Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization
Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chro...
Saved in:
Published in | Genome Biology Vol. 16; no. 1; p. 110 |
---|---|
Main Authors | , , |
Format | Journal Article |
Language | English |
Published |
England
BioMed Central
27.05.2015
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Abstract | Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata.
Here we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1.
We show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies. |
---|---|
AbstractList | Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata.
Here we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1.
We show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies. Background Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata. Results Here we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1. Conclusions We show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies. BACKGROUNDInterphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata.RESULTSHere we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1.CONCLUSIONSWe show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies. |
ArticleNumber | 110 |
Author | Aitken, Stuart Semple, Colin A Moore, Benjamin L |
Author_xml | – sequence: 1 givenname: Benjamin L surname: Moore fullname: Moore, Benjamin L email: ben.moore@igmm.ed.ac.uk organization: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK. ben.moore@igmm.ed.ac.uk – sequence: 2 givenname: Stuart surname: Aitken fullname: Aitken, Stuart email: stuart.aitken@igmm.ed.ac.uk organization: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK. stuart.aitken@igmm.ed.ac.uk – sequence: 3 givenname: Colin A surname: Semple fullname: Semple, Colin A email: colin.semple@igmm.ed.ac.uk organization: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK. colin.semple@igmm.ed.ac.uk |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26013771$$D View this record in MEDLINE/PubMed |
BookMark | eNpdUctqHDEQFMEmfiQfkEsQ5OKLYmn0nEsgmDwMBl8SyE1oNa3dMTPSRhotTr7e2qxjEp-66a4qqqgzdBRTBITeMPqeMaMuC-NU9oQySahSjNy_QKdMaEG0oj-O9ruSRPVUnaCzUu4oZb3o1Et00inKuNbsFNXruMA6u2XcAZ7TANMY1zjDDtxU8LIBvM1j9ON2goJTwHOdlpEU7ybAfpPT3JgRr1KNg8u_cEh5f0kRt-umzi7iWP0ELuOU1y6Ov_98X6Hj0PTh9eM8R98_f_p29ZXc3H65vvp4Q7xU3UKYkNprTaXRamC6pywEJoawoiC5MDwEQ3stun7wZhBBKGdcP4ieg5Srgff8HH046G7raobBQ1yym2yLNDe3NrnR_v-J48au084KIbiSoglcPArk9LNCWew8Fg_T5CKkWixThmspDDMN-u4Z9C7VHFs823VUC9N8qYZiB5TPqZQM4ckMo3Zfqj2Ualupdl-qvW-ct_-meGL8bZE_AC-Hojs |
CitedBy_id | crossref_primary_10_1038_s41467_022_28018_z crossref_primary_10_37349_emed_2021_00068 crossref_primary_10_1016_j_biopha_2022_113230 crossref_primary_10_1038_s41467_019_13423_8 crossref_primary_10_1186_s13059_019_1635_1 crossref_primary_10_1007_s00439_020_02121_x crossref_primary_10_1016_j_cels_2019_04_001 crossref_primary_10_1016_j_ygeno_2017_05_009 crossref_primary_10_1038_srep37324 crossref_primary_10_1186_s12859_022_04614_0 crossref_primary_10_1016_j_csbj_2021_05_013 crossref_primary_10_3389_fgene_2022_850108 crossref_primary_10_1016_j_arcmed_2022_11_010 crossref_primary_10_1016_j_cell_2019_01_020 crossref_primary_10_1016_j_isci_2024_109570 crossref_primary_10_1016_j_semcdb_2015_11_013 crossref_primary_10_1101_gr_249367_119 crossref_primary_10_15252_msb_20156492 crossref_primary_10_1016_j_coisb_2017_01_003 crossref_primary_10_1002_gcc_22732 crossref_primary_10_1186_s13059_018_1483_4 crossref_primary_10_1186_s13059_018_1484_3 crossref_primary_10_1186_s13059_016_1003_3 crossref_primary_10_1038_ng_3539 crossref_primary_10_1093_nar_gkaa087 crossref_primary_10_12688_f1000research_10792_1 crossref_primary_10_1016_j_coisb_2017_02_003 crossref_primary_10_1016_j_molcel_2017_07_022 |
Cites_doi | 10.1126/science.1181369 10.1038/nature13415 10.1101/gr.141028.112 10.1186/gb-2013-14-12-r148 10.1016/j.cell.2013.04.053 10.1158/0008-5472.CAN-11-3382 10.1182/blood-2009-09-240978 10.1038/nature13668 10.1038/nmeth.1923 10.1186/gb-2012-13-9-r53 10.1038/nbt.2057 10.1016/j.cell.2013.11.039 10.1016/j.cell.2013.02.001 10.1023/A:1010933404324 10.1038/nature11082 10.1073/pnas.1211427109 10.1038/nrg3454 10.3389/fimmu.2014.00045 10.1038/nature12593 10.1016/0092-8674(93)90662-A 10.1038/nature10953 10.1016/j.cell.2011.09.057 10.1038/nmeth.1906 10.1073/pnas.96.3.956 10.1038/nrg3663 10.1093/nar/gks1284 10.1371/journal.pgen.1003778 10.1890/07-0539.1 10.1007/b94608_6 10.1371/journal.pcbi.1003017 10.1101/gr.161620.113 10.1038/nmeth.2148 10.1016/j.ymeth.2014.10.031 10.1073/pnas.1317788111 10.1186/gb-2012-13-10-r85 10.1101/gr.099796.109 10.1038/cr.2012.175 10.1007/s00439-013-1337-9 10.1038/ni.2641 10.1186/gb-2008-9-9-r137 10.1137/0905052 10.1038/nature11049 10.1038/nature12420 10.1091/mbc.E12-07-0529 10.1016/j.cell.2012.08.033 10.1038/nature11247 10.1016/j.cell.2012.01.010 |
ContentType | Journal Article |
Copyright | 2015. This work is licensed under http://creativecommons.org/licenses/by/4.0 (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Moore et al.; licensee BioMed Central. 2015 |
Copyright_xml | – notice: 2015. This work is licensed under http://creativecommons.org/licenses/by/4.0 (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: Moore et al.; licensee BioMed Central. 2015 |
DBID | CGR CUY CVF ECM EIF NPM AAYXX CITATION 3V. 7X7 7XB 88E 8FE 8FH 8FI 8FJ 8FK ABUWG AFKRA AZQEC BBNVY BENPR BHPHI CCPQU DWQXO FYUFA GHDGH GNUQQ HCIFZ K9. LK8 M0S M1P M7P PIMPY PQEST PQQKQ PQUKI PRINS 7X8 5PM |
DOI | 10.1186/s13059-015-0661-x |
DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed CrossRef ProQuest Central (Corporate) Health & Medical Collection ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) ProQuest Central (Alumni) ProQuest Central ProQuest Central Essentials Biological Science Collection ProQuest Central Natural Science Collection ProQuest One Community College ProQuest Central Korea Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) Biological Sciences Health & Medical Collection (Alumni Edition) Medical Database Biological Science Database Publicly Available Content Database ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Academic ProQuest One Academic UKI Edition ProQuest Central China MEDLINE - Academic PubMed Central (Full Participant titles) |
DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) CrossRef Publicly Available Content Database ProQuest Central Student ProQuest Central Essentials ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) SciTech Premium Collection ProQuest One Community College ProQuest Natural Science Collection ProQuest Central China ProQuest Central Health Research Premium Collection Health and Medicine Complete (Alumni Edition) Natural Science Collection ProQuest Central Korea Biological Science Collection ProQuest Medical Library (Alumni) ProQuest Biological Science Collection ProQuest One Academic Eastern Edition ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database ProQuest SciTech Collection ProQuest Hospital Collection (Alumni) ProQuest Health & Medical Complete ProQuest Medical Library ProQuest One Academic UKI Edition ProQuest One Academic ProQuest Central (Alumni) MEDLINE - Academic |
DatabaseTitleList | MEDLINE Publicly Available Content Database 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 – sequence: 3 dbid: BENPR name: ProQuest Central url: https://www.proquest.com/central sourceTypes: Aggregation Database |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Biology |
EISSN | 1474-760X 1465-6906 1465-6914 |
EndPage | 110 |
ExternalDocumentID | 10_1186_s13059_015_0661_x 26013771 |
Genre | Research Support, Non-U.S. Gov't Journal Article |
GrantInformation_xml | – fundername: Medical Research Council |
GroupedDBID | --- 0R~ 29H 3V. 4.4 53G 5GY 5VS 7X7 88E 8FE 8FH 8FI 8FJ AAFWJ AAHBH AAJSJ ABUWG ACGFO ACGFS ACJQM ACPRK ACRMQ ADBBV ADINQ ADUKV AEGXH AFKRA AHBYD AHSBF AIAGR ALIPV ALMA_UNASSIGNED_HOLDINGS AMKLP AMTXH AOIAM AOIJS BAPOH BAWUL BBNVY BCNDV BENPR BFQNJ BHPHI BMC BPHCQ BVXVI C24 C6C CCPQU CGR CUY CVF EBD EBLON EBS ECM EIF EMOBN FYUFA GROUPED_DOAJ GX1 HCIFZ HMCUK HYE IAO IGS IHR ISR ITC KPI LK8 M1P M7P NPM PIMPY PQQKQ PROAC PSQYO ROL RPM RSV SJN SOJ SV3 UKHRP 2WC AAYXX AENEX AHYZX CITATION CS3 DIK E3Z EJD F5P HZ~ KQ8 O5R O5S OK1 RBZ SBL TR2 WOQ 7XB 8FK AZQEC DWQXO GNUQQ K9. PQEST PQUKI PRINS 7X8 5PM |
ID | FETCH-LOGICAL-c562t-1457c7705876d17901ff14dfb0e53483ff8097429dc8d4f46a8a9d493e55bd393 |
IEDL.DBID | 7X7 |
ISSN | 1465-6906 1474-7596 |
IngestDate | Tue Sep 17 21:28:39 EDT 2024 Fri Oct 25 21:59:57 EDT 2024 Thu Oct 10 18:02:33 EDT 2024 Fri Nov 22 01:38:38 EST 2024 Tue Oct 15 23:52:09 EDT 2024 |
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 (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
LinkModel | DirectLink |
MergedId | FETCHMERGED-LOGICAL-c562t-1457c7705876d17901ff14dfb0e53483ff8097429dc8d4f46a8a9d493e55bd393 |
Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
OpenAccessLink | https://www.proquest.com/docview/2207484936?pq-origsite=%requestingapplication% |
PMID | 26013771 |
PQID | 2207484936 |
PQPubID | 2040232 |
PageCount | 1 |
ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_4443654 proquest_miscellaneous_1683754818 proquest_journals_2207484936 crossref_primary_10_1186_s13059_015_0661_x pubmed_primary_26013771 |
PublicationCentury | 2000 |
PublicationDate | 2015-05-27 |
PublicationDateYYYYMMDD | 2015-05-27 |
PublicationDate_xml | – month: 05 year: 2015 text: 2015-05-27 day: 27 |
PublicationDecade | 2010 |
PublicationPlace | England |
PublicationPlace_xml | – name: England – name: London |
PublicationTitle | Genome Biology |
PublicationTitleAlternate | Genome Biol |
PublicationYear | 2015 |
Publisher | BioMed Central |
Publisher_xml | – name: BioMed Central |
References | 24614316 - Nat Rev Genet. 2014 Apr;15(4):234-46 24068952 - PLoS Genet. 2013;9(9):e1003778 25164757 - Nature. 2014 Aug 28;512(7515):453-6 23124521 - Genome Res. 2013 Feb;23(2):270-80 23924899 - Mol Biol Cell. 2013 Oct;24(19):3025-37 8649793 - Oncogene. 1996 Mar 7;12(5):1025-32 22198700 - Nat Biotechnol. 2012 Jan;30(1):90-8 23812095 - Nat Immunol. 2013 Aug;14(8):867-75 24575094 - Front Immunol. 2014 Feb 10;5:45 25164756 - Nature. 2014 Aug 28;512(7515):449-52 23247625 - Cell Res. 2013 Jan;23(1):49-69 19952138 - Genome Res. 2010 Feb;20(2):155-69 24380390 - Genome Biol. 2013;14(12):R148 24067610 - Nature. 2013 Oct 3;502(7469):59-64 23706625 - Cell. 2013 Jun 6;153(6):1281-95 22388813 - Nature. 2012 Mar 29;483(7391):598-602 23213261 - Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):21028-33 22196736 - Cell. 2011 Dec 23;147(7):1628-39 20498303 - Blood. 2010 Nov 4;116(18):3564-71 25448293 - Methods. 2015 Jan 15;72:65-75 22495300 - Nature. 2012 May 17;485(7398):376-80 22495304 - Nature. 2012 May 17;485(7398):381-5 18798982 - Genome Biol. 2008;9(9):R137 19815776 - Science. 2009 Oct 9;326(5950):289-93 23657480 - Nat Rev Genet. 2013 Jun;14(6):390-403 23883933 - Nature. 2013 Sep 12;501(7466):227-31 24360274 - Cell. 2013 Dec 19;155(7):1507-20 22315347 - Cancer Res. 2012 Mar 1;72(5):1051-4 24002784 - Genome Res. 2013 Dec;23(12):2066-77 22955616 - Nature. 2012 Sep 6;489(7414):57-74 22373907 - Nat Methods. 2012 Mar;9(3):215-6 23851939 - Hum Genet. 2013 Nov;132(11):1311-20 23498936 - Cell. 2013 Mar 14;152(6):1270-84 9927675 - Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):956-61 24335803 - Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):996-1001 23592965 - PLoS Comput Biol. 2013 Apr;9(4):e1003017 22265598 - Cell. 2012 Feb 3;148(3):458-72 22388286 - Nat Methods. 2012 Apr;9(4):357-9 23034477 - Genome Biol. 2012;13(10):R85 23221638 - Nucleic Acids Res. 2013 Jan;41(2):827-41 22941365 - Nat Methods. 2012 Oct;9(10):999-1003 23021216 - Cell. 2012 Sep 28;151(1):68-79 8425219 - Cell. 1993 Jan 29;72(2):223-32 18051647 - Ecology. 2007 Nov;88(11):2783-92 22950368 - Genome Biol. 2012;13(9):R53 TT Onder (661_CR32) 2012; 483 O Ram (661_CR3) 2011; 147 JWK Ho (661_CR44) 2014; 512 JR Dixon (661_CR9) 2012; 485 R Mansson (661_CR24) 2012; 109 E Pohl (661_CR25) 2013; 132 AG Evertts (661_CR27) 2013; 24 R Kalhor (661_CR40) 2012; 30 M Imakaev (661_CR41) 2012; 9 EC Svensson (661_CR26) 1999; 96 J Zuin (661_CR13) 2014; 111 C Müller-Tidow (661_CR37) 2010; 116 BM Hagmeyer (661_CR38) 1996; 12 Z Nie (661_CR18) 2012; 151 R Nechanitzky (661_CR23) 2013; 14 KR Kieffer-Kwon (661_CR19) 2013; 155 DR Cutler (661_CR49) 2007; 88 E de Wit (661_CR7) 2013; 501 Wa Bickmore (661_CR1) 2013; 152 EV Chambers (661_CR8) 2013; 9 T Sexton (661_CR35) 2012; 148 AS Zervos (661_CR20) 1993; 72 I Hiratani (661_CR11) 2010; 20 ENCODE (661_CR4) 2012; 489 G Liang (661_CR12) 2013; 23 CT Ong (661_CR39) 2014; 15 J Ernst (661_CR2) 2012; 9 661_CR48 E Lieberman-Aiden (661_CR15) 2009; 326 S Wold (661_CR21) 1984; 5 EP Nora (661_CR14) 2012; 485 PC Schwalie (661_CR29) 2013; 14 T Nagano (661_CR22) 2013; 502 M Ku (661_CR34) 2012; 13 L Breiman (661_CR46) 2001; 45 X Dong (661_CR16) 2012; 13 AP Boyle (661_CR43) 2014; 512 661_CR50 B Langmead (661_CR42) 2012; 9 BR Lajoie (661_CR17) 2015; 72 MM Hoffman (661_CR5) 2013; 41 W Meuleman (661_CR10) 2013; 23 A Liaw (661_CR47) 2002; 2 ML Atchison (661_CR28) 2014; 5 J Dekker (661_CR6) 2013; 14 Y Zwang (661_CR36) 2012; 72 Y Zhang (661_CR45) 2008; 9 VC Seitan (661_CR30) 2013; 23 JE Phillips-Cremins (661_CR31) 2013; 153 X Chai (661_CR33) 2013; 9 |
References_xml | – volume: 326 start-page: 289 year: 2009 ident: 661_CR15 publication-title: Science doi: 10.1126/science.1181369 contributor: fullname: E Lieberman-Aiden – volume: 512 start-page: 449 year: 2014 ident: 661_CR44 publication-title: Nature doi: 10.1038/nature13415 contributor: fullname: JWK Ho – volume: 23 start-page: 270 year: 2013 ident: 661_CR10 publication-title: Genome Res doi: 10.1101/gr.141028.112 contributor: fullname: W Meuleman – volume: 14 start-page: 148 year: 2013 ident: 661_CR29 publication-title: Genome Biol doi: 10.1186/gb-2013-14-12-r148 contributor: fullname: PC Schwalie – ident: 661_CR50 – volume: 153 start-page: 1281 year: 2013 ident: 661_CR31 publication-title: Cell doi: 10.1016/j.cell.2013.04.053 contributor: fullname: JE Phillips-Cremins – volume: 72 start-page: 1051 year: 2012 ident: 661_CR36 publication-title: Cancer Res doi: 10.1158/0008-5472.CAN-11-3382 contributor: fullname: Y Zwang – volume: 116 start-page: 3564 year: 2010 ident: 661_CR37 publication-title: Blood doi: 10.1182/blood-2009-09-240978 contributor: fullname: C Müller-Tidow – volume: 512 start-page: 453 year: 2014 ident: 661_CR43 publication-title: Nature doi: 10.1038/nature13668 contributor: fullname: AP Boyle – volume: 9 start-page: 357 year: 2012 ident: 661_CR42 publication-title: Nat Methods doi: 10.1038/nmeth.1923 contributor: fullname: B Langmead – volume: 2 start-page: 18 year: 2002 ident: 661_CR47 publication-title: R News contributor: fullname: A Liaw – volume: 13 start-page: 53 year: 2012 ident: 661_CR16 publication-title: Genome Biol doi: 10.1186/gb-2012-13-9-r53 contributor: fullname: X Dong – volume: 30 start-page: 90 year: 2012 ident: 661_CR40 publication-title: Nat Biotechnol doi: 10.1038/nbt.2057 contributor: fullname: R Kalhor – volume: 155 start-page: 1507 year: 2013 ident: 661_CR19 publication-title: Cell doi: 10.1016/j.cell.2013.11.039 contributor: fullname: KR Kieffer-Kwon – volume: 152 start-page: 1270 year: 2013 ident: 661_CR1 publication-title: Cell doi: 10.1016/j.cell.2013.02.001 contributor: fullname: Wa Bickmore – volume: 45 start-page: 5 year: 2001 ident: 661_CR46 publication-title: Mach Learn doi: 10.1023/A:1010933404324 contributor: fullname: L Breiman – volume: 485 start-page: 376 year: 2012 ident: 661_CR9 publication-title: Nature doi: 10.1038/nature11082 contributor: fullname: JR Dixon – volume: 109 start-page: 21028 year: 2012 ident: 661_CR24 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1211427109 contributor: fullname: R Mansson – volume: 14 start-page: 390 year: 2013 ident: 661_CR6 publication-title: Nat Rev Genet doi: 10.1038/nrg3454 contributor: fullname: J Dekker – volume: 5 start-page: 45 year: 2014 ident: 661_CR28 publication-title: Front Immunol doi: 10.3389/fimmu.2014.00045 contributor: fullname: ML Atchison – volume: 502 start-page: 59 year: 2013 ident: 661_CR22 publication-title: Nature doi: 10.1038/nature12593 contributor: fullname: T Nagano – volume: 72 start-page: 223 year: 1993 ident: 661_CR20 publication-title: Cell doi: 10.1016/0092-8674(93)90662-A contributor: fullname: AS Zervos – volume: 483 start-page: 598 year: 2012 ident: 661_CR32 publication-title: Nature doi: 10.1038/nature10953 contributor: fullname: TT Onder – volume: 147 start-page: 1628 year: 2011 ident: 661_CR3 publication-title: Cell doi: 10.1016/j.cell.2011.09.057 contributor: fullname: O Ram – volume: 9 start-page: 215 year: 2012 ident: 661_CR2 publication-title: Nat Methods doi: 10.1038/nmeth.1906 contributor: fullname: J Ernst – volume: 96 start-page: 956 year: 1999 ident: 661_CR26 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.96.3.956 contributor: fullname: EC Svensson – volume: 15 start-page: 234 year: 2014 ident: 661_CR39 publication-title: Nat Rev Genet doi: 10.1038/nrg3663 contributor: fullname: CT Ong – volume: 41 start-page: 827 year: 2013 ident: 661_CR5 publication-title: Nucleic Acids Res doi: 10.1093/nar/gks1284 contributor: fullname: MM Hoffman – volume: 9 start-page: 1003778 year: 2013 ident: 661_CR33 publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003778 contributor: fullname: X Chai – volume: 88 start-page: 2783 year: 2007 ident: 661_CR49 publication-title: Ecology doi: 10.1890/07-0539.1 contributor: fullname: DR Cutler – ident: 661_CR48 doi: 10.1007/b94608_6 – volume: 9 start-page: 1003017 year: 2013 ident: 661_CR8 publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1003017 contributor: fullname: EV Chambers – volume: 23 start-page: 2066 year: 2013 ident: 661_CR30 publication-title: Genome Res doi: 10.1101/gr.161620.113 contributor: fullname: VC Seitan – volume: 9 start-page: 999 year: 2012 ident: 661_CR41 publication-title: Nat Methods doi: 10.1038/nmeth.2148 contributor: fullname: M Imakaev – volume: 72 start-page: 65 year: 2015 ident: 661_CR17 publication-title: Methods doi: 10.1016/j.ymeth.2014.10.031 contributor: fullname: BR Lajoie – volume: 111 start-page: 996 year: 2014 ident: 661_CR13 publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.1317788111 contributor: fullname: J Zuin – volume: 13 start-page: 85 year: 2012 ident: 661_CR34 publication-title: Genome Biol doi: 10.1186/gb-2012-13-10-r85 contributor: fullname: M Ku – volume: 20 start-page: 155 year: 2010 ident: 661_CR11 publication-title: Genome Res doi: 10.1101/gr.099796.109 contributor: fullname: I Hiratani – volume: 23 start-page: 49 year: 2013 ident: 661_CR12 publication-title: Cell Res doi: 10.1038/cr.2012.175 contributor: fullname: G Liang – volume: 132 start-page: 1311 year: 2013 ident: 661_CR25 publication-title: Hum Genet doi: 10.1007/s00439-013-1337-9 contributor: fullname: E Pohl – volume: 14 start-page: 867 year: 2013 ident: 661_CR23 publication-title: Nat Immunol doi: 10.1038/ni.2641 contributor: fullname: R Nechanitzky – volume: 9 start-page: 137 year: 2008 ident: 661_CR45 publication-title: Genome Biol doi: 10.1186/gb-2008-9-9-r137 contributor: fullname: Y Zhang – volume: 5 start-page: 735 year: 1984 ident: 661_CR21 publication-title: SIAM J Sci Stat Comput doi: 10.1137/0905052 contributor: fullname: S Wold – volume: 485 start-page: 381 year: 2012 ident: 661_CR14 publication-title: Nature doi: 10.1038/nature11049 contributor: fullname: EP Nora – volume: 501 start-page: 227 year: 2013 ident: 661_CR7 publication-title: Nature doi: 10.1038/nature12420 contributor: fullname: E de Wit – volume: 24 start-page: 3025 year: 2013 ident: 661_CR27 publication-title: Mol Biol Cell doi: 10.1091/mbc.E12-07-0529 contributor: fullname: AG Evertts – volume: 151 start-page: 68 year: 2012 ident: 661_CR18 publication-title: Cell doi: 10.1016/j.cell.2012.08.033 contributor: fullname: Z Nie – volume: 489 start-page: 57 year: 2012 ident: 661_CR4 publication-title: Nature doi: 10.1038/nature11247 contributor: fullname: ENCODE – volume: 148 start-page: 458 year: 2012 ident: 661_CR35 publication-title: Cell doi: 10.1016/j.cell.2012.01.010 contributor: fullname: T Sexton – volume: 12 start-page: 1025 year: 1996 ident: 661_CR38 publication-title: Oncogene contributor: fullname: BM Hagmeyer |
SSID | ssj0019426 ssj0017866 |
Score | 2.3709605 |
Snippet | Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic... Background Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales,... BACKGROUNDInterphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from... |
SourceID | pubmedcentral proquest crossref pubmed |
SourceType | Open Access Repository Aggregation Database Index Database |
StartPage | 110 |
SubjectTerms | Boundaries CCCTC-Binding Factor Cell cycle Cell Line Chromatin Chromatin - genetics Chromosomes Comparative analysis Data collection Databases, Genetic Datasets Deoxyribonucleic acid DNA DNA methylation DNA Replication Timing DNA-binding protein DNA-Binding Proteins - genetics Epigenesis, Genetic Genetic Loci Genomes Humans K562 Cells Models, Molecular Multigene Family Proteins Regulation Repressor Proteins - genetics Repressor Proteins - metabolism Stem cells Transcription factors |
Title | Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization |
URI | https://www.ncbi.nlm.nih.gov/pubmed/26013771 https://www.proquest.com/docview/2207484936 https://search.proquest.com/docview/1683754818 https://pubmed.ncbi.nlm.nih.gov/PMC4443654 |
Volume | 16 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV3fa9wwDBZby2AvZb-Xrjs82NMgNI7txHkq7WjpBiujrHDsxcSJTfuS3C530P73lRxf2ttgL4HEgQRLlj_J0ieAz1Ln3iEMSImKPZXKoR1UDU-dJupNKxBxU2jgx0VxfiW_z9U8BtyGmFa5sYnBULd9QzHywzzPiPayEsXR4k9KXaPodDW20HgKuzzHrRz1uZxPDhcvNWGVeFPJfCw1ogREVRXxiBP_8XBAQ64obUhRQT5Pb7c3qX-Q598JlI92pLMXsBehJDseZf8SnrjuFTwbm0vevYb1t8gEgfaMhYY3uEsxYmxCjWOI-9hiE2gfWO9ZSC1MB5SZY831sico2zEb2i4t79hU5cjwaejsxzriQq6XrH9Uz_kGrs5Of309T2OThbRB6LNKuVRlU5aZQrPYEl0X957L1tvMKSG18F5n6HPkVdvoVnpZ1LquWpSDU8q2ohJvYafrO_cemEVrIDUivspK6a2zLbq6XmR5jZPKtU3gy2ZWzWLk0jDBB9GFGUVgUASGRGBuEzjYzLuJy2owD0qQwKdpGBcEnXLUnevXg-GFpra-CEQSeDeKafoa8aeJsuQJlFsCnF4gsu3tke7mOpBuSylFoeT-_3_rAzzPgxpRod8B7KyWa_cRUcvKzoJqzmD35PTi5-Us-P54vTz5fQ_mRe5O |
link.rule.ids | 230,314,780,784,864,885,12056,21388,27924,27925,31719,31720,33744,33745,43310,43805 |
linkProvider | ProQuest |
linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1La9wwEB7SDaW9lDZ9uU1bBXoqiNiWZMun0pSETZosISSQm7BsieRib9e7kPz7zthaJ9tCj7YMFprR6NM8vgH4KnXqHcIATlTsXCqHdlBVCXeaqDetQMRNroGzWTa9kifX6jo43LqQVrm2ib2hrtuKfOT7aRoT7WUhsu_z35y6RlF0NbTQeALbxJyuJrB9cDg7vxjjCLkmtBIeCpkOxUaUgqiKLAQ5cZb7HZpyRYlDikryE363eUz9gz3_TqF8dCYdvYQXAUyyH4P0X8GWa3bg6dBe8v41rI4DFwRaNNa3vMFzihFnE-ocQ-TH5mtXe8daz_rkQt6h1ByrbhYtgdmG2b7x0uKejXWODN_2vf1YQ2zI5YK1jyo638DV0eHlzykPbRZ4heBnyROp8irPY4WGsSbCrsT7RNbexk4JqYX3OsZbR1rUla6ll1mpy6JGSTilbC0K8RYmTdu498As2gOpEfMVVkpvna3xsutFnJa4qIm2EXxbr6qZD2wapr-F6MwMIjAoAkMiMHcR7K7X3YSN1ZkHNYhgbxzGLUFxjrJx7aozSaapsS9CkQjeDWIa_0YMaiLPkwjyDQGOHxDd9uZIc3vT025LKUWm5If_T-sLPJtenp2a0-PZr4_wPO1Visr-dmGyXKzcJ8QwS_s5KOofoG7vBg |
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=Integrative+modeling+reveals+the+principles+of+multi-scale+chromatin+boundary+formation+in+human+nuclear+organization&rft.jtitle=GenomeBiology.com&rft.au=Moore%2C+Benjamin+L&rft.au=Aitken%2C+Stuart&rft.au=Semple%2C+Colin+A&rft.date=2015-05-27&rft.issn=1465-6906&rft.eissn=1465-6906&rft.volume=16&rft.issue=1&rft_id=info:doi/10.1186%2Fs13059-015-0661-x&rft.externalDBID=n%2Fa&rft.externalDocID=10_1186_s13059_015_0661_x |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1465-6906&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1465-6906&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1465-6906&client=summon |