Defining the chromatin signature of inducible genes in T cells

Lim, Hardy Kristine, Bunting, Ma Lina, Peng Kaiman, Chen Xinxin, Shannon

Description

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.

Informations

• Publié par: biomed
• Publié le: 01 janvier 2009
• Nombre de lectures: 100
• Langue: English
• Poids de l'ouvrage: 4 Mo

Extrait

2eLVti0omal0lu.9me10,Issue10,ArticleR107 Open Access Research Defining the chromatin signature of inducible genes in T cells ¤ * ¤ * †* ‡ Pek S Lim, Kristine Hardy, Karen L Bunting, Lina Ma, Kaiman Peng, ‡ * Xinxin Chenand Mary F Shannon

* Addresses: GenomeBiology Program and ACRF Biomolecular Resource Facility, John Curtin School of Medical Research, The Australian † National University, Garran Road, Acton, ACT 0200, Australia.Current address: Department of Medicine/Hematology-Oncology, Weill ‡ Cornell Medical College, 68th St, New York, NY 10065, USA.Current address: Departments of Physiology and Pathology, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Beijing 100730, PR China.

¤ These authors contributed equally to this work.

Correspondence: Mary F Shannon. Email: [e-mail]

Published: 6 October 2009 GenomeBiology2009,10:R107 (doi:10.1186/gb-2009-10-10-r107) The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2009/10/10/R107

Received: 30 April 2009 Revised: 27 July 2009 Accepted: 6 October 2009

© 2009 Limet 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. A<pc>hIrnodmuactiibnlesigutanerniesenfhtwohssllceTiblegorinducetamorhcgneitevfcascoisticterharaincyheearimprfed,seggusitsetgn.</p>serotarsnnrcpiitno

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.

GenomeBiology2009,10:R107