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Series GSE194423 Query DataSets for GSE194423
Status Public on Jun 20, 2022
Title Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [Hi-C]
Organisms Gallus gallus; Mus musculus
Experiment type Other
Summary 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.
 
Overall design We used Capture Hi-C enriching the Hoxd locus and its flanking TADs to using mouse E9.5 and chicken HH18 posterior trunks to evaluate the conservation of chromatin architecture in amniotes.
 
Contributor(s) Hintermann A, Guerreiro I, Lopez-Delisle L, Bolt CC, Gitto S, Duboule D, Beccari L
Citation(s) 35770682
Submission date Jan 25, 2022
Last update date Aug 16, 2022
Contact name Aurelie Hintermann
E-mail(s) aur.hin@gmail.com
Organization name University of Geneva
Department Genetics and Evolution
Street address 30 quai Ernest-Ansermet
City Geneva
ZIP/Postal code 1205
Country Switzerland
 
Platforms (2)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL23499 Illumina HiSeq 4000 (Gallus gallus)
Samples (2)
GSM5835528 CHiC E9.5 posterior trunks
GSM5835529 CHiC HH18 posterior trunks
This SubSeries is part of SuperSeries:
GSE195592 Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds
Relations
BioProject PRJNA800469

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE194423_RAW.tar 125.8 Mb (http)(custom) TAR (of BED, COOL, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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