Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Wang, Ya-Mei, Zhou, Ping, Wang, Li-Yong, Li, Zhen-Hua, Zhang, Yao-Nan, Zhang, Yu-Xiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416863/
https://www.ncbi.nlm.nih.gov/pubmed/22900019
http://dx.doi.org/10.1371/journal.pone.0042414
_version_ 1782240461740572672
author Wang, Ya-Mei
Zhou, Ping
Wang, Li-Yong
Li, Zhen-Hua
Zhang, Yao-Nan
Zhang, Yu-Xiang
author_facet Wang, Ya-Mei
Zhou, Ping
Wang, Li-Yong
Li, Zhen-Hua
Zhang, Yao-Nan
Zhang, Yu-Xiang
author_sort Wang, Ya-Mei
collection PubMed
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 Online
Article
Text
id pubmed-3416863
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-34168632012-08-16 Correlation Between DNase I Hypersensitive Site Distribution and Gene Expression in HeLa S3 Cells Wang, Ya-Mei Zhou, Ping Wang, Li-Yong Li, Zhen-Hua Zhang, Yao-Nan Zhang, Yu-Xiang PLoS One Research Article 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. Public Library of Science 2012-08-10 /pmc/articles/PMC3416863/ /pubmed/22900019 http://dx.doi.org/10.1371/journal.pone.0042414 Text en © 2012 Wang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Wang, Ya-Mei
Zhou, Ping
Wang, Li-Yong
Li, Zhen-Hua
Zhang, Yao-Nan
Zhang, Yu-Xiang
Correlation Between DNase I Hypersensitive Site Distribution and Gene Expression in HeLa S3 Cells
title 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_short 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
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416863/
https://www.ncbi.nlm.nih.gov/pubmed/22900019
http://dx.doi.org/10.1371/journal.pone.0042414
work_keys_str_mv AT wangyamei correlationbetweendnaseihypersensitivesitedistributionandgeneexpressioninhelas3cells
AT zhouping correlationbetweendnaseihypersensitivesitedistributionandgeneexpressioninhelas3cells
AT wangliyong correlationbetweendnaseihypersensitivesitedistributionandgeneexpressioninhelas3cells
AT lizhenhua correlationbetweendnaseihypersensitivesitedistributionandgeneexpressioninhelas3cells
AT zhangyaonan correlationbetweendnaseihypersensitivesitedistributionandgeneexpressioninhelas3cells
AT zhangyuxiang correlationbetweendnaseihypersensitivesitedistributionandgeneexpressioninhelas3cells