An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wid...

Full description

Saved in:
Bibliographic Details
Published in:BMC genomics 2018-06, Vol.19 (1), p.476-476, Article 476
Main Authors: Kennedy, Elizabeth M, Goehring, George N, Nichols, Michael H, Robins, Chloe, Mehta, Divya, Klengel, Torsten, Eskin, Eleazar, Smith, Alicia K, Conneely, Karen N
Format: Article
Language:English
Subjects:
Adolescent
Adult
Aged
Analysis
Atherosclerosis
Binding sites
Biological effects
Blood
Blood cells
Blood Cells - metabolism
Chromatin
Cohort Studies
CpG Islands
Data mining
Data processing
Deoxyribonucleic acid
DNA
DNA Methylation
Enhancers
Enrichment
Epigenesis, Genetic
Epigenetic inheritance
Epigenetics
Female
Gene expression
Gene Expression Profiling
Gene Ontology
Genes
Genetic transcription
Genomes
Genomics
Humans
Insulators
Male
Methylation
MicroRNAs
Middle Aged
miRNA
Promoters
Regulatory sequences
Ribonucleic acid
RNA
Studies
Transcriptional regulation
Young Adult
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c594t-54e3ab9c345df1bb734a6ee19174e176fc38485a9870b3047120a4e3c49ae1543
cites cdi_FETCH-LOGICAL-c594t-54e3ab9c345df1bb734a6ee19174e176fc38485a9870b3047120a4e3c49ae1543
container_end_page 476
container_issue 1
container_start_page 476
container_title BMC genomics
container_volume 19
creator Kennedy, Elizabeth M
Goehring, George N
Nichols, Michael H
Robins, Chloe
Mehta, Divya
Klengel, Torsten
Eskin, Eleazar
Smith, Alicia K
Conneely, Karen N
description Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), > 50% are distal (> 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P 
doi_str_mv 10.1186/s12864-018-4842-3
format article
fullrecord <record><control><sourceid>gale_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_66a8978a0f964e29a988cd512072b3c3</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A546872049</galeid><doaj_id>oai_doaj_org_article_66a8978a0f964e29a988cd512072b3c3</doaj_id><sourcerecordid>A546872049</sourcerecordid><originalsourceid>FETCH-LOGICAL-c594t-54e3ab9c345df1bb734a6ee19174e176fc38485a9870b3047120a4e3c49ae1543</originalsourceid><addsrcrecordid>eNptkstr3DAQh01padK0f0AvRdBLe3Cql_W4FJbQx0Kg0MdZjOWxV4vX2lp2SP77ytk07Jbig83om8_M6FcUrxm9ZMyoD4lxo2RJmSmlkbwUT4pzJjUrOVPy6dH3WfEipS2lTBtePS_OuLVMCiXPC1gNJAwTdiNM2JAy7oJPBAbo71JIJLZk2iDBfehwwCl40sPQJA97XM6WIsHb_YgphbiYyGbewUDqPsaGeOz79LJ41kKf8NXD-6L49fnTz6uv5fW3L-ur1XXpKyunspIooLZeyKppWV1rIUEhMsu0RKZV64WRpgJrNK0FzZNxCrnHSwvIKikuivXB20TYuv0YdjDeuQjB3Rfi2DkY8wQ9OqXAWG2AtlZJ5DZLjW-qbNS8Fl5k18eDaz_XO2w8DtMI_Yn09GQIG9fFG6coVVrrLHj3IBjj7xnT5HYhLeuAAeOcHKeVZsLqimf07T_oNs5jvoB7ShlmxTHVQR4gDG3M__WL1K0qqYzmVNpMXf6Hyk-D-V7jgG3I9ZOG9ycNmZnwdupgTsmtf3w_ZdmB9WNMacT2cR-MuiWP7pBHl_Poljy6ZZFvjhf52PE3gOIP3n3YGA</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2056819352</pqid></control><display><type>article</type><title>An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells</title><source>Open Access: PubMed Central</source><source>Publicly Available Content Database</source><creator>Kennedy, Elizabeth M ; Goehring, George N ; Nichols, Michael H ; Robins, Chloe ; Mehta, Divya ; Klengel, Torsten ; Eskin, Eleazar ; Smith, Alicia K ; Conneely, Karen N</creator><creatorcontrib>Kennedy, Elizabeth M ; Goehring, George N ; Nichols, Michael H ; Robins, Chloe ; Mehta, Divya ; Klengel, Torsten ; Eskin, Eleazar ; Smith, Alicia K ; Conneely, Karen N</creatorcontrib><description>Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), &gt; 50% are distal (&gt; 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P &lt; 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60-70% of occurrences and are enriched for annotated gene promoters and enhancers (P &lt; 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control. This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-018-4842-3</identifier><identifier>PMID: 29914364</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Adolescent ; Adult ; Aged ; Analysis ; Atherosclerosis ; Binding sites ; Biological effects ; Blood ; Blood cells ; Blood Cells - metabolism ; Chromatin ; Cohort Studies ; CpG Islands ; Data mining ; Data processing ; Deoxyribonucleic acid ; DNA ; DNA Methylation ; Enhancers ; Enrichment ; Epigenesis, Genetic ; Epigenetic inheritance ; Epigenetics ; Female ; Gene expression ; Gene Expression Profiling ; Gene Ontology ; Genes ; Genetic transcription ; Genomes ; Genomics ; Humans ; Insulators ; Male ; Methylation ; MicroRNAs ; Middle Aged ; miRNA ; Promoters ; Regulatory sequences ; Ribonucleic acid ; RNA ; Studies ; Transcriptional regulation ; Young Adult</subject><ispartof>BMC genomics, 2018-06, Vol.19 (1), p.476-476, Article 476</ispartof><rights>COPYRIGHT 2018 BioMed Central Ltd.</rights><rights>Copyright © 2018. 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.</rights><rights>The Author(s). 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c594t-54e3ab9c345df1bb734a6ee19174e176fc38485a9870b3047120a4e3c49ae1543</citedby><cites>FETCH-LOGICAL-c594t-54e3ab9c345df1bb734a6ee19174e176fc38485a9870b3047120a4e3c49ae1543</cites><orcidid>0000-0003-0074-2840</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006777/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2056819352?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29914364$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kennedy, Elizabeth M</creatorcontrib><creatorcontrib>Goehring, George N</creatorcontrib><creatorcontrib>Nichols, Michael H</creatorcontrib><creatorcontrib>Robins, Chloe</creatorcontrib><creatorcontrib>Mehta, Divya</creatorcontrib><creatorcontrib>Klengel, Torsten</creatorcontrib><creatorcontrib>Eskin, Eleazar</creatorcontrib><creatorcontrib>Smith, Alicia K</creatorcontrib><creatorcontrib>Conneely, Karen N</creatorcontrib><title>An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), &gt; 50% are distal (&gt; 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P &lt; 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60-70% of occurrences and are enriched for annotated gene promoters and enhancers (P &lt; 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control. This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Aged</subject><subject>Analysis</subject><subject>Atherosclerosis</subject><subject>Binding sites</subject><subject>Biological effects</subject><subject>Blood</subject><subject>Blood cells</subject><subject>Blood Cells - metabolism</subject><subject>Chromatin</subject><subject>Cohort Studies</subject><subject>CpG Islands</subject><subject>Data mining</subject><subject>Data processing</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>Enhancers</subject><subject>Enrichment</subject><subject>Epigenesis, Genetic</subject><subject>Epigenetic inheritance</subject><subject>Epigenetics</subject><subject>Female</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Ontology</subject><subject>Genes</subject><subject>Genetic transcription</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Humans</subject><subject>Insulators</subject><subject>Male</subject><subject>Methylation</subject><subject>MicroRNAs</subject><subject>Middle Aged</subject><subject>miRNA</subject><subject>Promoters</subject><subject>Regulatory sequences</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Studies</subject><subject>Transcriptional regulation</subject><subject>Young Adult</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptkstr3DAQh01padK0f0AvRdBLe3Cql_W4FJbQx0Kg0MdZjOWxV4vX2lp2SP77ytk07Jbig83om8_M6FcUrxm9ZMyoD4lxo2RJmSmlkbwUT4pzJjUrOVPy6dH3WfEipS2lTBtePS_OuLVMCiXPC1gNJAwTdiNM2JAy7oJPBAbo71JIJLZk2iDBfehwwCl40sPQJA97XM6WIsHb_YgphbiYyGbewUDqPsaGeOz79LJ41kKf8NXD-6L49fnTz6uv5fW3L-ur1XXpKyunspIooLZeyKppWV1rIUEhMsu0RKZV64WRpgJrNK0FzZNxCrnHSwvIKikuivXB20TYuv0YdjDeuQjB3Rfi2DkY8wQ9OqXAWG2AtlZJ5DZLjW-qbNS8Fl5k18eDaz_XO2w8DtMI_Yn09GQIG9fFG6coVVrrLHj3IBjj7xnT5HYhLeuAAeOcHKeVZsLqimf07T_oNs5jvoB7ShlmxTHVQR4gDG3M__WL1K0qqYzmVNpMXf6Hyk-D-V7jgG3I9ZOG9ycNmZnwdupgTsmtf3w_ZdmB9WNMacT2cR-MuiWP7pBHl_Poljy6ZZFvjhf52PE3gOIP3n3YGA</recordid><startdate>20180619</startdate><enddate>20180619</enddate><creator>Kennedy, Elizabeth M</creator><creator>Goehring, George N</creator><creator>Nichols, Michael H</creator><creator>Robins, Chloe</creator><creator>Mehta, Divya</creator><creator>Klengel, Torsten</creator><creator>Eskin, Eleazar</creator><creator>Smith, Alicia K</creator><creator>Conneely, Karen N</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><general>BMC</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0003-0074-2840</orcidid></search><sort><creationdate>20180619</creationdate><title>An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells</title><author>Kennedy, Elizabeth M ; Goehring, George N ; Nichols, Michael H ; Robins, Chloe ; Mehta, Divya ; Klengel, Torsten ; Eskin, Eleazar ; Smith, Alicia K ; Conneely, Karen N</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c594t-54e3ab9c345df1bb734a6ee19174e176fc38485a9870b3047120a4e3c49ae1543</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>Aged</topic><topic>Analysis</topic><topic>Atherosclerosis</topic><topic>Binding sites</topic><topic>Biological effects</topic><topic>Blood</topic><topic>Blood cells</topic><topic>Blood Cells - metabolism</topic><topic>Chromatin</topic><topic>Cohort Studies</topic><topic>CpG Islands</topic><topic>Data mining</topic><topic>Data processing</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>Enhancers</topic><topic>Enrichment</topic><topic>Epigenesis, Genetic</topic><topic>Epigenetic inheritance</topic><topic>Epigenetics</topic><topic>Female</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Ontology</topic><topic>Genes</topic><topic>Genetic transcription</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Humans</topic><topic>Insulators</topic><topic>Male</topic><topic>Methylation</topic><topic>MicroRNAs</topic><topic>Middle Aged</topic><topic>miRNA</topic><topic>Promoters</topic><topic>Regulatory sequences</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Studies</topic><topic>Transcriptional regulation</topic><topic>Young Adult</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kennedy, Elizabeth M</creatorcontrib><creatorcontrib>Goehring, George N</creatorcontrib><creatorcontrib>Nichols, Michael H</creatorcontrib><creatorcontrib>Robins, Chloe</creatorcontrib><creatorcontrib>Mehta, Divya</creatorcontrib><creatorcontrib>Klengel, Torsten</creatorcontrib><creatorcontrib>Eskin, Eleazar</creatorcontrib><creatorcontrib>Smith, Alicia K</creatorcontrib><creatorcontrib>Conneely, Karen N</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium &amp; Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Health &amp; Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kennedy, Elizabeth M</au><au>Goehring, George N</au><au>Nichols, Michael H</au><au>Robins, Chloe</au><au>Mehta, Divya</au><au>Klengel, Torsten</au><au>Eskin, Eleazar</au><au>Smith, Alicia K</au><au>Conneely, Karen N</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2018-06-19</date><risdate>2018</risdate><volume>19</volume><issue>1</issue><spage>476</spage><epage>476</epage><pages>476-476</pages><artnum>476</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), &gt; 50% are distal (&gt; 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P &lt; 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60-70% of occurrences and are enriched for annotated gene promoters and enhancers (P &lt; 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control. This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>29914364</pmid><doi>10.1186/s12864-018-4842-3</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-0074-2840</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1471-2164
ispartof BMC genomics, 2018-06, Vol.19 (1), p.476-476, Article 476
issn 1471-2164
1471-2164
language eng
recordid cdi_doaj_primary_oai_doaj_org_article_66a8978a0f964e29a988cd512072b3c3
source Open Access: PubMed Central; Publicly Available Content Database
subjects Adolescent
Adult
Aged
Analysis
Atherosclerosis
Binding sites
Biological effects
Blood
Blood cells
Blood Cells - metabolism
Chromatin
Cohort Studies
CpG Islands
Data mining
Data processing
Deoxyribonucleic acid
DNA
DNA Methylation
Enhancers
Enrichment
Epigenesis, Genetic
Epigenetic inheritance
Epigenetics
Female
Gene expression
Gene Expression Profiling
Gene Ontology
Genes
Genetic transcription
Genomes
Genomics
Humans
Insulators
Male
Methylation
MicroRNAs
Middle Aged
miRNA
Promoters
Regulatory sequences
Ribonucleic acid
RNA
Studies
Transcriptional regulation
Young Adult
title An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-29T15%3A24%3A21IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=An%20integrated%20-omics%20analysis%20of%20the%20epigenetic%20landscape%20of%20gene%20expression%20in%20human%20blood%20cells&rft.jtitle=BMC%20genomics&rft.au=Kennedy,%20Elizabeth%20M&rft.date=2018-06-19&rft.volume=19&rft.issue=1&rft.spage=476&rft.epage=476&rft.pages=476-476&rft.artnum=476&rft.issn=1471-2164&rft.eissn=1471-2164&rft_id=info:doi/10.1186/s12864-018-4842-3&rft_dat=%3Cgale_doaj_%3EA546872049%3C/gale_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c594t-54e3ab9c345df1bb734a6ee19174e176fc38485a9870b3047120a4e3c49ae1543%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2056819352&rft_id=info:pmid/29914364&rft_galeid=A546872049&rfr_iscdi=true