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Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [4C-seq]

ABSTRACT: Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [4C-seq]

PROVIDER: PRJNA801313 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17791913.fastq.gz	Fastqsanger.gz
	SRR17791914.fastq.gz	Fastqsanger.gz
	SRR17791915.fastq.gz	Fastqsanger.gz
	SRR17791916.fastq.gz	Fastqsanger.gz
	SRR17791917.fastq.gz	Fastqsanger.gz

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Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds

Project description:Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds

| PRJNA801310 | ENA

Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [4C-seq]

Project description:Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. During vertebrate evolution, Hox genes were redeployed in different organs in a class-specific manner, while maintaining the same basic function in organizing the primary body axis. Since a large part of the relevant enhancers are located in a conserved regulatory landscape, this gene cluster represents an interesting paradigm to study the emergence of regulatory innovations. In this work, we analyzed Hoxd gene regulation in both murine vibrissae and chicken feather primordia, two mammalian- and avian-specific skin appendages which express different subsets of Hoxd genes, and compared their regulatory modalities with the regulations at work during the elongation of the posterior trunk, a mechanism highly conserved in amniotes. We show that in the former two structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, likely as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the regulations implemented in the mouse and chicken embryonic trunk partially rely on conserved CREs. Nevertheless, a high proportion of these non-coding sequences active in the trunk appear to have functionally diverged between the two species, suggesting that transcriptional robustness is maintained despite a considerable divergence in CREs’ sequence, an observation supported by a genome-wide comparative approach.

2022-06-20 | GSE195591 | GEO

Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ATAC-Seq]

Project description:Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ATAC-Seq]

| PRJNA838207 | ENA

Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [Hi-C]

Project description:Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [Hi-C]

| PRJNA800469 | ENA

Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ChIP-seq]

Project description:Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ChIP-seq]

| PRJNA800459 | ENA

Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ATAC-Seq]

2022-06-20 | GSE203031 | GEO

Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [Hi-C]

2022-06-20 | GSE194423 | GEO

Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ChIP-seq]

2022-06-20 | GSE194418 | GEO

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

Viral Metagenomes of Antarctic Birds and Mammals

Project description:Viral Metagenomes of Antarctic Birds and Mammals

| PRJNA529359 | ENA