Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines.

Joseph W Foley,Arend Sidow

doi:10.1186/1471-2164-14-720

Abstract

BackgroundHigh-occupancy target (HOT) regions are compact genome loci occupied by many different transcription factors (TFs). HOT regions were initially defined in invertebrate model organisms, and we here show that they are a ubiquitous feature of the human gene-regulation landscape.ResultsWe identified HOT regions by a comprehensive analysis of ChIP-seq data from 96 DNA-associated proteins in 5 human cell lines. Most HOT regions co-localize with RNA polymerase II binding sites, but many are not near the promoters of annotated genes. At HOT promoters, TF occupancy is strongly predictive of transcription preinitiation complex recruitment and moderately predictive of initiating Pol II recruitment, but only weakly predictive of elongating Pol II and RNA transcript abundance. TF occupancy varies quantitatively within human HOT regions; we used this variation to discover novel associations between TFs. The sequence motif associated with any given TF’s direct DNA binding is somewhat predictive of its empirical occupancy, but a great deal of occupancy occurs at sites without the TF’s motif, implying indirect recruitment by another TF whose motif is present.ConclusionsMammalian HOT regions are regulatory hubs that integrate the signals from diverse regulatory pathways to quantitatively tune the promoter for RNA polymerase II recruitment.

Highlights

High-occupancy target (HOT) regions are compact genome loci occupied by many different transcription factors (TFs)
Unlike other peak-callers for ChIP-seq, UniPeak does not directly use “input” or other negative controls to filter enriched regions initially; rather, though these samples do not contribute to the region-calling step, negative-control reads are counted within the regions called from ChIP samples, and reported alongside read counts from TF ChIP samples
We present a quantitative analysis of a large volume of ChIP-seq data, constituting the genome-wide occupancy profiles of a large number of TFs in five human cell types, from the ENCODE consortium [8]

Summary

Introduction

High-occupancy target (HOT) regions are compact genome loci occupied by many different transcription factors (TFs). Transcription factors (TFs) are proteins that regulate the expression of genes by binding the DNA at their regulatory elements (promoters or enhancers) and either preventing or facilitating the recruitment, in eukaryotes, of the transcription preinitiation complex (PIC). The PIC in turn recruits RNA polymerase II (Pol II) to the transcription start site (TSS) to synthesize an RNA transcript. This is a primary mechanism for the regulation of gene expression in response to environmental stimuli or developmental programs. Some regulatory regions (“high-occupancy target”, or HOT, regions) are occupied by a large number of transcription factors [1,2,3,4,5,6]. Less is known about the interactions among TFs at HOT regions and how these interactions contribute combinatorially to the regulation of transcription, and until recently, insufficient data existed to search for HOT regions in human cells

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