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

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

PROVIDER: PRJNA475490 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7288060.fastq.gz	Fastqsanger.gz
	SRR7288070.fastq.gz	Fastqsanger.gz
	SRR7288061.fastq.gz	Fastqsanger.gz
	SRR7288071.fastq.gz	Fastqsanger.gz
	SRR7288062.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 | GSE115560 | 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]

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

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

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Spatial organization of chromatin at the HoxD locus in developing caeca (4C-seq)

Project description:Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Chromosome Conformation Capture (4C seq) at the HoxD locus in developing caeca at E13.5

2013-10-23 | E-GEOD-44360 | biostudies-arrayexpress

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Spatial organization of chromatin at the HoxD locus in developing caeca (4C tiling chip)

Project description:Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Chromosome Conformation Capture-on-chip analysis (4C) at the Hoxd locus in developing caeca at E13.5, Array data were quantile normalized within 4C/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp.

2013-10-23 | E-GEOD-44357 | biostudies-arrayexpress

2018-11-27 | GSE115562 | GEO