NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE232882 Query DataSets for GSE232882
Status Public on Jun 01, 2024
Title A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival [ATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Gene deserts spanning more than 500kb of non-protein coding genomic sequence are considered evolutionarily ancient and stable and are enriched in the vicinity of developmental regulator genes (Ovcharenko 2005). These extensive genomic regions typically harbor numerous conserved elements with predicted gene regulatory potential pointing to critical tissue-specific functions during development. Nevertheless, the biological necessity and underlying funtional enhancer landscapes of most gene deserts near developmental transcription factors (TFs) remain unknown, and it is unclear how precise pleiotropic expression patterns emerge from gene desert sequence. Here, we investigated the cis-regulatory architecture and function of a gene desert flanking the mouse Shox2 transcriptional regulator which itself is essential for embryonic limb, craniofacial, and cardiac pacemaker development. By combining epigenomic enhancer prediction, transgenic reporter validation and region-specific chromatin capture (C-HiC), we define the embryonic in vivo enhancer landscape and chromatin topology of the Shox2 gene desert. Targeted and context-specific genomic deletions uncover the gene desert not only as a regulator of embryonic survival through enhancer-mediated control of cardiac Shox2 expression, but also link distinct subsets of tissue-specific gene desert enhancers to the regulation of craniofacial patterning and proximal limb development. Our results hence identify the Shox2 gene desert as a fundamental genomic unit indispensable for pleiotropic patterning, robust organ morphogenesis and embryonic development progression by serving as a dynamic hub for tissue-specific developmental enhancers.
 
Overall design ATAC-seq from whole-mount mouse embryonic hearts to determine genome-wide cardiac open chromatin regions
 
Contributor(s) Zoia M, Mannion B, Barozzi I, Visel A, Pennacchio L, Osterwalder M
Citation(s) 39389973
Submission date May 19, 2023
Last update date Oct 16, 2024
Contact name Marco Osterwalder
E-mail(s) olheartdev@gmail.com
Organization name Universiy of Bern
Department DBMR
Lab Osterwalder Lab
Street address Murtenstrasse 24
City Bern
ZIP/Postal code 3008
Country Switzerland
 
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (2)
GSM7385432 ATAC_H_E115-WT_rep1
GSM7385433 ATAC_H_E115-WT_rep2
This SubSeries is part of SuperSeries:
GSE232887 A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival
Relations
BioProject PRJNA974367

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

Supplementary file Size Download File type/resource
GSE232882_RAW.tar 388.0 Mb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap