Kinetic profiles of p300 occupancy in vivo predict common features of promoter structure and coactivator recruitment

Abstract

Understanding the language encrypted in the gene regulatory regions of the human genome is a challenging goal for the genomic era. Although customary extrapolations from steady-state mRNA levels have been effective, deciphering these regulatory codes will require additional empirical data sets that more closely reflect the dynamic progression of molecular events responsible for inducible transcription. We describe an approach using chromatin immunoprecipitation to profile the kinetic occupancy of the transcriptional coactivator and histone acetyltransferase p300 at numerous mitogen-induced genes in activated T cells. Comparison of these profiles reveals a class of promoters that share common patterns of inducible expression, p300 recruitment, dependence on selective p300 domains, and sensitivity to histone deacetylase inhibitors. Remarkably, this class also shares an evolutionarily conserved promoter composition and structure that accurately predicts additional human genes with similar functional attributes. This ''reverse genomic'' approach will have broad application for the genome-wide classification of promoter structure and function.

Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes

“…Cells were stimulated with 1 M ionomycin (Calbiochem) and 50 ng/mL PMA (Sigma-Aldrich) at indicated time points as previously described (5). Cells were then fixed in 1% formaldehyde for 5 min and subjected to ChIP analysis as previously described (6). The complete protocol is provided in SI Materials and Methods.…”

“…Prior studies from our group showed that p300 associates rapidly with the promoters of several genes in Jurkat human T cells following mitogen stimulation with phorbol ester and ionomycin (P/I) (5,6). We expanded this observation using ChIP-chip strategies and qChIP to profile genome-wide changes in promoter occupancy of p300 and pol II 45 min following mitogen stimulation ( Fig.…”

“…2A). Prior observation of the kinetics of mitogen-stimulated p300 assembly at rapidly induced genes using semiquantitative PCR showed dynamic changes as the promoter evolved over 15-min intervals within 1 h following mitogen activation, where p300 appears to leave the template shortly after transcriptional stimulation in some cases (6). To assess these dynamic changes over a longer time frame and at higher resolution, similar but more sensitive measurements were done using ChIP followed by quantitative real-time PCR.…”

Temporal cross‐talk between TCR and STAT signals for CD8 T cell effector differentiation

“…Interestingly, ChIP assays using an anti-p300 mAb to examine the kinetics of the association of p300 with multiple promoter regions in activated T cells revealed a class of promoters with common patterns of p300 recruitment. These also share aspects of gene-regulatory control and present evolutionarily conserved features of promoter structure [72].…”

Ethanol-responsive genes: identification of transcription factors and their role in metabolomics

“…10 In higher eukaryotes, most promoters and gene-regulatory regions are comprised of an integrated network of modular or 'composite' TF-binding sites (TFBS) [10][11][12] whose specific arrangement determines the expression specificity of the gene(s). A set of distinct TFBS that make up a regulatory constituent is called a cis-regulatory module.…”