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HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ChIP-seq]

ABSTRACT: HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ChIP-seq]

PROVIDER: PRJNA508887 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11164810_1.fastq.gz	Fastqsanger.gz
	SRR11164810_2.fastq.gz	Fastqsanger.gz
	SRR11164811_1.fastq.gz	Fastqsanger.gz
	SRR11164811_2.fastq.gz	Fastqsanger.gz
	SRR8290670_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

HOX13-dependent chromatin accessibility underlies the transition towards the digit development program

Project description:HOX13-dependent chromatin accessibility underlies the transition towards the digit development program

| PRJNA508886 | ENA

HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ChIP-seq]

Project description:Pioneer factors are transcription factors able to recognize their target site even concealed in “closed” chromatin, eventually eliciting the switch to accessible targets for other transcription factors and the transcriptional machinery. As such, pioneer factors play a key role in switching cell fate. Here, we provide evidence that HOXA13 and HOXD13 (HOX13 hereafter), two transcription factors of the Hox family of developmental genes, act as pioneer factors in the developing limb. We show that Hox13 function is mandatory for switching a series of target loci to an accessible chromatin state, allowing the binding of other transcription factors. These target loci include an enhancer previously identified as essential for the pentadactyl state, providing evidence that the pioneer activity of HOX13 is key for digit patterning. Based on the data reported here and previous studies, we propose that, during the fin-to-limb transition, the implementation of digit-specific enhancer elements had required an ancestral pioneer function of the HOX13 TFs.

2020-03-25 | GSE123480 | GEO

HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ATAC-Seq]

2020-04-03 | GSE123481 | GEO

HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ATAC-Seq]

Project description:HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ATAC-Seq]

| PRJNA508888 | ENA

HOX13-dependent chromatin accessibility underlies the transition towards the digit development program.

Project description:Hox genes encode transcription factors (TFs) that establish morphological diversity in the developing embryo. The similar DNA-binding motifs of the various HOX TFs contrast with the wide-range of HOX-dependent genetic programs. The influence of the chromatin context on HOX binding specificity remains elusive. Here, we used the developing limb as a model system to compare the binding specificity of HOXA13 and HOXD13 (HOX13 hereafter), which are required for digit formation, and HOXA11, involved in forearm/leg development. We find that upon ectopic expression in distal limb buds, HOXA11 binds sites normally HOX13-specific. Importantly, these sites are loci whose chromatin accessibility relies on HOX13. Moreover, we show that chromatin accessibility specific to the distal limb requires HOX13 function. Based on these results, we propose that HOX13 TFs pioneer the distal limb-specific chromatin accessibility landscape for the proper implementation of the distal limb developmental program.

| S-EPMC7237422 | biostudies-literature

HOX13-dependent chromatin accessibility underlies the transition towards the digit development program

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-03-25 | GSE123482 | GEO

HOX13 activity reprograms cis-regulatory modules during digit development (RNA-Seq)

Project description:The combinatorial expression of the Hox genes along the body axes, referred to as the HOX code, is a major determinant of cell fate and plays a prevailing role in generating the animal body plan. In developing limb buds, the paralogous group 13 genes of the HoxA and HoxD clusters are essential for patterning the distal-most limb structures, the digits. Inactivation of HOXA13 and HOXD13 transcription factors (HOX13) leads to complete digit agenesis in mice, but how HOX13 regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here we performed genome-wide profiling of HOX13 by chromatin immunoprecipitation and analyzed the transcriptome and chromatin state of wild type early and late-distal limb buds, as well as Hoxa13-/-;Hoxd13-/- compound mutant limb buds. Our results show that inactivation of HOX13 impairs the activation and repression of putative cis-regulatory modules specific to the late-distal limb cells. Loss of HOX13 also disrupts the specific, spatial patterning of gene expression along the proximal-distal axis of the developing limb buds. These results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.

2016-12-14 | GSE81357 | GEO

HOX13 activity reprograms cis-regulatory modules during digit development (ChIP-Seq)

2016-12-14 | GSE81356 | GEO

HOX13 activity reprograms cis-regulatory modules during digit development

Project description:HOX13 activity reprograms cis-regulatory modules during digit development

| PRJNA321343 | ENA

Acquisition of a unique mesenchymal precursor-like blastema state underlies successful adult mammalian digit tip regeneration

Project description:Here, we investigate the origin and nature of blastema cells that regenerate the adult murine digit tip. We show that Pdgfra-expressing mesenchymal cells in uninjured digits establish the regenerative blastema and are essential for regeneration. Single cell profiling shows that the mesenchymal blastema cells are distinct from both uninjured digit and embryonic limb/digit Pdgfra-positive cells. This unique blastema state is environmentally determined; dermal fibroblasts transplanted into the regenerative, but not non-regenerative, digit express blastema markers and contribute to bone regeneration. Moreover, lineage tracing with single cell profiling indicates that endogenous osteoblasts/osteocytes acquire a blastema mesenchymal transcriptional state and contribute to both dermis and bone regeneration. Thus, mammalian digit tip regeneration occurs via a distinct adult mechanism where the regenerative environment promotes acquisition of a unique blastema state that allows cells from tissues like bone to contribute to regeneration of other mesenchymal tissues such as the dermis.

2019-11-15 | GSE135985 | GEO

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