Defining the chromatin signature of inducible genes in T cells
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Lim, Pek S; Hardy, Kristine; Bunting, Karen; Ma, Lina; Peng, Kaiman; Chen, Xinxin; Shannon, Mary F
Description
BACKGROUND Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with active and inactive genes. There is growing evidence that genes that respond to environmental or developmental signals may possess distinct chromatin marks. Using a T cell model and both genome-wide and gene-focused approaches, we examined the chromatin characteristics of genes that respond to T cell activation. RESULTS To facilitate comparison of genes with...[Show more]
dc.contributor.author | Lim, Pek S | |
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dc.contributor.author | Hardy, Kristine | |
dc.contributor.author | Bunting, Karen | |
dc.contributor.author | Ma, Lina | |
dc.contributor.author | Peng, Kaiman | |
dc.contributor.author | Chen, Xinxin | |
dc.contributor.author | Shannon, Mary F | |
dc.date.accessioned | 2016-01-04T03:37:52Z | |
dc.date.available | 2016-01-04T03:37:52Z | |
dc.identifier.issn | 1465-6906 | |
dc.identifier.uri | http://hdl.handle.net/1885/95207 | |
dc.description.abstract | BACKGROUND Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with active and inactive genes. There is growing evidence that genes that respond to environmental or developmental signals may possess distinct chromatin marks. Using a T cell model and both genome-wide and gene-focused approaches, we examined the chromatin characteristics of genes that respond to T cell activation. RESULTS To facilitate comparison of genes with similar basal expression levels, we used expression-profiling data to bin genes according to their basal expression levels. We found that inducible genes in the lower basal expression bins, especially rapidly induced primary response genes, were more likely than their non-responsive counterparts to display the histone modifications of active genes, have RNA polymerase II (Pol II) at their promoters and show evidence of ongoing basal elongation. There was little or no evidence for the presence of active chromatin marks in the absence of promoter Pol II on these inducible genes. In addition, we identified a subgroup of genes with active promoter chromatin marks and promoter Pol II but no evidence of elongation. Following T cell activation, we find little evidence for a major shift in the active chromatin signature around inducible gene promoters but many genes recruit more Pol II and show increased evidence of elongation. CONCLUSIONS These results suggest that the majority of inducible genes are primed for activation by having an active chromatin signature and promoter Pol II with or without ongoing elongation. | |
dc.publisher | BioMed Central | |
dc.rights | © 2009 Lim et al.; licensee BioMed Central Ltd. 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. | |
dc.source | Genome Biology | |
dc.subject | acetylation | |
dc.subject | base composition | |
dc.subject | cd4-positive t-lymphocytes | |
dc.subject | chromatin | |
dc.subject | chromatin immunoprecipitation | |
dc.subject | cpg islands | |
dc.subject | histones | |
dc.subject | humans | |
dc.subject | lymphocyte activation | |
dc.subject | methylation | |
dc.subject | promoter regions, genetic | |
dc.subject | protein binding | |
dc.subject | rna polymerase ii | |
dc.subject | transcription, genetic | |
dc.subject | gene expression regulation | |
dc.title | Defining the chromatin signature of inducible genes in T cells | |
dc.type | Journal article | |
local.description.notes | Imported from ARIES | |
local.identifier.citationvolume | 10 | |
dc.date.issued | 2009-10-06 | |
local.identifier.absfor | 060199 | |
local.identifier.ariespublication | u4020362xPUB162 | |
local.publisher.url | http://www.biomedcentral.com/ | |
local.type.status | Published Version | |
local.contributor.affiliation | Lim, Pek (Chloe), College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, Genome Sciences, The Australian National University | |
local.contributor.affiliation | Hardy, Kristine, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, Genome Sciences, The Australian National University | |
local.contributor.affiliation | Bunting, Karen L, Weill Cornell Medical College, United States of America | |
local.contributor.affiliation | Ma, Lina, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, Genome Sciences, The Australian National University | |
local.contributor.affiliation | Peng, Kaiman, Institute of Basic Medical Sciences (Beijing), China | |
local.contributor.affiliation | Chen, Xinxin, Chinese Academy of Medical Sciences , China | |
local.contributor.affiliation | Shannon, M Frances, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, Genome Sciences, The Australian National University | |
local.identifier.essn | 1474-760X | |
local.bibliographicCitation.issue | 10 | |
local.bibliographicCitation.startpage | R107 | |
local.bibliographicCitation.lastpage | 107.18 | |
local.identifier.doi | 10.1186/gb-2009-10-10-r107 | |
dc.date.updated | 2016-02-24T10:26:56Z | |
local.identifier.scopusID | 2-s2.0-75349108276 | |
local.identifier.thomsonID | 000272227000009 | |
Collections | ANU Research Publications |
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