Identification of cell states using super-enhancer RNA

Abstract Background A new class of regulatory elements called super-enhancers, comprised of multiple neighboring enhancers, have recently been reported to be the key transcriptional drivers of cellular, developmental, and disease states. Results Here, we defined super-enhancer RNAs as highly express...

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Autores principales:	Yueh-Hua Tu, Hsueh-Fen Juan, Hsuan-Cheng Huang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Super enhancer Enhancer RNA Super-enhancer RNA Cell state FANTOM5 Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/984823a71155488da684c57a2649353d
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spelling	oai:doaj.org-article:984823a71155488da684c57a2649353d2021-11-08T10:57:20ZIdentification of cell states using super-enhancer RNA10.1186/s12864-021-08092-11471-2164https://doaj.org/article/984823a71155488da684c57a2649353d2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08092-1https://doaj.org/toc/1471-2164Abstract Background A new class of regulatory elements called super-enhancers, comprised of multiple neighboring enhancers, have recently been reported to be the key transcriptional drivers of cellular, developmental, and disease states. Results Here, we defined super-enhancer RNAs as highly expressed enhancer RNAs that are transcribed from a cluster of localized genomic regions. Using the cap analysis of gene expression sequencing data from FANTOM5, we systematically explored the enhancer and messenger RNA landscapes in hundreds of different cell types in response to various environments. Applying non-negative matrix factorization (NMF) to super-enhancer RNA profiles, we found that different cell types were well classified. In addition, through the NMF of individual time-course profiles from a single cell-type, super-enhancer RNAs were clustered into several states with progressive patterns. We further investigated the enriched biological functions of the proximal genes involved in each pattern, and found that they were associated with the corresponding developmental process. Conclusions The proposed super-enhancer RNAs can act as a good alternative, without the complicated measurement of histone modifications, for identifying important regulatory elements of cell type specification and identifying dynamic cell states.Yueh-Hua TuHsueh-Fen JuanHsuan-Cheng HuangBMCarticleSuper enhancerEnhancer RNASuper-enhancer RNACell stateFANTOM5BiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss S3, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Super enhancer Enhancer RNA Super-enhancer RNA Cell state FANTOM5 Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Super enhancer Enhancer RNA Super-enhancer RNA Cell state FANTOM5 Biotechnology TP248.13-248.65 Genetics QH426-470 Yueh-Hua Tu Hsueh-Fen Juan Hsuan-Cheng Huang Identification of cell states using super-enhancer RNA
description	Abstract Background A new class of regulatory elements called super-enhancers, comprised of multiple neighboring enhancers, have recently been reported to be the key transcriptional drivers of cellular, developmental, and disease states. Results Here, we defined super-enhancer RNAs as highly expressed enhancer RNAs that are transcribed from a cluster of localized genomic regions. Using the cap analysis of gene expression sequencing data from FANTOM5, we systematically explored the enhancer and messenger RNA landscapes in hundreds of different cell types in response to various environments. Applying non-negative matrix factorization (NMF) to super-enhancer RNA profiles, we found that different cell types were well classified. In addition, through the NMF of individual time-course profiles from a single cell-type, super-enhancer RNAs were clustered into several states with progressive patterns. We further investigated the enriched biological functions of the proximal genes involved in each pattern, and found that they were associated with the corresponding developmental process. Conclusions The proposed super-enhancer RNAs can act as a good alternative, without the complicated measurement of histone modifications, for identifying important regulatory elements of cell type specification and identifying dynamic cell states.
format	article
author	Yueh-Hua Tu Hsueh-Fen Juan Hsuan-Cheng Huang
author_facet	Yueh-Hua Tu Hsueh-Fen Juan Hsuan-Cheng Huang
author_sort	Yueh-Hua Tu
title	Identification of cell states using super-enhancer RNA
title_short	Identification of cell states using super-enhancer RNA
title_full	Identification of cell states using super-enhancer RNA
title_fullStr	Identification of cell states using super-enhancer RNA
title_full_unstemmed	Identification of cell states using super-enhancer RNA
title_sort	identification of cell states using super-enhancer rna
publisher	BMC
publishDate	2021
url	https://doaj.org/article/984823a71155488da684c57a2649353d
work_keys_str_mv	AT yuehhuatu identificationofcellstatesusingsuperenhancerrna AT hsuehfenjuan identificationofcellstatesusingsuperenhancerrna AT hsuanchenghuang identificationofcellstatesusingsuperenhancerrna
_version_	1718442450487345152

Identification of cell states using super-enhancer RNA

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