title: Genome-wide analysis of gene expression in T cells to identify targets of the NF-kappa B transcription factor c-Rel.
abstract: It is well established that the NF-kappaB family of transcription factors serves a major role in controlling gene expression in response to T cell activation, but the genome-wide roles of individual family members remain to be determined. c-Rel, a member of the NF-kappaB family, appears to play a specific role in T cell function because T cells from c-Rel(-/-) animals are defective in their response to immune signals. We have used expression profiling to identify sets of genes that are affected by either deletion or overexpression of c-Rel in T cells. Very few of these genes exhibit a strong requirement for c-Rel; rather, c-Rel appears to modulate the expression of a large number of genes in these cells. The sets of c-Rel-affected genes are significantly enriched for genes containing consensus NF-kappaB/Rel sites in their proximal promoter regions. In addition, their promoters contain a higher average density of NF-kappaB/Rel sites compared with all genes represented on the microarrays. A transcriptional module comprised of two closely spaced c-Rel consensus sites is found with higher frequency in the c-Rel-affected gene sets and may represent an important control module for genes regulated by c-Rel or other NF-kappaB family members. We confirmed the importance of these findings on a subgroup of genes by using quantitative PCR to monitor gene expression as well as in vitro c-Rel/DNA binding assays and luciferase reporter assays. The c-Rel-regulated genes identified here support a role for c-Rel in inflammatory responses as well as in the promotion of cell growth and survival.
authors.affiliation: Division of Molecular Bioscience, John Curtin School of Medical Research, Australian National University, Canberra, Australia.
authors.forename: Karen
authors.initials: K
authors.lastname: Bunting
authors.forename: Sudha
authors.initials: S
authors.lastname: Rao
authors.forename: Kristine
authors.initials: K
authors.lastname: Hardy
authors.forename: Donna
authors.initials: D
authors.lastname: Woltring
authors.forename: Gareth S
authors.initials: GS
authors.lastname: Denyer
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Steve
authors.initials: S
authors.lastname: Gerondakis
authors.forename: M Frances
authors.initials: MF
authors.lastname: Shannon
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism*; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000276:immunology*; D018390:Gene Targeting; D006801:Humans; D019169:Jurkat Cells; D008213:Lymphocyte Activation / Q000235:genetics; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D020569:Proto-Oncogene Proteins c-rel / Q000172:deficiency / Q000235:genetics / Q000378:metabolism / Q000502:physiology*
chemical_list: D016328:NF-kappa B; D020569:Proto-Oncogene Proteins c-rel