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Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [Capture Hi-C]

ABSTRACT: Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [Capture Hi-C]

PROVIDER: PRJNA475488 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7288112_1.fastq.gz	Fastqsanger.gz
	SRR7288112_2.fastq.gz	Fastqsanger.gz
	SRR7288113_1.fastq.gz	Fastqsanger.gz
	SRR7288113_2.fastq.gz	Fastqsanger.gz

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Project description:Hoxd genes are important for limb development in all tetrapods examined thus far. In mouse, they are controlled by a complex bimodal regulation, which regulates first the proximal patterning, then the distal structure, allowing at the same time the formation of the wrist and ankle articulations. We analyzed the existence of this regulatory mechanism in chicken, i.e. in an animal where large morphological differences exist between fore- and hindlimbs. We report that while this bimodal regulation is globally conserved between mammals and avian, some important modifications evolved at least between these two model systems, in particular regarding the activity of specific enhancer and the position of the TAD boundary and the forelimb versus hindlimb comparative regulations. Some aspects of these regulations seem to be more conserved between chick and bats than with the mouse situation, which may relate to the extent to which forelimbs and hindlimbs of these various animals differ in their functions.

2018-11-27 | GSE115562 | GEO

Project description:Similarities and differences in the regulation of HoxD genes during chick and mouse limb development.

| PRJNA475482 | ENA

Project description:Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [ChIP-Seq]

| PRJNA475489 | ENA

Project description:Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [4C-seq]

| PRJNA475490 | ENA

Project description:Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [RNA-Seq]

| PRJNA475487 | ENA

2018-11-27 | GSE115561 | GEO

2018-11-27 | GSE115560 | GEO

2018-11-27 | GSE115559 | GEO

A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [Hi-C]

Project description:The mammalian HoxD cluster is positioned at the boundary between two topologically associating domains (TADs), each of them matching a distinct, enhancer-rich regulatory landscape. During limb development, the telomeric TAD controls the early phase of Hoxd gene transcription in future forearm cells, whereas the centromeric TAD subsequently regulates transcription of more posterior Hoxd genes in presumptive digit cells. The TAD boundary is essential as it prevents the terminal Hoxd13 gene to respond to potent forearm enhancers, thereby allowing the formation of proper proximal limb structures. Here we apply chromosome conformation capture onto embryonic proximal and distal limb bud cells micro-dissected from a set of nested deletions involving part- or all- of this boundary region to try to understand the nature and function of this CTCF- and cohesin-rich DNA region. We document a progressive release of the boundary effect, allowing for inter-TAD contacts to be established, which were favoured by the functional status of the newly accessed enhancers. However, the boundary was highly resilient and only a 400kb large deletion including the whole gene cluster was eventually able to merge the two neighbouring TADs into a single structure. We propose that the whole HoxD cluster is a dynamic transcriptional boundary, showing slight variations depending on both the transcriptional status and the ontogenetic context

2017-12-22 | GSE101715 | GEO

Project description:In all tetrapods examined thus far, the development and patterning of limbs require the activation of gene members of the HoxD cluster. In mammals, they are regulated by a complex bimodal process that controls first the proximal patterning and then the distal structure. During the shift from the former to the latter regulation, this bimodal regulatory mechanism allows the production of a domain with low Hoxd gene expression, at which both telomeric (T-DOM) and centromeric regulatory domains (C-DOM) are silent. These cells generate the future wrist and ankle articulations. We analyzed the implementation of this regulatory mechanism in chicken, i.e., in an animal for which large morphological differences exist between fore- and hindlimbs. We report that although this bimodal regulation is globally conserved between the mouse and the chick, some important modifications evolved at least between these two model systems, in particular regarding the activity of specific enhancers, the width of the TAD boundary separating the two regulations, and the comparison between the forelimb versus hindlimb regulatory controls. At least one aspect of these regulations seems to be more conserved between chick and bats than with mouse, which may relate to the extent to which forelimbs and hindlimbs of these various animals differ in their morphologies.

| S-EPMC6283595 | biostudies-literature

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