Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning
We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2022-03, Vol.114 (2), p.110296-110296, Article 110296 |
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| container_title | Genomics (San Diego, Calif.) |
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| creator | Gao, Yahui Liu, Shuli Baldwin VI, Ransom L. Connor, Erin E. Cole, John B. Ma, Li Fang, Lingzhao Li, Cong-jun Liu, George E. |
| description | We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development.
•We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning.•The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined•Each chromatin state presented specific enrichment for functional regulatory elements.•During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states.•With in vivo rumen tissues, we showed the roles of cell interactions and mitochondrial activities in tissue development. |
| doi_str_mv | 10.1016/j.ygeno.2022.110296 |
| format | Article |
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•We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning.•The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined•Each chromatin state presented specific enrichment for functional regulatory elements.•During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states.•With in vivo rumen tissues, we showed the roles of cell interactions and mitochondrial activities in tissue development.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2022.110296</identifier><identifier>PMID: 35143887</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Animals ; Butyrate ; Cattle - genetics ; Cattle genome ; Cell interaction ; Chromatin - genetics ; Chromatin - metabolism ; Chromatin state ; DNA Methylation ; Functional annotation ; Rumen - metabolism ; Rumen development ; Transcription Initiation Site ; Weaning</subject><ispartof>Genomics (San Diego, Calif.), 2022-03, Vol.114 (2), p.110296-110296, Article 110296</ispartof><rights>2022</rights><rights>Copyright © 2022. Published by Elsevier Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c404t-cabc841858100cbe4095bae654235921bfa90da2067664ffe2aaa3c96f25f863</citedby><cites>FETCH-LOGICAL-c404t-cabc841858100cbe4095bae654235921bfa90da2067664ffe2aaa3c96f25f863</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ygeno.2022.110296$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,864,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35143887$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gao, Yahui</creatorcontrib><creatorcontrib>Liu, Shuli</creatorcontrib><creatorcontrib>Baldwin VI, Ransom L.</creatorcontrib><creatorcontrib>Connor, Erin E.</creatorcontrib><creatorcontrib>Cole, John B.</creatorcontrib><creatorcontrib>Ma, Li</creatorcontrib><creatorcontrib>Fang, Lingzhao</creatorcontrib><creatorcontrib>Li, Cong-jun</creatorcontrib><creatorcontrib>Liu, George E.</creatorcontrib><title>Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development.
•We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning.•The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined•Each chromatin state presented specific enrichment for functional regulatory elements.•During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states.•With in vivo rumen tissues, we showed the roles of cell interactions and mitochondrial activities in tissue development.</description><subject>Animals</subject><subject>Butyrate</subject><subject>Cattle - genetics</subject><subject>Cattle genome</subject><subject>Cell interaction</subject><subject>Chromatin - genetics</subject><subject>Chromatin - metabolism</subject><subject>Chromatin state</subject><subject>DNA Methylation</subject><subject>Functional annotation</subject><subject>Rumen - metabolism</subject><subject>Rumen development</subject><subject>Transcription Initiation Site</subject><subject>Weaning</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kU9v1DAQxS1E1W7_fAIk5COXLLbjeJ0DB1RRqFSJS-_WxJnsepXYi-0U9pPx9XB2C0dOMyO9934aPULecbbmjKuP-_Vxiz6sBRNizTkTrXpDVpzpttJKqrdkxbTW1aaR9RW5TmnPGGtrLS7JVd1wWWu9WZHfD7O32QUPIwXvQ4bloGGgEbfzCDnEI8URJ_Q5UeephZxHpAt5wiJ6QRgTzbuyhxHT4sRfOYLFcSz-WDwZy3mKBd_T_uhhcpbaHfgtLnq7i2EqXE9TweMJE-dCpH2JH8NhgdN-js5v6U8EX-YtuRgKGO9e5w15fvjyfP-tevr-9fH-81NlJZO5stBZLbluNGfMdihZ23SAqpGiblrBuwFa1oNgaqOUHAYUAFDbVg2iGbSqb8iHc-whhh8zpmwml5bXwGOYkxFK6JrxjWBFWp-lNoaUIg7mEN0E8Wg4M0thZm9OhZmlMHMurLjevwLmbsL-n-dvQ0Xw6SzA8uWLw2iSdegt9i6izaYP7r-AP2OIrbA</recordid><startdate>202203</startdate><enddate>202203</enddate><creator>Gao, Yahui</creator><creator>Liu, Shuli</creator><creator>Baldwin VI, Ransom L.</creator><creator>Connor, Erin E.</creator><creator>Cole, John B.</creator><creator>Ma, Li</creator><creator>Fang, Lingzhao</creator><creator>Li, Cong-jun</creator><creator>Liu, George E.</creator><general>Elsevier Inc</general><scope>6I.</scope><scope>AAFTH</scope><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>7X8</scope></search><sort><creationdate>202203</creationdate><title>Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning</title><author>Gao, Yahui ; Liu, Shuli ; Baldwin VI, Ransom L. ; Connor, Erin E. ; Cole, John B. ; Ma, Li ; Fang, Lingzhao ; Li, Cong-jun ; Liu, George E.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c404t-cabc841858100cbe4095bae654235921bfa90da2067664ffe2aaa3c96f25f863</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Animals</topic><topic>Butyrate</topic><topic>Cattle - genetics</topic><topic>Cattle genome</topic><topic>Cell interaction</topic><topic>Chromatin - genetics</topic><topic>Chromatin - metabolism</topic><topic>Chromatin state</topic><topic>DNA Methylation</topic><topic>Functional annotation</topic><topic>Rumen - metabolism</topic><topic>Rumen development</topic><topic>Transcription Initiation Site</topic><topic>Weaning</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gao, Yahui</creatorcontrib><creatorcontrib>Liu, Shuli</creatorcontrib><creatorcontrib>Baldwin VI, Ransom L.</creatorcontrib><creatorcontrib>Connor, Erin E.</creatorcontrib><creatorcontrib>Cole, John B.</creatorcontrib><creatorcontrib>Ma, Li</creatorcontrib><creatorcontrib>Fang, Lingzhao</creatorcontrib><creatorcontrib>Li, Cong-jun</creatorcontrib><creatorcontrib>Liu, George E.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gao, Yahui</au><au>Liu, Shuli</au><au>Baldwin VI, Ransom L.</au><au>Connor, Erin E.</au><au>Cole, John B.</au><au>Ma, Li</au><au>Fang, Lingzhao</au><au>Li, Cong-jun</au><au>Liu, George E.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2022-03</date><risdate>2022</risdate><volume>114</volume><issue>2</issue><spage>110296</spage><epage>110296</epage><pages>110296-110296</pages><artnum>110296</artnum><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development.
•We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning.•The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined•Each chromatin state presented specific enrichment for functional regulatory elements.•During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states.•With in vivo rumen tissues, we showed the roles of cell interactions and mitochondrial activities in tissue development.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>35143887</pmid><doi>10.1016/j.ygeno.2022.110296</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Butyrate Cattle - genetics Cattle genome Cell interaction Chromatin - genetics Chromatin - metabolism Chromatin state DNA Methylation Functional annotation Rumen - metabolism Rumen development Transcription Initiation Site Weaning |
| title | Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning |
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