Cargando…
Determination of enriched histone modifications in non-genic portions of the human genome
BACKGROUND: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers. RESULTS: We have extended the analysis of histone modif...
Autores principales: | , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2009
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667539/ https://www.ncbi.nlm.nih.gov/pubmed/19335899 http://dx.doi.org/10.1186/1471-2164-10-143 |
_version_ | 1782166146198274048 |
---|---|
author | Rosenfeld, Jeffrey A Wang, Zhibin Schones, Dustin E Zhao, Keji DeSalle, Rob Zhang, Michael Q |
author_facet | Rosenfeld, Jeffrey A Wang, Zhibin Schones, Dustin E Zhao, Keji DeSalle, Rob Zhang, Michael Q |
author_sort | Rosenfeld, Jeffrey A |
collection | PubMed |
description | BACKGROUND: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers. RESULTS: We have extended the analysis of histone modifications to gene deserts, pericentromeres and subtelomeres. Using data from human CD4(+ )T cells, we have found that each of these non-genic regions has a particular profile of histone modifications that distinguish it from the other non-coding regions. Different methylation states of H4K20, H3K9 and H3K27 were found to be enriched in each region relative to the other regions. These findings indicate that non-genic regions of the genome are variable with respect to histone modification patterns, rather than being monolithic. We furthermore used consensus sequences for unassembled centromeres and telomeres to identify the significant histone modifications in these regions. Finally, we compared the modification patterns in non-genic regions to those at silent genes and genes with higher levels of expression. For all tested methylations with the exception of H3K27me3, the enrichment level of each modification state for silent genes is between that of non-genic regions and expressed genes. For H3K27me3, the highest levels are found in silent genes. CONCLUSION: In addition to the histone modification pattern difference between euchromatin and heterochromatin regions, as is illustrated by the enrichment of H3K9me2/3 in non-genic regions while H3K9me1 is enriched at active genes; the chromatin modifications within non-genic (heterochromatin-like) regions (e.g. subtelomeres, pericentromeres and gene deserts) are also quite different. |
format | Text |
id | pubmed-2667539 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26675392009-04-10 Determination of enriched histone modifications in non-genic portions of the human genome Rosenfeld, Jeffrey A Wang, Zhibin Schones, Dustin E Zhao, Keji DeSalle, Rob Zhang, Michael Q BMC Genomics Research Article BACKGROUND: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers. RESULTS: We have extended the analysis of histone modifications to gene deserts, pericentromeres and subtelomeres. Using data from human CD4(+ )T cells, we have found that each of these non-genic regions has a particular profile of histone modifications that distinguish it from the other non-coding regions. Different methylation states of H4K20, H3K9 and H3K27 were found to be enriched in each region relative to the other regions. These findings indicate that non-genic regions of the genome are variable with respect to histone modification patterns, rather than being monolithic. We furthermore used consensus sequences for unassembled centromeres and telomeres to identify the significant histone modifications in these regions. Finally, we compared the modification patterns in non-genic regions to those at silent genes and genes with higher levels of expression. For all tested methylations with the exception of H3K27me3, the enrichment level of each modification state for silent genes is between that of non-genic regions and expressed genes. For H3K27me3, the highest levels are found in silent genes. CONCLUSION: In addition to the histone modification pattern difference between euchromatin and heterochromatin regions, as is illustrated by the enrichment of H3K9me2/3 in non-genic regions while H3K9me1 is enriched at active genes; the chromatin modifications within non-genic (heterochromatin-like) regions (e.g. subtelomeres, pericentromeres and gene deserts) are also quite different. BioMed Central 2009-03-31 /pmc/articles/PMC2667539/ /pubmed/19335899 http://dx.doi.org/10.1186/1471-2164-10-143 Text en Copyright © 2009 Rosenfeld et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Rosenfeld, Jeffrey A Wang, Zhibin Schones, Dustin E Zhao, Keji DeSalle, Rob Zhang, Michael Q Determination of enriched histone modifications in non-genic portions of the human genome |
title | Determination of enriched histone modifications in non-genic portions of the human genome |
title_full | Determination of enriched histone modifications in non-genic portions of the human genome |
title_fullStr | Determination of enriched histone modifications in non-genic portions of the human genome |
title_full_unstemmed | Determination of enriched histone modifications in non-genic portions of the human genome |
title_short | Determination of enriched histone modifications in non-genic portions of the human genome |
title_sort | determination of enriched histone modifications in non-genic portions of the human genome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667539/ https://www.ncbi.nlm.nih.gov/pubmed/19335899 http://dx.doi.org/10.1186/1471-2164-10-143 |
work_keys_str_mv | AT rosenfeldjeffreya determinationofenrichedhistonemodificationsinnongenicportionsofthehumangenome AT wangzhibin determinationofenrichedhistonemodificationsinnongenicportionsofthehumangenome AT schonesdustine determinationofenrichedhistonemodificationsinnongenicportionsofthehumangenome AT zhaokeji determinationofenrichedhistonemodificationsinnongenicportionsofthehumangenome AT desallerob determinationofenrichedhistonemodificationsinnongenicportionsofthehumangenome AT zhangmichaelq determinationofenrichedhistonemodificationsinnongenicportionsofthehumangenome |