Nov 7, 2018

Occupancy patterns of 208 DNA-associated proteins in a single human cell type

BioRxiv : the Preprint Server for Biology
E. Christopher PartridgeEric M. Mendenhall

Abstract

Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes, but only a small fraction of the >1,600 transcription factors (TFs) encoded in the human genome has been assayed. Here we present data and analyses of ChIP-seq experiments for 208 DNA-associated proteins (DAPs) in the HepG2 hepatocellular carcinoma line, spanning nearly a quarter of its expressed TFs, transcriptional co-factors, and chromatin regulator proteins. The DAP binding profiles classify into major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalog of DNA sequence motifs; 77 factors showed similar motifs to those previously described using in vivo and/or in vitro methods, and 17 yielded novel motifs. We also describe motifs corresponding to other TFs that co-enrich with the primary ChIP target. FOX family motifs are, for example, significantly enriched in ChIP-seq peaks of 37 other DAPs. We show that promoters and enhancers can be discriminated based on motif content and occupancy patterns. This large catalog reveals High Occupancy Target (HOT) regions at which many DAPs associate, although each contains...Continue Reading

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Mentioned in this Paper

Genome-Wide Association Study
In Vivo
Transcriptional Regulation
Patterns
Diaminopyrimidine
Classification
Genome
Transcription, Genetic
DNA, Viral
Liver Carcinoma

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