Identifying synergistic regulation involving c-Myc and sp1 in human tissues.
Combinatorial gene regulation largely contributes to phenotypic versatility in higher eukaryotes. Genome-wide chromatin immuno-precipitation (ChIP) combined with expression profiling can dissect regulatory circuits around transcriptional regulators. Here, we integrate tiling array measurements of DNA-binding sites for c-Myc, sp1, TFIID and modified histones with a tissue expression atlas to establish the functional correspondence between physical binding, promoter activity and transcriptional regulation. For this we develop SLM, a methodology to map c-Myc and sp1-binding sites and then classify sites as sp1-only, c-Myc-only or dual. Dual sites show several distinct features compared to the single regulator sites: specifically, they exhibit overall higher degree of conservation between human and rodents, stronger correlation with TFIID-bound promoters, and preference for permissive chromatin state. By applying regression models to an expression atlas we identified a functionally distinct signature for strong dual c-Myc/sp1 sites. Namely, the correlation with c-Myc expression in promoters harboring dual-sites is increased for stronger sp1 sites by strong sp1 binding and the effect is largest in proliferating tissues. Our approach shows how integrated functional analyses can uncover tissue-specific and combinatorial regulatory dependencies in mammals.
Parisi
Fabio
F
Swiss Institute for Experimental Cancer Research (ISREC) and NCCR Molecular Oncology, Lausanne, Switzerland.
Wirapati
Pratyaksha
P
Naef
Felix
F
D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic; D016271:Proto-Oncogene Proteins c-myc / Q000378:metabolism*; D051381:Rats; D016329:Sp1 Transcription Factor / Q000378:metabolism*; D014018:Tissue Distribution
D002843:Chromatin; C489427:MYC protein, human; D016271:Proto-Oncogene Proteins c-myc; D016329:Sp1 Transcription Factor