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Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome

The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites is an accurate method for identifying the location of functional regulatory elem...

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Autores principales: Xi, Hualin, Shulha, Hennady P, Lin, Jane M, Vales, Teresa R, Fu, Yutao, Bodine, David M, McKay, Ronald D. G, Chenoweth, Josh G, Tesar, Paul J, Furey, Terrence S, Ren, Bing, Weng, Zhiping, Crawford, Gregory E
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950163/
https://www.ncbi.nlm.nih.gov/pubmed/17708682
http://dx.doi.org/10.1371/journal.pgen.0030136
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author Xi, Hualin
Shulha, Hennady P
Lin, Jane M
Vales, Teresa R
Fu, Yutao
Bodine, David M
McKay, Ronald D. G
Chenoweth, Josh G
Tesar, Paul J
Furey, Terrence S
Ren, Bing
Weng, Zhiping
Crawford, Gregory E
author_facet Xi, Hualin
Shulha, Hennady P
Lin, Jane M
Vales, Teresa R
Fu, Yutao
Bodine, David M
McKay, Ronald D. G
Chenoweth, Josh G
Tesar, Paul J
Furey, Terrence S
Ren, Bing
Weng, Zhiping
Crawford, Gregory E
author_sort Xi, Hualin
collection PubMed
description The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites is an accurate method for identifying the location of functional regulatory elements. We used a high throughput method called DNase-chip to identify 3,904 DNaseI HS sites from six cell types across 1% of the human genome. A significant number (22%) of DNaseI HS sites from each cell type are ubiquitously present among all cell types studied. Surprisingly, nearly all of these ubiquitous DNaseI HS sites correspond to either promoters or insulator elements: 86% of them are located near annotated transcription start sites and 10% are bound by CTCF, a protein with known enhancer-blocking insulator activity. We also identified a large number of DNaseI HS sites that are cell type specific (only present in one cell type); these regions are enriched for enhancer elements and correlate with cell type–specific gene expression as well as cell type–specific histone modifications. Finally, we found that approximately 8% of the genome overlaps a DNaseI HS site in at least one the six cell lines studied, indicating that a significant percentage of the genome is potentially functional.
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spelling pubmed-19501632007-08-18 Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome Xi, Hualin Shulha, Hennady P Lin, Jane M Vales, Teresa R Fu, Yutao Bodine, David M McKay, Ronald D. G Chenoweth, Josh G Tesar, Paul J Furey, Terrence S Ren, Bing Weng, Zhiping Crawford, Gregory E PLoS Genet Research Article The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites is an accurate method for identifying the location of functional regulatory elements. We used a high throughput method called DNase-chip to identify 3,904 DNaseI HS sites from six cell types across 1% of the human genome. A significant number (22%) of DNaseI HS sites from each cell type are ubiquitously present among all cell types studied. Surprisingly, nearly all of these ubiquitous DNaseI HS sites correspond to either promoters or insulator elements: 86% of them are located near annotated transcription start sites and 10% are bound by CTCF, a protein with known enhancer-blocking insulator activity. We also identified a large number of DNaseI HS sites that are cell type specific (only present in one cell type); these regions are enriched for enhancer elements and correlate with cell type–specific gene expression as well as cell type–specific histone modifications. Finally, we found that approximately 8% of the genome overlaps a DNaseI HS site in at least one the six cell lines studied, indicating that a significant percentage of the genome is potentially functional. Public Library of Science 2007-08 2007-08-17 /pmc/articles/PMC1950163/ /pubmed/17708682 http://dx.doi.org/10.1371/journal.pgen.0030136 Text en This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
spellingShingle Research Article
Xi, Hualin
Shulha, Hennady P
Lin, Jane M
Vales, Teresa R
Fu, Yutao
Bodine, David M
McKay, Ronald D. G
Chenoweth, Josh G
Tesar, Paul J
Furey, Terrence S
Ren, Bing
Weng, Zhiping
Crawford, Gregory E
Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome
title Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome
title_full Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome
title_fullStr Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome
title_full_unstemmed Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome
title_short Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome
title_sort identification and characterization of cell type–specific and ubiquitous chromatin regulatory structures in the human genome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950163/
https://www.ncbi.nlm.nih.gov/pubmed/17708682
http://dx.doi.org/10.1371/journal.pgen.0030136
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