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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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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 |
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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 |
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