007 ident: 10.1093/mp/sst018_bib3 article-title: The complex language of chromatin regulation during transcription publication-title: Nature doi: 10.1038/nature05915 – volume: 12 start-page: R83 year: 2011 ident: 10.1093/mp/sst018_bib19 article-title: Cistrome: an integrative platform for transcriptional regulation studies publication-title: Genome Biol doi: 10.1186/gb-2011-12-8-r83 – volume: 9 start-page: R137 year: 2008 ident: 10.1093/mp/sst018_bib38 article-title: Model-based analysis of ChIP-Seq (MACS) publication-title: Genome Biol doi: 10.1186/gb-2008-9-9-r137 – volume: 21 start-page: 3732 year: 2009 ident: 10.1093/mp/sst018_bib4 article-title: Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis publication-title: Plant Cell doi: 10.1105/tpc.109.066845 – volume: 17 start-page: 175 year: 2007 ident: 10.1093/mp/sst018_bib10 article-title: Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana publication-title: Genome Res doi: 10.1101/gr.5509507 – volume: 12 start-page: 7 year: 2010 ident: 10.1093/mp/sst018_bib39 article-title: Charting histone modifications and the functional organization of mammalian genomes publication-title: Nat. Rev. Genet doi: 10.1038/nrg2905 – volume: 22 start-page: 17 year: 2010 ident: 10.1093/mp/sst018_bib7 article-title: Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids publication-title: Plant Cell doi: 10.1105/tpc.109.072041 – volume: 37 start-page: 426 year: 2004 ident: 10.1093/mp/sst018_bib21 article-title: Definition and interactions of a positive regulatory element of the Arabidopsis INNER NO OUTER promoter publication-title: Plant J doi: 10.1046/j.1365-313X.2003.01971.x – volume: 21 start-page: 447 year: 2011 ident: 10.1093/mp/sst018_bib25 article-title: Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data publication-title: Genome Res doi: 10.1101/gr.112623.110 – volume: 7 start-page: 1773 year: 1995 ident: 10.1093/mp/sst018_bib1 article-title: Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco publication-title: Plant Cell – volume: 163 start-page: 1221 year: 2003 ident: 10.1093/mp/sst018_bib22 article-title: Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres publication-title: Genetics doi: 10.1093/genetics/163.3.1221 – volume: 10 start-page: 645 year: 2007 ident: 10.1093/mp/sst018_bib24 article-title: Histone modifications and dynamic regulation of genome accessibility in plants publication-title: Curr. Opin. Plant Biol doi: 10.1016/j.pbi.2007.07.013 – volume: 12 start-page: 119 year: 2012 ident: 10.1093/mp/sst018_bib29 article-title: Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells publication-title: Funct. Integr. Genomics doi: 10.1007/s10142-012-0263-6 – volume: 10 start-page: 238 year: 2010 ident: 10.1093/mp/sst018_bib32 article-title: Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana publication-title: BMC Plant Biol doi: 10.1186/1471-2229-10-238 – volume: 31 start-page: 374 year: 2003 ident: 10.1093/mp/sst018_bib20 article-title: TRANSFAC®: transcriptional regulation, from patterns to profiles publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg108 – reference: 22110044 - Genome Res. 2012 Jan;22(1):151-62 – reference: 11247607 - Plant Mol Biol. 2001 Jan;45(1):63-73 – reference: 18250624 - Nat Rev Genet. 2008 Mar;9(3):179-91 – reference: 18263775 - Plant Cell. 2008 Feb;20(2):259-76 – reference: 8535134 - Plant Cell. 1995 Nov;7(11):1773-85 – reference: 17522673 - Nature. 2007 May 24;447(7143):407-12 – reference: 21859476 - Genome Biol. 2011;12(8):R83 – reference: 20086188 - Plant Cell. 2010 Jan;22(1):17-33 – reference: 12045153 - Genome Res. 2002 Jun;12(6):996-1006 – reference: 19204718 - Nat Rev Genet. 2009 Mar;10(3):161-72 – reference: 17210932 - Genome Res. 2007 Feb;17(2):175-83 – reference: 21356108 - BMC Genomics. 2011;12:134 – reference: 12000681 - Plant J. 2002 May;30(3):337-48 – reference: 18798982 - Genome Biol. 2008;9(9):R137 – reference: 21750106 - Genome Res. 2011 Oct;21(10):1757-67 – reference: 21050490 - BMC Plant Biol. 2010;10:238 – reference: 18552846 - Nat Genet. 2008 Jul;40(7):897-903 – reference: 8253077 - EMBO J. 1993 Sep;12(9):3507-17 – reference: 17884714 - Curr Opin Plant Biol. 2007 Dec;10(6):645-52 – reference: 21116306 - Nat Rev Genet. 2011 Jan;12(1):7-18 – reference: 19299119 - Curr Opin Genet Dev. 2009 Apr;19(2):127-34 – reference: 20436464 - Nat Biotechnol. 2010 May;28(5):511-5 – reference: 21324879 - Genome Res. 2011 Apr;21(4):590-8 – reference: 21317377 - Plant Cell. 2011 Feb;23(2):459-70 – reference: 21394438 - Chromosoma. 2011 Aug;120(4):353-65 – reference: 19508735 - Genome Biol. 2009;10(6):R62 – reference: 14731261 - Plant J. 2004 Feb;37(3):426-38 – reference: 17145706 - Nucleic Acids Res. 2007 Jan;35(Database issue):D883-7 – reference: 17512414 - Cell. 2007 May 18;129(4):823-37 – reference: 17277777 - Nat Genet. 2007 Mar;39(3):311-8 – reference: 19451168 - Bioinformatics. 2009 Jul 15;25(14):1754-60 – reference: 20008096 - Plant Cell. 2009 Dec;21(12):3732-48 – reference: 12520026 - Nucleic Acids Res. 2003 Jan 1;31(1):374-8 – reference: 21106759 - Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6 – reference: 22249597 - Funct Integr Genomics. 2012 Mar;12(1):119-30 – reference: 12678559 - Plant Mol Biol. 2003 Mar;51(5):719-29 – reference: 12663558 - Genetics. 2003 Mar;163(3):1221-5 – reference: 19689956 - Bioinformatics. 2009 Oct 1;25(19):2605-6 – reference: 21106904 - Genome Res. 2011 Mar;21(3):447-55 |
| SSID | ssj0060863 |
| Score | 2.3621707 |
| Snippet | While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about... While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the... SUMMARY H3K4me2/3, H3K9ac, and H3K27ac investigated by ChIP-Seq showed enrichment in generic regions and transcription start sites, and associated with active... H3K4me2/3, H3K9ac, and H3K27ac investigated by ChIP-Seq showed enrichment in generic regions and transcription start sites, and associated with active... |
| SourceID | pubmedcentral proquest pubmed crossref elsevier chongqing |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 1463 |
| SubjectTerms | acylation Base Sequence binding sites Binding Sites - genetics bioinformatics Chromatin chromatin structure and remodeling Deoxyribonucleases - metabolism DNA Transposable Elements - genetics epigenetics Gene expression gene regulation genes Genes, Plant - genetics Genome, Plant - genetics Genomes genomics growth and development high-throughput nucleotide sequencing histones Histones - metabolism Lysine - metabolism Molecular Sequence Annotation Molecular Sequence Data Oryza - genetics Oryza - metabolism Oryza sativa Plant growth precipitin tests prediction Protein Processing, Post-Translational Reproducibility of Results Rice Sequence Analysis, DNA Studies transcription (genetics) Transcription factors Transcription Factors - metabolism Transcription Initiation Site Transcription, Genetic 基因组分析 基因转录 染色质免疫沉淀 水稻基因组 粳稻 组蛋白修饰 转录因子结合位点 转录起始位点 |
| Title | Genome-Wide Analysis of Histone Modifications： H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica |
| URI | http://lib.cqvip.com/qk/90143B/201305/47523352.html https://dx.doi.org/10.1093/mp/sst018 https://www.ncbi.nlm.nih.gov/pubmed/23355544 https://www.proquest.com/docview/1500255034 https://www.proquest.com/docview/1434742682 https://www.proquest.com/docview/2000319208 https://pubmed.ncbi.nlm.nih.gov/PMC3842134 |
| Volume | 6 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Lb9QwELaqggQXxJstpTKIA4cNcW0ncbi1FWVpaTlAxd4sO3YgEuuE7hap_Hpm8hIL7YGblYwSP2bG3yQznwl5KY3xDpUXrK2I5K5hUZ5nNhLKZUlqUm4VFgqfnKazM3k0T-Yb5GCohcG0yt73dz699db9lbifzbipqvgT5s9zrD2VKZaLIuOnkKot4pvvD944BcjeJtmDcITSA7tQLuJFEy-XK4bnfdwCXxO-_oDd4rr96V_8-Xca5R_70uFdcqcHlHSv6_M9suHDfXJzvwbQd_mANO98qBc--lI5TwcCElqXtKUHCZ6e1A6Thbrvdm_oTBzLhefTviHaRm6KKTXBYZtnpqBVoB_PL38ZiqlAPw398JoemQZJds1Dcnb49vPBLOoPWYiKhPFVJJ0XYMWcAw5EmqPECQiaSgjNRAnhcbHrWZZ7m_skKRXEL6xMuWLOc-FKb5kTj8hmgP4-ITSRNgOEU0ibGukLoVLlvLKClYXlyvMJ2RqnWTcdmYaWGYTCgAIn5NUw77ro6cnxlIzvuvtNLvSi0d1yTciLUXR4zBVC02Hx9JpCadgrrhLfHhZY91a81ACWMeRiQk7I8_E22B_-VDHB1xcgI4UEPUwVv14Gy6HA1XEGr3nc6czYcRw8QDp4Q7amTaMA8n-v3wnVt5YHXCiJfHxb_zfSp-Q2b4_0wDy5bbK5Or_wzwBYrewOubH3_nh2utNa0G_MsSI2 |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Lb9QwELZKQSoXxJstBQziwGFDXNtJHG60omzb3XKgFXuz7NiBSGwSuluk8uuZyUsstAduVjJK_JgZf5PMfCbktTTGO1ResLYskLuGBWma2EAol0SxiblVWCg8O4knZ_JoHs03yH5fC4NplZ3vb3164627K2E3m2FdFOFnzJ_nWHsqYywXFTfITUADCVrn4Xyvd8cxYPYmyx6kAxTv6YVSES7qcLlcMTzwYwucTfn1B2wX121Q_wLQv_Mo_9iYDu6SOx2ipO_bTt8jG768T27tVYD6Lh-Q-qMvq4UPvhTO056BhFY5bfhBSk9nlcNsofbD3Ts6Ecdy4fm4a4imkZpsTE3psM0Tk9GipJ_OL38ZirlAPw2dvqVHpkaWXfOQnB18ON2fBN0pC0EWMb4KpPMCzJhzAILIcxQ5AVFTDrGZyCE-znY9S1JvUx9FuYIAhuUxV8x5LlzuLXPiEdksob9PCI2kTQDiZNLGRvpMqFg5r6xgeWa58nxEtodp1nXLpqFlArEwwMARedPPu846fnI8JuO7bv-TC72odbtcI_JqEO0fc4XQuF88vaZRGjaLq8R3-gXWnRkvNaBljLmYkCPycrgNBoh_VUzpqwuQkUKCIsaKXy-D9VDg6ziD1zxudWboOA4eMB28IVnTpkEACcDX75TFt4YIXCiJhHzb_zfSF2Rrcjqb6unhyfFTcps353tg0twO2VydX_hngLJW9nljRb8BP5EjyA |
| 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=Genome-Wide+Analysis+of+Histone+Modifications%3A+H3K4me2%2C+H3K4me3%2C+H3K9ac%2C+and+H3K27ac+in+Oryza+sativa+L.+Japonica&rft.jtitle=Molecular+plant&rft.au=Du%2C+Zhou&rft.au=Li%2C+Hui&rft.au=Wei%2C+Qiang&rft.au=Zhao%2C+Xin&rft.date=2013-09-01&rft.issn=1674-2052&rft.volume=6&rft.issue=5&rft.spage=1463&rft.epage=1472&rft_id=info:doi/10.1093%2Fmp%2Fsst018&rft.externalDBID=n%2Fa&rft.externalDocID=10_1093_mp_sst018 |
| thumbnail_s | http://utb.summon.serialssolutions.com/2.0.0/image/custom?url=http%3A%2F%2Fimage.cqvip.com%2Fvip1000%2Fqk%2F90143B%2F90143B.jpg |