Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections

Abstract Recent advances in genome‐wide technologies have enabled analyses using small cell numbers of even single cells. However, obtaining tissue epigenomes with cell‐type resolution from large organs and tissues still remains challenging, especially when the available material is limited. Here, w...

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Autores principales:	Kazumitsu Maehara, Kosuke Tomimatsu, Akihito Harada, Kaori Tanaka, Shoko Sato, Megumi Fukuoka, Seiji Okada, Tetsuya Handa, Hitoshi Kurumizaka, Noriko Saitoh, Hiroshi Kimura, Yasuyuki Ohkawa
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	dissociation‐free epigenome analysis in situ epigenomics on single thin tissue section tissue‐specific enhancers transcriptional state decomposition traveling ratio Biology (General) QH301-705.5 Medicine (General) R5-920
Acceso en línea:	https://doaj.org/article/a14215197b00491ea6506a7f9089eef7
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spelling	oai:doaj.org-article:a14215197b00491ea6506a7f9089eef72021-11-29T08:21:36ZModeling population size independent tissue epigenomes by ChIL‐seq with single thin sections1744-429210.15252/msb.202110323https://doaj.org/article/a14215197b00491ea6506a7f9089eef72021-11-01T00:00:00Zhttps://doi.org/10.15252/msb.202110323https://doaj.org/toc/1744-4292Abstract Recent advances in genome‐wide technologies have enabled analyses using small cell numbers of even single cells. However, obtaining tissue epigenomes with cell‐type resolution from large organs and tissues still remains challenging, especially when the available material is limited. Here, we present a ChIL‐based approach for analyzing the diverse cellular dynamics at the tissue level using high‐depth epigenomic data. “ChIL for tissues” allows the analysis of a single tissue section and can reproducibly generate epigenomic profiles from several tissue types, based on the distribution of target epigenomic states, tissue morphology, and number of cells. The proposed method enabled the independent evaluation of changes in cell populations and gene activation in cells from regenerating skeletal muscle tissues, using a statistical model of RNA polymerase II distribution on gene loci. Thus, the integrative analyses performed using ChIL can elucidate in vivo cell‐type dynamics of tissues.Kazumitsu MaeharaKosuke TomimatsuAkihito HaradaKaori TanakaShoko SatoMegumi FukuokaSeiji OkadaTetsuya HandaHitoshi KurumizakaNoriko SaitohHiroshi KimuraYasuyuki OhkawaWileyarticledissociation‐free epigenome analysisin situ epigenomics on single thin tissue sectiontissue‐specific enhancerstranscriptional state decompositiontraveling ratioBiology (General)QH301-705.5Medicine (General)R5-920ENMolecular Systems Biology, Vol 17, Iss 11, Pp n/a-n/a (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	dissociation‐free epigenome analysis in situ epigenomics on single thin tissue section tissue‐specific enhancers transcriptional state decomposition traveling ratio Biology (General) QH301-705.5 Medicine (General) R5-920
spellingShingle	dissociation‐free epigenome analysis in situ epigenomics on single thin tissue section tissue‐specific enhancers transcriptional state decomposition traveling ratio Biology (General) QH301-705.5 Medicine (General) R5-920 Kazumitsu Maehara Kosuke Tomimatsu Akihito Harada Kaori Tanaka Shoko Sato Megumi Fukuoka Seiji Okada Tetsuya Handa Hitoshi Kurumizaka Noriko Saitoh Hiroshi Kimura Yasuyuki Ohkawa Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections
description	Abstract Recent advances in genome‐wide technologies have enabled analyses using small cell numbers of even single cells. However, obtaining tissue epigenomes with cell‐type resolution from large organs and tissues still remains challenging, especially when the available material is limited. Here, we present a ChIL‐based approach for analyzing the diverse cellular dynamics at the tissue level using high‐depth epigenomic data. “ChIL for tissues” allows the analysis of a single tissue section and can reproducibly generate epigenomic profiles from several tissue types, based on the distribution of target epigenomic states, tissue morphology, and number of cells. The proposed method enabled the independent evaluation of changes in cell populations and gene activation in cells from regenerating skeletal muscle tissues, using a statistical model of RNA polymerase II distribution on gene loci. Thus, the integrative analyses performed using ChIL can elucidate in vivo cell‐type dynamics of tissues.
format	article
author	Kazumitsu Maehara Kosuke Tomimatsu Akihito Harada Kaori Tanaka Shoko Sato Megumi Fukuoka Seiji Okada Tetsuya Handa Hitoshi Kurumizaka Noriko Saitoh Hiroshi Kimura Yasuyuki Ohkawa
author_facet	Kazumitsu Maehara Kosuke Tomimatsu Akihito Harada Kaori Tanaka Shoko Sato Megumi Fukuoka Seiji Okada Tetsuya Handa Hitoshi Kurumizaka Noriko Saitoh Hiroshi Kimura Yasuyuki Ohkawa
author_sort	Kazumitsu Maehara
title	Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections
title_short	Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections
title_full	Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections
title_fullStr	Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections
title_full_unstemmed	Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections
title_sort	modeling population size independent tissue epigenomes by chil‐seq with single thin sections
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/a14215197b00491ea6506a7f9089eef7
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_version_	1718407478726623232

Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections

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