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...
| Huvudupphovsmän: | , , , , , , , , , , , , |
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| Materialtyp: | Artikel |
| Språk: | English |
| Publicerad: |
Public Library of Science (PLoS)
2007-08-01
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| Serie: | PLoS Genetics |
| Länkar: | http://europepmc.org/articles/PMC1950163?pdf=render |
| _version_ | 1828340256367181824 |
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| author | Hualin Xi Hennady P Shulha Jane M Lin Teresa R Vales Yutao Fu David M Bodine Ronald D G McKay Josh G Chenoweth Paul J Tesar Terrence S Furey Bing Ren Zhiping Weng Gregory E Crawford |
| author_facet | Hualin Xi Hennady P Shulha Jane M Lin Teresa R Vales Yutao Fu David M Bodine Ronald D G McKay Josh G Chenoweth Paul J Tesar Terrence S Furey Bing Ren Zhiping Weng Gregory E Crawford |
| author_sort | Hualin Xi |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-13T22:53:08Z |
| format | Article |
| id | doaj.art-9202a350102e4d898c3c40a9ef7b46e1 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-13T22:53:08Z |
| publishDate | 2007-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-9202a350102e4d898c3c40a9ef7b46e12022-12-22T02:26:06ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042007-08-0138e13610.1371/journal.pgen.0030136Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.Hualin XiHennady P ShulhaJane M LinTeresa R ValesYutao FuDavid M BodineRonald D G McKayJosh G ChenowethPaul J TesarTerrence S FureyBing RenZhiping WengGregory E CrawfordThe 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.http://europepmc.org/articles/PMC1950163?pdf=render |
| spellingShingle | Hualin Xi Hennady P Shulha Jane M Lin Teresa R Vales Yutao Fu David M Bodine Ronald D G McKay Josh G Chenoweth Paul J Tesar Terrence S Furey Bing Ren Zhiping Weng Gregory E Crawford Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genetics |
| 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 |
| url | http://europepmc.org/articles/PMC1950163?pdf=render |
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