Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.

Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also cal...

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Autores principales:	Ya-Mei Wang, Ping Zhou, Li-Yong Wang, Zhen-Hua Li, Yao-Nan Zhang, Yu-Xiang Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/37aae5bc55fa4bd6881e47f43c27f94f
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spelling	oai:doaj.org-article:37aae5bc55fa4bd6881e47f43c27f94f2021-11-18T07:09:09ZCorrelation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.1932-620310.1371/journal.pone.0042414https://doaj.org/article/37aae5bc55fa4bd6881e47f43c27f94f2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22900019/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100-500 bp. Therefore, we used short DNA fragments released by DNase I digestion to generate DNA libraries for next generation sequencing. The short segments are 100-300 bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by this DHS assay are consistent with those identified by longer fragments in previous studies. We also found: (1) the distribution of DHSs in promoter and other gene regions of similarly expressed genes differs among different chromosomes; (2) silenced genes had a more open chromatin structure than previously thought; (3) DHSs in 3'untranslated regions (3'UTRs) are negatively correlated with level of gene expression.Ya-Mei WangPing ZhouLi-Yong WangZhen-Hua LiYao-Nan ZhangYu-Xiang ZhangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e42414 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ya-Mei Wang Ping Zhou Li-Yong Wang Zhen-Hua Li Yao-Nan Zhang Yu-Xiang Zhang Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
description	Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100-500 bp. Therefore, we used short DNA fragments released by DNase I digestion to generate DNA libraries for next generation sequencing. The short segments are 100-300 bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by this DHS assay are consistent with those identified by longer fragments in previous studies. We also found: (1) the distribution of DHSs in promoter and other gene regions of similarly expressed genes differs among different chromosomes; (2) silenced genes had a more open chromatin structure than previously thought; (3) DHSs in 3'untranslated regions (3'UTRs) are negatively correlated with level of gene expression.
format	article
author	Ya-Mei Wang Ping Zhou Li-Yong Wang Zhen-Hua Li Yao-Nan Zhang Yu-Xiang Zhang
author_facet	Ya-Mei Wang Ping Zhou Li-Yong Wang Zhen-Hua Li Yao-Nan Zhang Yu-Xiang Zhang
author_sort	Ya-Mei Wang
title	Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
title_short	Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
title_full	Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
title_fullStr	Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
title_full_unstemmed	Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
title_sort	correlation between dnase i hypersensitive site distribution and gene expression in hela s3 cells.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/37aae5bc55fa4bd6881e47f43c27f94f
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_version_	1718423845295095808

Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.

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