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Genome-wide map of binding sites for HNF4a during hepatic specification of iPS cells

ABSTRACT: HNF4a has been shown to be critical for hepatocyte differentiation from iPS cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE104613 | GEO | 2019/01/28

REPOSITORIES: GEO

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Genome-wide map of binding sites for HNF4a during hepatic specification of iPS cells

Project description:Genome-wide map of binding sites for HNF4a during hepatic specification of iPS cells

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Project description:HNF4a has been shown to be a central regulator of hepatocyte differentiation and function in adult mice. It was recently shown the HNF4a regulates the onset of hepatic gene expression during liver differentiation in vitro and is critical for the specification of liver towards a hepatic fate We examined the global gene expression of the differentiaiton of iPS cells into specified hepatic cells on consecutive days of liver differentiation (Mallanna et al 2013) to determine the onset of hepatic gene expression and the role HNF4a plays during hepatic specification.

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HNF4A-binding sites in HepG2 hepatoblastoma cells treated with TGF-beta

Project description:Specific regulation of target genes by transforming growth factor-β (TGF-β) in a given cellular context is determined in part by transcription factors and cofactors that interact with the Smad complex. In the present study, we determined Smad2 and Smad3 (Smad2/3) binding regions in the promoters of known genes in HepG2 hepatoblastoma cells, and compared them to those in HaCaT epidermal keratinocytes to elucidate the mechanisms of cell type- and context-dependent regulation of transcription induced by TGF-β. Our results show that 81% of the Smad2/3 binding regions in HepG2 cells were not shared with those found in HaCaT cells. Hepatocyte nuclear factor 4α (HNF4α) is expressed in HepG2 cells, but not in HaCaT cells, and the HNF4α binding motif was identified as an enriched motif in the HepG2-specific Smad2/3 binding regions. ChIP-sequencing analysis of HNF4A binding regions under TGF-β stimulation revealed that 32.5% of the Smad2/3 binding regions overlapped HNF4A bindings. MIXL1 was identified as a new combinatorial target of HNF4A and Smad2/3, and both the HNF4A protein and its binding motif were required for the induction of MIXL1 by TGF-β in HepG2 cells. These findings generalize the importance of binding of HNF4A on Smad2/3 binding genomic regions for HepG2-specific regulation of transcription by TGF-β, and suggest that certain transcription factors expressed in a cell-type-specific manner play important roles in the transcription regulated by the TGF-β-Smad signaling pathway. HepG2 cells were treated with TGF-beta for 1.5 h or left untreated. anti-HNF4A ChIP-seq was performed. One lane was used for each sample.

2011-06-08 | E-GEOD-28845 | biostudies-arrayexpress

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Project description:We performed bulk RNA-seq and compared complehensive gene expression profiles of kidney organoids induced from wild type, HNF4A-KO, HNF4G-KO, and HNF4A/4G-DKO iPS cell lines.

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TAF4 promotes pre-initiation complex formation and HNF4A occupancy of regulatory elements required to activation post-natal gene expression programme in hepatocytes (ChIP-seq)

Project description:The nuclear receptor HNF4A regulates embryonic and post-natal hepatocyte gene expression. Using hepatocyte-specific inactivation in mice, we show that the TAF4 subunit of TFIID acts as a cofactor for HNF4A in vivo and that HNF4A interacts directly with the TAF4-TAF12 heterodimer in vitro. In vivo, TAF4 is required to maintain HNF4A-directed embryonic gene expression at post-natal stages and for HNF4A-directed activation of post-natal gene expression. TAF4 promotes HNF4A occupancy of functional cis-regulatory elements located adjacent to the transcription start sites of post-natal expressed genes and for pre-initiation complex formation required for their expression. Promoter-proximal HNF4A-TFIID interactions are therefore required for pre-initiation complex formation and stable HNF4A occupancy of regulatory elements as two concomitant mutually dependent processes. Examination of PIC, H3k4me3, Ctcf and Hnf4a occupancy in wild-type and Taf4-/- livers by deep sequencing

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TAF4 promotes pre-initiation complex formation and HNF4A occupancy of regulatory elements required to activation post-natal gene expression programme in hepatocytes (RNA-seq)

Project description:The nuclear receptor HNF4A regulates embryonic and post-natal hepatocyte gene expression. Using hepatocyte-specific inactivation in mice, we show that the TAF4 subunit of TFIID acts as a cofactor for HNF4A in vivo and that HNF4A interacts directly with the TAF4-TAF12 heterodimer in vitro. In vivo, TAF4 is required to maintain HNF4A-directed embryonic gene expression at post-natal stages and for HNF4A-directed activation of post-natal gene expression. TAF4 promotes HNF4A occupancy of functional cis-regulatory elements located adjacent to the transcription start sites of post-natal expressed genes and for pre-initiation complex formation required for their expression. Promoter-proximal HNF4A-TFIID interactions are therefore required for pre-initiation complex formation and stable HNF4A occupancy of regulatory elements as two concomitant mutually dependent processes. RNA profiles in wild-type and Taf4-/- livers by deep sequencing

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Project description:HNF4a and FOXA2 are two liver enriched transcription factors that have been shown capable of reprogramming fibroblasts into hepatocyte-like cells. However to date it is not yet understood how these master regulators, expressed in both embryonic and adult liver contribute to the transcriptional changes necessary for hepatocyte maturation during development. Consequently we undertook to identify binding sites and target genes for HNF4a and FOXA2 in the embryonic liver. A comparison of embryonic and adult liver TF binding patterns revealed widespread differentiation-dependent genome occupancy associated with changes in target gene expression during liver development.

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