Differential contribution to gene expression prediction of histone modifications at enhancers or promoters
The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop quantitative models to characterize the relationship of gene expression with his...
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Published in | PLoS computational biology Vol. 17; no. 9; p. e1009368 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
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Public Library of Science
01.09.2021
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Abstract | The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop quantitative models to characterize the relationship of gene expression with histone modifications at enhancers or promoters. We use embryonic stem cells (ESCs), which contain a full spectrum of active and repressed (poised) enhancers, to train predictive models. As many poised enhancers in ESCs switch towards an active state during differentiation, predictive models can also be trained on poised enhancers throughout differentiation and in development. Remarkably, we determine that histone modifications at enhancers, as well as promoters, are predictive of gene expression in ESCs and throughout differentiation and development. Importantly, we demonstrate that their contribution to the predictive models varies depending on their location in enhancers or promoters. Moreover, we use a local regression (LOESS) to normalize sequencing data from different sources, which allows us to apply predictive models trained in a specific cellular context to a different one. We conclude that the relationship between gene expression and histone modifications at enhancers is universal and different from promoters. Our study provides new insight into how histone modifications relate to gene expression based on their location in enhancers or promoters. |
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AbstractList | The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop quantitative models to characterize the relationship of gene expression with histone modifications at enhancers or promoters. We use embryonic stem cells (ESCs), which contain a full spectrum of active and repressed (poised) enhancers, to train predictive models. As many poised enhancers in ESCs switch towards an active state during differentiation, predictive models can also be trained on poised enhancers throughout differentiation and in development. Remarkably, we determine that histone modifications at enhancers, as well as promoters, are predictive of gene expression in ESCs and throughout differentiation and development. Importantly, we demonstrate that their contribution to the predictive models varies depending on their location in enhancers or promoters. Moreover, we use a local regression (LOESS) to normalize sequencing data from different sources, which allows us to apply predictive models trained in a specific cellular context to a different one. We conclude that the relationship between gene expression and histone modifications at enhancers is universal and different from promoters. Our study provides new insight into how histone modifications relate to gene expression based on their location in enhancers or promoters. The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop quantitative models to characterize the relationship of gene expression with histone modifications at enhancers or promoters. We use embryonic stem cells (ESCs), which contain a full spectrum of active and repressed (poised) enhancers, to train predictive models. As many poised enhancers in ESCs switch towards an active state during differentiation, predictive models can also be trained on poised enhancers throughout differentiation and in development. Remarkably, we determine that histone modifications at enhancers, as well as promoters, are predictive of gene expression in ESCs and throughout differentiation and development. Importantly, we demonstrate that their contribution to the predictive models varies depending on their location in enhancers or promoters. Moreover, we use a local regression (LOESS) to normalize sequencing data from different sources, which allows us to apply predictive models trained in a specific cellular context to a different one. We conclude that the relationship between gene expression and histone modifications at enhancers is universal and different from promoters. Our study provides new insight into how histone modifications relate to gene expression based on their location in enhancers or promoters. Gene expression can be properly predicted by the ChIP-seq signal of histone modifications at promoters, but whether this is also true at enhancers is unclear. In this study we develop predictive models of gene expression that demonstrate the predictive power of histone modifications at enhancers in the context of mouse embryonic stem cells, during differentiation, and in animal development. Moreover, by assessing the contribution of each histone modification, we found that enhancer predictive models and promoter predictive models have different histone modification requirement. Therefore, different histone modifications relate better to enhancer or promoter function(s). Finally, by applying predictive models trained in a specific cellular context to a different one, we concluded that the relationship between gene expression and histone modifications at enhancers is universal. |
Audience | Academic |
Author | González-Ramírez, Mar Ballaré, Cecilia Santanach, Alexandra Mugianesi, Francesca Beringer, Malte Blanco, Enrique Di Croce, Luciano |
AuthorAffiliation | 3 Universitat Pompeu Fabra (UPF), Barcelona, Spain 4 ICREA, Pg. Barcelona, Spain 2 CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain University of Virginia, UNITED STATES 1 Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain |
AuthorAffiliation_xml | – name: 2 CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain – name: 4 ICREA, Pg. Barcelona, Spain – name: 1 Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain – name: 3 Universitat Pompeu Fabra (UPF), Barcelona, Spain – name: University of Virginia, UNITED STATES |
Author_xml | – sequence: 1 givenname: Mar orcidid: 0000-0003-2297-2671 surname: González-Ramírez fullname: González-Ramírez, Mar organization: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain – sequence: 2 givenname: Cecilia orcidid: 0000-0002-9442-807X surname: Ballaré fullname: Ballaré, Cecilia organization: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain – sequence: 3 givenname: Francesca surname: Mugianesi fullname: Mugianesi, Francesca organization: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain – sequence: 4 givenname: Malte surname: Beringer fullname: Beringer, Malte organization: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain – sequence: 5 givenname: Alexandra surname: Santanach fullname: Santanach, Alexandra organization: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain – sequence: 6 givenname: Enrique orcidid: 0000-0001-6261-7370 surname: Blanco fullname: Blanco, Enrique organization: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain – sequence: 7 givenname: Luciano orcidid: 0000-0003-3488-6228 surname: Di Croce fullname: Di Croce, Luciano organization: ICREA, Pg. Barcelona, Spain |
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CitedBy_id | crossref_primary_10_1016_j_molcel_2023_07_003 crossref_primary_10_1016_j_stemcr_2022_03_014 crossref_primary_10_1016_j_xpro_2022_101948 crossref_primary_10_1038_s41594_023_01195_1 crossref_primary_10_1093_nar_gkac550 |
Cites_doi | 10.1073/pnas.082249499 10.1101/gr.163519.113 10.1038/emboj.2011.295 10.1073/pnas.1016071107 10.1016/j.cell.2007.02.005 10.1016/j.stem.2012.07.006 10.1093/nar/gkt826 10.1186/gb-2011-12-2-r15 10.1038/ng.3393 10.1101/gad.225565.113 10.7554/eLife.21926 10.1016/j.molcel.2010.05.004 10.1016/j.ydbio.2004.02.013 10.1038/msb.2012.23 10.1186/gb-2012-13-9-r53 10.1074/jbc.M500796200 10.1093/bioinformatics/btp120 10.1371/journal.pcbi.1007329 10.1101/gr.201574.115 10.1371/journal.pcbi.1005665 10.1093/bioinformatics/btg405 10.1016/j.stem.2017.02.004 10.1038/nature09692 10.1038/s41586-020-2493-4 10.1038/nbt.1621 10.1016/j.tig.2019.11.004 10.1073/pnas.0909344107 10.1126/science.aad7701 10.1016/j.celrep.2017.11.097 10.1038/s41588-018-0218-5 10.1093/nar/gks304 10.1038/ncb1076 10.1186/gb-2009-10-3-r25 10.1016/j.cell.2012.07.035 10.1093/nar/gkr752 10.1093/nar/gkv1189 10.1073/pnas.0904863106 10.1126/science.1076997 10.1186/gb-2008-9-9-r137 10.1016/j.molcel.2016.10.018 10.1093/bioinformatics/19.2.185 10.1186/s13072-020-0327-0 10.1038/nmeth.2221 10.1038/nmeth.1906 10.1016/j.cell.2017.09.043 10.1016/j.cell.2007.05.009 10.1038/s41588-019-0538-0 10.1093/nar/gkw377 10.1128/MCB.23.12.4207-4218.2003 10.1093/nar/gky064 10.4161/trns.2.6.18747 10.1038/nature01080 10.1073/pnas.1704553114 10.1038/ng.154 10.1101/gr.122382.111 10.1186/s13059-018-1432-2 10.1038/ng1966 |
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Copyright | COPYRIGHT 2021 Public Library of Science 2021 González-Ramírez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2021 González-Ramírez et al 2021 González-Ramírez et al |
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References | P Freire-Pritchett (pcbi.1009368.ref031) 2017; 6 MP Creyghton (pcbi.1009368.ref033) 2010; 107 C Trapnell (pcbi.1009368.ref056) 2010; 28 R Schneider (pcbi.1009368.ref005) 2004; 6 Y Zhu (pcbi.1009368.ref050) 2013; 41 F Koch (pcbi.1009368.ref027) 2011; 2 MV Kuleshov (pcbi.1009368.ref029) 2016; 44 X Dong (pcbi.1009368.ref014) 2012; 13 Z Duren (pcbi.1009368.ref016) 2017; 114 G Mas (pcbi.1009368.ref051) 2018; 50 S Heinz (pcbi.1009368.ref060) 2010; 38 NA O’Leary (pcbi.1009368.ref024) 2016; 44 S Wang (pcbi.1009368.ref018) 2016; 26 BE Bernstein (pcbi.1009368.ref004) 2002; 99 O Symmons (pcbi.1009368.ref032) 2014; 24 NJ Krogan (pcbi.1009368.ref039) 2003; 23 J Ernst (pcbi.1009368.ref054) 2012; 9 ND Heintzman (pcbi.1009368.ref008) 2007; 39 C Wang (pcbi.1009368.ref012) 2012; 40 A Rada-Iglesias (pcbi.1009368.ref044) 2012; 11 B Langmead (pcbi.1009368.ref052) 2009; 10 A Barski (pcbi.1009368.ref025) 2007; 129 TH Chang (pcbi.1009368.ref046) 2004; 269 F Schmidt (pcbi.1009368.ref017); 13 F. Hounkpe BWC (pcbi.1009368.ref038) 2019 E Blanco (pcbi.1009368.ref020) 2020; 36 H Santos-Rosa (pcbi.1009368.ref003) 2002; 419 B Bonev (pcbi.1009368.ref030) 2017; 171 R Cao (pcbi.1009368.ref007) 2002; 298 CP Fulco (pcbi.1009368.ref019) 2019; 51 M Beringer (pcbi.1009368.ref023) 2016; 64 GE Zentner (pcbi.1009368.ref022) 2011; 21 Y. H. Dudoit SY (pcbi.1009368.ref036) 2002; 12 D Karolchik (pcbi.1009368.ref062) 2007 M Kuhn (pcbi.1009368.ref045) 2008; 28 EP Consortium (pcbi.1009368.ref041) 2020; 583 TA Hait (pcbi.1009368.ref048) 2018; 19 N Link (pcbi.1009368.ref047) 2013; 27 A Rada-Iglesias (pcbi.1009368.ref043) 2011; 470 F Serra (pcbi.1009368.ref057) 2017; 13 BE Russ (pcbi.1009368.ref028) 2017; 21 L Gautier (pcbi.1009368.ref061) 2004; 20 R Karlic (pcbi.1009368.ref009) 2010; 107 SC Tippmann (pcbi.1009368.ref013) 2012; 8 S Schoenfelder (pcbi.1009368.ref042) 2015; 47 S Cruz-Molina (pcbi.1009368.ref021) 2017; 20 E Vidal (pcbi.1009368.ref059) 2018; 46 Z Wang (pcbi.1009368.ref006) 2008; 40 BM Bolstad (pcbi.1009368.ref037) 2003; 19 T Kouzarides (pcbi.1009368.ref002) 2007; 128 DF Read (pcbi.1009368.ref015) 2019; 15 Z Ouyang (pcbi.1009368.ref049) 2009; 106 C Trapnell (pcbi.1009368.ref055) 2009; 25 C Cheng (pcbi.1009368.ref010) 2011; 12 S Marco-Sola (pcbi.1009368.ref058) 2012; 9 E Shema (pcbi.1009368.ref034) 2016; 352 JA Wamstad (pcbi.1009368.ref035) 2012; 151 M Gasperini (pcbi.1009368.ref001) 2020 C Cheng (pcbi.1009368.ref011) 2012; 40 A Pekowska (pcbi.1009368.ref026) 2011; 30 AJ Bannister (pcbi.1009368.ref040) 2005; 280 Y Zhang (pcbi.1009368.ref053) 2008; 9 |
References_xml | – volume: 99 start-page: 8695 issue: 13 year: 2002 ident: pcbi.1009368.ref004 article-title: Methylation of histone H3 Lys 4 in coding regions of active genes publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.082249499 contributor: fullname: BE Bernstein – volume: 24 start-page: 390 issue: 3 year: 2014 ident: pcbi.1009368.ref032 article-title: Functional and topological characteristics of mammalian regulatory domains publication-title: Genome Res doi: 10.1101/gr.163519.113 contributor: fullname: O Symmons – volume: 30 start-page: 4198 issue: 20 year: 2011 ident: pcbi.1009368.ref026 article-title: H3K4 tri-methylation provides an epigenetic signature of active enhancers publication-title: EMBO J doi: 10.1038/emboj.2011.295 contributor: fullname: A Pekowska – volume: 107 start-page: 21931 issue: 50 year: 2010 ident: pcbi.1009368.ref033 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 contributor: fullname: MP Creyghton – volume: 128 start-page: 693 issue: 4 year: 2007 ident: pcbi.1009368.ref002 article-title: Chromatin modifications and their function publication-title: Cell doi: 10.1016/j.cell.2007.02.005 contributor: fullname: T Kouzarides – volume: 11 start-page: 633 issue: 5 year: 2012 ident: pcbi.1009368.ref044 article-title: Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest publication-title: Cell Stem Cell doi: 10.1016/j.stem.2012.07.006 contributor: fullname: A Rada-Iglesias – volume: 41 start-page: 10032 issue: 22 year: 2013 ident: pcbi.1009368.ref050 article-title: Predicting enhancer transcription and activity from chromatin modifications publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt826 contributor: fullname: Y Zhu – volume: 12 start-page: R15 issue: 2 year: 2011 ident: pcbi.1009368.ref010 article-title: A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets publication-title: Genome Biol doi: 10.1186/gb-2011-12-2-r15 contributor: fullname: C Cheng – volume: 47 start-page: 1179 issue: 10 year: 2015 ident: pcbi.1009368.ref042 article-title: Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome publication-title: Nat Genet doi: 10.1038/ng.3393 contributor: fullname: S Schoenfelder – volume-title: The UCSC Genome Browser. Curr Protoc BioinformaticsChapter 1:Unit 1 4 year: 2007 ident: pcbi.1009368.ref062 contributor: fullname: D Karolchik – volume: 27 start-page: 2433 issue: 22 year: 2013 ident: pcbi.1009368.ref047 article-title: A p53 enhancer region regulates target genes through chromatin conformations in cis and in trans publication-title: Genes Dev doi: 10.1101/gad.225565.113 contributor: fullname: N Link – volume: 6 year: 2017 ident: pcbi.1009368.ref031 article-title: Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells publication-title: Elife doi: 10.7554/eLife.21926 contributor: fullname: P Freire-Pritchett – volume: 38 start-page: 576 issue: 4 year: 2010 ident: pcbi.1009368.ref060 article-title: Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities publication-title: Mol Cell doi: 10.1016/j.molcel.2010.05.004 contributor: fullname: S Heinz – volume: 269 start-page: 595 issue: 2 year: 2004 ident: pcbi.1009368.ref046 article-title: An enhancer directs differential expression of the linked Mrf4 and Myf5 myogenic regulatory genes in the mouse publication-title: Dev Biol doi: 10.1016/j.ydbio.2004.02.013 contributor: fullname: TH Chang – volume: 8 start-page: 593 year: 2012 ident: pcbi.1009368.ref013 article-title: Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels publication-title: Mol Syst Biol doi: 10.1038/msb.2012.23 contributor: fullname: SC Tippmann – volume: 13 start-page: R53 issue: 9 year: 2012 ident: pcbi.1009368.ref014 article-title: Modeling gene expression using chromatin features in various cellular contexts publication-title: Genome Biol doi: 10.1186/gb-2012-13-9-r53 contributor: fullname: X Dong – volume: 280 start-page: 17732 issue: 18 year: 2005 ident: pcbi.1009368.ref040 article-title: Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes publication-title: J Biol Chem doi: 10.1074/jbc.M500796200 contributor: fullname: AJ Bannister – year: 2020 ident: pcbi.1009368.ref001 article-title: Towards a comprehensive catalogue of validated and target-linked human enhancers publication-title: Nat Rev Genet contributor: fullname: M Gasperini – volume: 25 start-page: 1105 issue: 9 year: 2009 ident: pcbi.1009368.ref055 article-title: TopHat: discovering splice junctions with RNA-Seq publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp120 contributor: fullname: C Trapnell – volume: 15 start-page: e1007329 issue: 9 year: 2019 ident: pcbi.1009368.ref015 article-title: Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features publication-title: PLoS Comput Biol. doi: 10.1371/journal.pcbi.1007329 contributor: fullname: DF Read – volume: 26 start-page: 1417 issue: 10 year: 2016 ident: pcbi.1009368.ref018 article-title: Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles publication-title: Genome Res doi: 10.1101/gr.201574.115 contributor: fullname: S Wang – volume: 13 start-page: e1005665 issue: 7 year: 2017 ident: pcbi.1009368.ref057 article-title: Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1005665 contributor: fullname: F Serra – volume: 20 start-page: 307 issue: 3 year: 2004 ident: pcbi.1009368.ref061 article-title: affy—analysis of Affymetrix GeneChip data at the probe level publication-title: Bioinformatics doi: 10.1093/bioinformatics/btg405 contributor: fullname: L Gautier – volume: 20 start-page: 689 issue: 5 year: 2017 ident: pcbi.1009368.ref021 article-title: PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation publication-title: Cell Stem Cell doi: 10.1016/j.stem.2017.02.004 contributor: fullname: S Cruz-Molina – volume: 470 start-page: 279 issue: 7333 year: 2011 ident: pcbi.1009368.ref043 article-title: A unique chromatin signature uncovers early developmental enhancers in humans publication-title: Nature doi: 10.1038/nature09692 contributor: fullname: A Rada-Iglesias – volume: 583 start-page: 699 issue: 7818 year: 2020 ident: pcbi.1009368.ref041 article-title: Expanded encyclopaedias of DNA elements in the human and mouse genomes publication-title: Nature doi: 10.1038/s41586-020-2493-4 contributor: fullname: EP Consortium – volume: 28 start-page: 511 issue: 5 year: 2010 ident: pcbi.1009368.ref056 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 contributor: fullname: C Trapnell – volume: 36 start-page: 118 issue: 2 year: 2020 ident: pcbi.1009368.ref020 article-title: The Bivalent Genome: Characterization, Structure, and Regulation. publication-title: Trends Genet. doi: 10.1016/j.tig.2019.11.004 contributor: fullname: E Blanco – volume: 28 start-page: 1 issue: 5 year: 2008 ident: pcbi.1009368.ref045 article-title: Building Predictive Models in R Using the caret Package publication-title: Journal of Statistical Software, Articles contributor: fullname: M Kuhn – volume: 107 start-page: 2926 issue: 7 year: 2010 ident: pcbi.1009368.ref009 article-title: Histone modification levels are predictive for gene expression publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0909344107 contributor: fullname: R Karlic – volume: 352 start-page: 717 issue: 6286 year: 2016 ident: pcbi.1009368.ref034 article-title: Single-molecule decoding of combinatorially modified nucleosomes publication-title: Science doi: 10.1126/science.aad7701 contributor: fullname: E Shema – volume: 21 start-page: 3624 issue: 12 year: 2017 ident: pcbi.1009368.ref028 article-title: Regulation of H3K4me3 at Transcriptional Enhancers Characterizes Acquisition of Virus-Specific CD8(+) T Cell-Lineage-Specific Function publication-title: Cell Rep doi: 10.1016/j.celrep.2017.11.097 contributor: fullname: BE Russ – volume: 50 start-page: 1452 issue: 10 year: 2018 ident: pcbi.1009368.ref051 article-title: Promoter bivalency favors an open chromatin architecture in embryonic stem cells publication-title: Nat Genet doi: 10.1038/s41588-018-0218-5 contributor: fullname: G Mas – volume: 40 start-page: 6414 issue: 14 year: 2012 ident: pcbi.1009368.ref012 article-title: Computational inference of mRNA stability from histone modification and transcriptome profiles publication-title: Nucleic Acids Res doi: 10.1093/nar/gks304 contributor: fullname: C Wang – volume: 6 start-page: 73 issue: 1 year: 2004 ident: pcbi.1009368.ref005 article-title: Histone H3 lysine 4 methylation patterns in higher eukaryotic genes publication-title: Nat Cell Biol doi: 10.1038/ncb1076 contributor: fullname: R Schneider – volume: 10 start-page: R25 issue: 3 year: 2009 ident: pcbi.1009368.ref052 article-title: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome publication-title: Genome Biol doi: 10.1186/gb-2009-10-3-r25 contributor: fullname: B Langmead – volume: 151 start-page: 206 issue: 1 year: 2012 ident: pcbi.1009368.ref035 article-title: Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage publication-title: Cell doi: 10.1016/j.cell.2012.07.035 contributor: fullname: JA Wamstad – volume: 40 start-page: 553 issue: 2 year: 2012 ident: pcbi.1009368.ref011 article-title: Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells publication-title: Nucleic Acids Res doi: 10.1093/nar/gkr752 contributor: fullname: C Cheng – volume: 44 start-page: D733 issue: D1 year: 2016 ident: pcbi.1009368.ref024 article-title: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation publication-title: Nucleic Acids Res doi: 10.1093/nar/gkv1189 contributor: fullname: NA O’Leary – volume: 106 start-page: 21521 issue: 51 year: 2009 ident: pcbi.1009368.ref049 article-title: ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0904863106 contributor: fullname: Z Ouyang – volume: 298 start-page: 1039 issue: 5595 year: 2002 ident: pcbi.1009368.ref007 article-title: Role of histone H3 lysine 27 methylation in Polycomb-group silencing publication-title: Science doi: 10.1126/science.1076997 contributor: fullname: R Cao – volume: 9 start-page: R137 issue: 9 year: 2008 ident: pcbi.1009368.ref053 article-title: Model-based analysis of ChIP-Seq (MACS) publication-title: Genome Biol doi: 10.1186/gb-2008-9-9-r137 contributor: fullname: Y Zhang – volume: 64 start-page: 645 issue: 4 year: 2016 ident: pcbi.1009368.ref023 article-title: EPOP Functionally Links Elongin and Polycomb in Pluripotent Stem Cells publication-title: Mol Cell doi: 10.1016/j.molcel.2016.10.018 contributor: fullname: M Beringer – volume: 19 start-page: 185 issue: 2 year: 2003 ident: pcbi.1009368.ref037 article-title: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias publication-title: Bioinformatics doi: 10.1093/bioinformatics/19.2.185 contributor: fullname: BM Bolstad – volume: 13 start-page: 4 issue: 1 ident: pcbi.1009368.ref017 article-title: Integrative prediction of gene expression with chromatin accessibility and conformation data publication-title: Epigenetics Chromatin. 2020 doi: 10.1186/s13072-020-0327-0 contributor: fullname: F Schmidt – volume: 9 start-page: 1185 issue: 12 year: 2012 ident: pcbi.1009368.ref058 article-title: The GEM mapper: fast, accurate and versatile alignment by filtration publication-title: Nat Methods. doi: 10.1038/nmeth.2221 contributor: fullname: S Marco-Sola – volume: 9 start-page: 215 issue: 3 year: 2012 ident: pcbi.1009368.ref054 article-title: ChromHMM: automating chromatin-state discovery and characterization publication-title: Nat Methods doi: 10.1038/nmeth.1906 contributor: fullname: J Ernst – volume: 171 start-page: 557 issue: 3 year: 2017 ident: pcbi.1009368.ref030 article-title: Multiscale 3D Genome Rewiring during Mouse Neural Development publication-title: Cell doi: 10.1016/j.cell.2017.09.043 contributor: fullname: B Bonev – volume: 12 start-page: 111 issue: 1 year: 2002 ident: pcbi.1009368.ref036 article-title: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments publication-title: Stat Sin contributor: fullname: Y. H. Dudoit SY – volume: 129 start-page: 823 issue: 4 year: 2007 ident: pcbi.1009368.ref025 article-title: High-resolution profiling of histone methylations in the human genome publication-title: Cell doi: 10.1016/j.cell.2007.05.009 contributor: fullname: A Barski – volume: 51 start-page: 1664 issue: 12 year: 2019 ident: pcbi.1009368.ref019 article-title: Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations publication-title: Nat Genet doi: 10.1038/s41588-019-0538-0 contributor: fullname: CP Fulco – volume: 44 start-page: W90 issue: W1 year: 2016 ident: pcbi.1009368.ref029 article-title: Enrichr: a comprehensive gene set enrichment analysis web server 2016 update publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw377 contributor: fullname: MV Kuleshov – volume: 23 start-page: 4207 issue: 12 year: 2003 ident: pcbi.1009368.ref039 article-title: Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II publication-title: Mol Cell Biol doi: 10.1128/MCB.23.12.4207-4218.2003 contributor: fullname: NJ Krogan – year: 2019 ident: pcbi.1009368.ref038 article-title: HT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets publication-title: bioRxiv contributor: fullname: F. Hounkpe BWC – volume: 46 start-page: e49 issue: 8 year: 2018 ident: pcbi.1009368.ref059 article-title: OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes publication-title: Nucleic Acids Res doi: 10.1093/nar/gky064 contributor: fullname: E Vidal – volume: 2 start-page: 263 issue: 6 year: 2011 ident: pcbi.1009368.ref027 article-title: Initiating RNA polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity publication-title: Transcription doi: 10.4161/trns.2.6.18747 contributor: fullname: F Koch – volume: 419 start-page: 407 issue: 6905 year: 2002 ident: pcbi.1009368.ref003 article-title: Active genes are tri-methylated at K4 of histone H3 publication-title: Nature doi: 10.1038/nature01080 contributor: fullname: H Santos-Rosa – volume: 114 start-page: E4914 issue: 25 year: 2017 ident: pcbi.1009368.ref016 article-title: Modeling gene regulation from paired expression and chromatin accessibility data publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1704553114 contributor: fullname: Z Duren – volume: 40 start-page: 897 issue: 7 year: 2008 ident: pcbi.1009368.ref006 article-title: Combinatorial patterns of histone acetylations and methylations in the human genome publication-title: Nat Genet doi: 10.1038/ng.154 contributor: fullname: Z Wang – volume: 21 start-page: 1273 issue: 8 year: 2011 ident: pcbi.1009368.ref022 article-title: Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions publication-title: Genome Res doi: 10.1101/gr.122382.111 contributor: fullname: GE Zentner – volume: 19 start-page: 56 issue: 1 year: 2018 ident: pcbi.1009368.ref048 article-title: FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map publication-title: Genome Biol doi: 10.1186/s13059-018-1432-2 contributor: fullname: TA Hait – volume: 39 start-page: 311 issue: 3 year: 2007 ident: pcbi.1009368.ref008 article-title: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome publication-title: Nat Genet doi: 10.1038/ng1966 contributor: fullname: ND Heintzman |
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SubjectTerms | Animals Biology and Life Sciences Cell Differentiation - genetics Cells, Cultured Chromatin Immunoprecipitation Sequencing - statistics & numerical data Computational Biology Differentiation Embryo cells Enhancer Elements, Genetic Enhancers Epigenetics Experiments Gene Expression Genetic aspects Genomes Histone Code - genetics Histones Humans Mice Models, Genetic Mouse Embryonic Stem Cells - metabolism Physical Sciences Physiological aspects Prediction models Promoter Regions, Genetic Promoters Regression Analysis Research and Analysis Methods Stem cells |
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Title | Differential contribution to gene expression prediction of histone modifications at enhancers or promoters |
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