title: Defining the chromatin signature of inducible genes in T cells.
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.
authors.affiliation: Genome Biology Program and ACRF Biomolecular Resource Facility, John Curtin School of Medical Research, The Australian National University, Garran Road, Acton, ACT 0200, Australia. chloe.lim@anu.edu.au
authors.forename: Pek S
authors.initials: PS
authors.lastname: Lim
authors.forename: Kristine
authors.initials: K
authors.lastname: Hardy
authors.forename: Karen L
authors.initials: KL
authors.lastname: Bunting
authors.forename: Lina
authors.initials: L
authors.lastname: Ma
authors.forename: Kaiman
authors.initials: K
authors.lastname: Peng
authors.forename: Xinxin
authors.initials: X
authors.lastname: Chen
authors.forename: Mary F
authors.initials: MF
authors.lastname: Shannon
mesh_terms: D000107:Acetylation; D001482:Base Composition / Q000235:genetics; D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands / Q000235:genetics; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism; D006801:Humans; D008213:Lymphocyte Activation / Q000235:genetics; D008745:Methylation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012319:RNA Polymerase II / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D006657:Histones; D012319:RNA Polymerase II