Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs.

Anagha Joshi

doi:10.1186/s12859-014-0412-0

Abstract

BackgroundTranscriptional hotspots are defined as genomic regions bound by multiple factors. They have been identified recently as cell type specific enhancers regulating developmentally essential genes in many species such as worm, fly and humans. The in-depth analysis of hotspots across multiple cell types in same species still remains to be explored and can bring new biological insights.ResultsWe therefore collected 108 transcription-related factor (TF) ChIP sequencing data sets in ten murine cell types and classified the peaks in each cell type in three groups according to binding occupancy as singletons (low-occupancy), combinatorials (mid-occupancy) and hotspots (high-occupancy). The peaks in the three groups clustered largely according to the occupancy, suggesting priming of genomic loci for mid occupancy irrespective of cell type. We then characterized hotspots for diverse structural functional properties. The genes neighbouring hotspots had a small overlap with hotspot genes in other cell types and were highly enriched for cell type specific function. Hotspots were enriched for sequence motifs of key TFs in that cell type and more than 90% of hotspots were occupied by pioneering factors. Though we did not find any sequence signature in the three groups, the H3K4me1 binding profile had bimodal peaks at hotspots, distinguishing hotspots from mono-modal H3K4me1 singletons. In ES cells, differentially expressed genes after perturbation of activators were enriched for hotspot genes suggesting hotspots primarily act as transcriptional activator hubs. Finally, we proposed that ES hotspots might be under control of SetDB1 and not DNMT for silencing.ConclusionTranscriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes. In ES cells, they are predicted to act as transcriptional activator hubs and might be under SetDB1 control for silencing.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0412-0) contains supplementary material, which is available to authorized users.

Highlights

Transcriptional hotspots are defined as genomic regions bound by multiple factors
The number of transcription-related factor (TF) at binding sites followed an exponential curve such that about half of the regions were bound by only one TF in any given cell type and less than 0.5% occupied by all TFs studied
We divided all peaks in a cell type into three groups: singletons or low-occupancy, peaks bound by only one transcription-related factor (Figure 1A), combinatorials or mid-occupancy, peaks bound by a combination of transcription-related factors (Figure 1A) and hotspots or high-occupancy, peaks bound by more than five TFs studied in a given cell type (Figure 1A, Additional file 1: Table S31)

Summary

Introduction

Transcriptional hotspots are defined as genomic regions bound by multiple factors They have been identified recently as cell type specific enhancers regulating developmentally essential genes in many species such as worm, fly and humans. As ChIP sequencing protocols mature, peaks of multiple transcription factors have been characterized in single cell types to study combinatorial control [1]. In 2006, Moorman et al [2] generated genome-wide binding profiles of seven transcription factors in D. melanogaster and identified a subset of peaks bound by all seven TFs (hotspots). Of these 108 hotspots, when tested using transgenic assays, 94% acted as enhancers strongly activating the neighbouring developmentally

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