Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors

ABSTRACT: FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: First, FOXA facilitate signal-dependent lineage initiation via enhancer priming, and second, FOXA enforce organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE148368 | GEO | 2021/10/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors

Project description:Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors

| PRJNA624086 | ENA

FoxK1 Associated Gene Regulatory Network in Hepatic Insulin Action and It’s Relationship to FoxO and Insulin Receptor Mediated Transcriptional Regulation

Project description:ChIP-seq analysis demonstrates FoxK1 binding to proximal promoters and enhancers, especially to genes containing a TGTTTAC motif, which is similar to the FoxA/FoxO motifs.

2023-11-22 | GSE230344 | GEO

Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate [RNA-seq]

Project description:Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF Forkhead box A (FOXA), required for endoderm lineage commitment, coordinates with the PR domain zinc finger 1 (PRDM1) TF to recruit Polycomb repressive complexes, which establish bivalent enhancers and repress alternative lineage programs. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to repress cell differentiation programs in pluripotent stem cells, suggesting this is a common feature of pioneer TFs. We propose that pioneer and PRDM TFs coordinate recruitment of Polycomb complexes to safeguard cell fate.

2024-01-10 | GSE215435 | GEO

Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate [CUT&Run and ChIP-seq]

2024-01-10 | GSE215434 | GEO

FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity

Project description:Tissue-specific DNA methylation patterns are created by transcription factors that recruit methylation and demethylation enzymes to cis-regulatory elements. To date, it is not known whether transcription factors are needed to continuously maintain methylation profiles in development and mature tissues or whether they only establish these marks during organ development. We queried the role of the pioneer factor FoxA in generating hypomethylated DNA at liver enhancers. We discovered a set of FoxA binding sites that undergo regional, FoxA-dependent demethylation during organ development. Conditional ablation of FoxA genes in the adult liver demonstrated that continued FoxA presence was not required to maintain the hypomethylated state, even when massive cell proliferation was induced. This study provides strong evidence for the stable, epigenetic nature of tissue-specific DNA methylation patterns directed by lineage-determining transcription factors during organ development.

2021-04-20 | GSE124384 | GEO

Influence of osmopriming on rape seeds germination

Project description:Transcriptomic study of the impact of osmopriming on rape seeds (Brassica napus L.; cv 'Libomir') during priming process and after germination. The assays were replicated twice on two independent priming and germination experiments. Seeds were osmoprimed in PEG solution (-1.2 MPa osmotic potential) during 7 days, dried to initial moisture content and then germinated for 7 hours on water. The analysis during different phases of priming procedure (soaking and drying), after whole osmopriming process and germination were done. 10 samples, four condition experiment; non dried primed seeds (Pnd) vs. dry unprimed seeds (UPd) (PEG soaking), non dried primed seeds (Pnd) vs dry primed seeds (Pd) (drying after soaking), dry primed seeds (Pd) vs. dry unprimed seeds (UPd) (full osmopriming process), primed seeds imbibed on water (P7h) vs unprimed seeds imbibed on water (UP7h) (germination after osmopriming). Biological replicates: 2 replicates for comparison PEG soaking, drying after soaking, full osmopriming process and germination after osmopriming.

2014-11-23 | E-GEOD-61702 | biostudies-arrayexpress

Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

Project description:Enhancers and silencers often depend on the same transcription factors (TFs) and are imperfectly distinguished from each other by genomic assays of TF binding or chromatin state. To identify sequence features that define enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF CRX and found instances of enhancer, silencer, or no activity. Both enhancers and silencers contain more TF motifs than inactive sequences, but enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. Our results indicate that enhancers contain motifs for a diverse but degenerate collection of TFs, while silencers depend on a smaller and less diverse collection of TFs.

2021-01-30 | GSE165812 | GEO

The within-host dynamics of infection in trans-generationally primed beetles

Project description:We report the temporal dynamics of differential gene expression between primed and unprimed beetles infected with the entomopathogen Bt

2017-02-28 | GSE95387 | GEO

Identification of Nkx6.1 regulated genes in mature pancreatic islets.

Project description:Nkx6.1 target genes were identified in mature pancreatic islets by comparing gene expression in conditional Nkx6.1-ablated islets versus control islets using microarray analysis. Nkx6.1 was conditionally ablated in mature pancreatic islets by recombination of a Nkx6.1-flox allele using the tamoxifen-inducible Pdx1-CreERTM allele (Gu et al 2002). Mice were injected with 2 mg/25 g tamoxifen in corn oil four times between 4 and 6 weeks of age. Islets were isolated after the final tamoxifen injection. Total RNA was isolated and pooled from pancreata of 6 week old Nkx6.1fl/-;Pdx1-CreERTM (mutant) versus Nkx6.1fl/+;Pdx1-CreERTM (control) littermates for 3 biological replicates.

2013-09-12 | E-GEOD-40470 | biostudies-arrayexpress

Identification of Nkx6.1 regulated genes in mature pancreatic islets.

2013-09-12 | GSE40470 | GEO