Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

Abstract

Foxa2 (HNF3β) is a one of three, closely related transcription factors that are critical to the development and function of the mouse liver. We have used chromatin immunoprecipitation and massively parallel Illumina 1G sequencing (ChIP–Seq) to create a genome-wide profile of in vivo Foxa2-binding sites in the adult liver. More than 65% of the ∼11.5 k genomic sites associated with Foxa2 binding, mapped to extended gene regions of annotated genes, while more than 30% of intragenic sites were located within first introns. 20.5% of all sites were further than 50 kb from any annotated gene, suggesting an association with novel gene regions. QPCR analysis demonstrated a strong positive correlation between peak height and fold enrichment for Foxa2-binding sites. We measured the relationship between Foxa2 and liver gene expression by overlapping Foxa2-binding sites with a SAGE transcriptome profile, and found that 43.5% of genes expressed in the liver were also associated with Foxa2 binding. We also identified potential Foxa2-interacting transcription factors whose motifs were enriched near Foxa2-binding sites. Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function.

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

“…Interestingly, 98% of all ORegAnno elements overlapping UMRs belong to binding sites for Esr1 and Foxa2. The Foxa 2 gene codes for the forkhead box protein A2, which is a transcriptional activator for liver-specific genes (25), and the Esr1 gene codes for the nuclear estrogen receptor α. This is the major estrogen receptor expressed in the liver, where it regulates glucose homeostasis as well as lipid metabolism (26).…”

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

“…We used data for FOXA2 binding in mouse adult liver (Wederell et al 2008) to assess whether the histone modification patterns that were associated with STAT1 in HeLa cells were unique to that transcription factor (TF) and cell line or were more general (Table 1).…”

“…In the work described here, we took advantage of this resolution to assess, for the first time, the direct relationship of H3K4me1 and H3K4me3 at regulatory elements inferred from profiles for two functionally different transcription factors. We assessed STAT1 in the immortalized HeLa S3 cell line, with and without interferon-gamma (IFNG) stimulation (Robertson et al 2007), and FOXA2 in a normal, non-immortalized tissue, mouse adult liver (Wederell et al 2008). We profiled H3K4me1 and H3K4me3 in these cells and determined combinations of modifications that were associated with transcription factor binding.…”

Next-generation tag sequencing for cancer gene expression profiling

“…Such technologies offer up to two orders of magnitude increase in per base cost efficiency compared to capillary sequencing (von Bubnoff 2008). These platforms have made feasible previously cost-prohibitive projects such as genome resequencing (Green et al 2006;Bentley et al 2008;Ley et al 2008;Wang et al 2008b) and deep transcriptome and noncoding RNA sequencing (Nielsen et al 2006;Weber et al 2007;Marioni et al 2008;Morin et al 2008;Rosenkranz et al 2008), as well as genome-wide protein bindingsite surveys (ChIP-seq) (Jothi et al 2008;Wederell et al 2008). …”