A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues

Super-enhancers (SEs) and broad H3K4me3 domains (BDs) are crucial regulators in the control of tissue identity in human and mouse. However, their features in pig remain largely unknown. In this study, by integrative computational analyses of epigenomic and transcriptomic data, we have characterized...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yanling Peng, Huifang Kang, Jing Luo, Yubo Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	super-enhancers broad H3K4me3 domains functional conservation tissue-specific pig Genetics QH426-470
Acceso en línea:	https://doaj.org/article/892e5823013d49d28516629a061c04eb
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:892e5823013d49d28516629a061c04eb
record_format	dspace
spelling	oai:doaj.org-article:892e5823013d49d28516629a061c04eb2021-11-30T19:07:16ZA Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues1664-802110.3389/fgene.2021.701049https://doaj.org/article/892e5823013d49d28516629a061c04eb2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.701049/fullhttps://doaj.org/toc/1664-8021Super-enhancers (SEs) and broad H3K4me3 domains (BDs) are crucial regulators in the control of tissue identity in human and mouse. However, their features in pig remain largely unknown. In this study, by integrative computational analyses of epigenomic and transcriptomic data, we have characterized SEs and BDs in six pig tissues and analyzed their conservation in comparison with human and mouse tissues. Similar to human and mouse, pig SEs and BDs display higher tissue specificity than their typical counterparts. Genes proximal to SEs and BDs are associated with tissue identity in most tissues. About 55–182 SEs (5–17% in total) and 99–309 BDs (8–16% in total) across pig tissues are considered as functionally conserved elements because they have orthologous SEs and BDs in human and mouse. However, these elements do not necessarily exhibit sequence conservation. The functionally conserved SEs are correlated to tissue identity in majority of pig tissues, while those conserved BDs are linked to tissue identity in a few tissues. Our study provides resources for future gene regulatory studies in pig. It highlights that SEs are more effective in defining tissue identity than BDs, which is contrasting to a previous study. It also provides novel insights on understanding the sequence features of functionally conserved elements.Yanling PengHuifang KangJing LuoYubo ZhangFrontiers Media S.A.articlesuper-enhancersbroad H3K4me3 domainsfunctional conservationtissue-specificpigGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	super-enhancers broad H3K4me3 domains functional conservation tissue-specific pig Genetics QH426-470
spellingShingle	super-enhancers broad H3K4me3 domains functional conservation tissue-specific pig Genetics QH426-470 Yanling Peng Huifang Kang Jing Luo Yubo Zhang A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues
description	Super-enhancers (SEs) and broad H3K4me3 domains (BDs) are crucial regulators in the control of tissue identity in human and mouse. However, their features in pig remain largely unknown. In this study, by integrative computational analyses of epigenomic and transcriptomic data, we have characterized SEs and BDs in six pig tissues and analyzed their conservation in comparison with human and mouse tissues. Similar to human and mouse, pig SEs and BDs display higher tissue specificity than their typical counterparts. Genes proximal to SEs and BDs are associated with tissue identity in most tissues. About 55–182 SEs (5–17% in total) and 99–309 BDs (8–16% in total) across pig tissues are considered as functionally conserved elements because they have orthologous SEs and BDs in human and mouse. However, these elements do not necessarily exhibit sequence conservation. The functionally conserved SEs are correlated to tissue identity in majority of pig tissues, while those conserved BDs are linked to tissue identity in a few tissues. Our study provides resources for future gene regulatory studies in pig. It highlights that SEs are more effective in defining tissue identity than BDs, which is contrasting to a previous study. It also provides novel insights on understanding the sequence features of functionally conserved elements.
format	article
author	Yanling Peng Huifang Kang Jing Luo Yubo Zhang
author_facet	Yanling Peng Huifang Kang Jing Luo Yubo Zhang
author_sort	Yanling Peng
title	A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues
title_short	A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues
title_full	A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues
title_fullStr	A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues
title_full_unstemmed	A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues
title_sort	comparative analysis of super-enhancers and broad h3k4me3 domains in pig, human, and mouse tissues
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/892e5823013d49d28516629a061c04eb
work_keys_str_mv	AT yanlingpeng acomparativeanalysisofsuperenhancersandbroadh3k4me3domainsinpighumanandmousetissues AT huifangkang acomparativeanalysisofsuperenhancersandbroadh3k4me3domainsinpighumanandmousetissues AT jingluo acomparativeanalysisofsuperenhancersandbroadh3k4me3domainsinpighumanandmousetissues AT yubozhang acomparativeanalysisofsuperenhancersandbroadh3k4me3domainsinpighumanandmousetissues AT yanlingpeng comparativeanalysisofsuperenhancersandbroadh3k4me3domainsinpighumanandmousetissues AT huifangkang comparativeanalysisofsuperenhancersandbroadh3k4me3domainsinpighumanandmousetissues AT jingluo comparativeanalysisofsuperenhancersandbroadh3k4me3domainsinpighumanandmousetissues AT yubozhang comparativeanalysisofsuperenhancersandbroadh3k4me3domainsinpighumanandmousetissues
_version_	1718406337607499776

A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues

Ejemplares similares