Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

Abstract

The liver and pancreas share a common origin and coexpress several transcription factors. To gain insight into the transcriptional networks regulating the function of these tissues, we globally identify binding sites for FOXA2 in adult mouse islets and liver, PDX1 in islets, and HNF4A in liver. Because most eukaryotic transcription factors bind thousands of loci, many of which are thought to be inactive, methods that can discriminate functionally active binding events are essential for the interpretation of genome-wide transcription factor binding data. To develop such a method, we also generated genome-wide H3K4me1 and H3K4me3 localization data in these tissues. By analyzing our binding and histone methylation data in combination with comprehensive gene expression data, we show that H3K4me1 enrichment profiles discriminate transcription factor occupied loci into three classes: those that are functionally active, those that are poised for activation, and those that reflect pioneer-like transcription factor activity. Furthermore, we demonstrate that the regulated presence of H3K4me1-marked nucleosomes at transcription factor occupied promoters and enhancers controls their activity, implicating both tissue-specific transcription factor binding and nucleosome remodeling complex recruitment in determining tissue-specific gene expression. Finally, we apply these approaches to generate novel insights into how FOXA2, PDX1, and HNF4A cooperate to drive islet-and liver-specific gene expression.

Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome

“…Among the remaining 2% of regulatory elements, we also found tissuerelated transcription-binding sites (i.e., Hnf4A). The hepatocyte nuclear factor 4α is a transcription factor found upstream in the regulation pathways of several hepatic genes (27). Surprisingly, the non-CGI UMRs produced, on average, a threefold greater enrichment in regulatory elements than the CGI-like UMRs.…”

Pioneer transcription factors: establishing competence for gene expression

“…Simple target site affinity was not a predictor of FoxA occupancy, at least in terminally differentiated cells. While the nature of this is discussed in detail below (and see also Hoffman et al 2010), Tuteja et al (2008) did find that medium-and lower-affinity, liver-specific targets were highly enriched for binding of other hepatic nuclear factors, suggesting a role for cooperative binding during the maintenance of differentiation. Furthermore, in adult liver tissue, FoxA1 and FoxA2 binding was not required to maintain local nucleosome organization (Z Li et al 2011).…”

Paracrine signalling loops in adult human and mouse pancreatic islets: netrins modulate beta cell apoptosis signalling via dependence receptors

“…Human islet genes were also confirmed in the Massively parallel signature sequencing (MPSS) data set of Kutlu et al [29]. A mouse islet tag sequencing library was analysed for RefSeq accessions with tag counts greater than five as described [30,31] (see also Electronic supplementary material [ESM] Methods). Briefly, DNaseI-treated total RNA isolated from hand-picked islets was used for tag sequencing libraries, sequenced to a depth of 7,481,000 tags.…”