Genomics,Multiomics

Dataset Information

0

A Genome-Scale Analysis of the Cis-Regulatory Circuitry Underlying Hedgehog Mediated Patterning of the Mammalian Limb


ABSTRACT: Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified approximately 5,000 high quality Gli3 binding sites, including all known Gli-dependent enhancers. Discrete binding regions exhibit a higher-order clustering, highlighting the complexity of cis-regulatory interactions. Further, Gli3 binds inertly to previously identified neural-specific Gli enhancers, demonstrating the accessibility of their cis-regulatory elements. Intersection of DNA binding data with gene expression profiles predicted 205 putative limb target genes. A subset of putative cis-regulatory regions were analyzed in transgenic embryos, establishing Blimp1 as a direct Gli target and identifying Gli-activator signaling in a direct, long-range regulation of the BMP antagonist Gremlin. In contrast, a long range silencer cassette downstream of Hand2 likely mediates Gli3 repression in the anterior limb. These studies provide the first comprehensive characterization of the transcriptional output of a Shh-patterning process in the mammalian embryo and a framework for elaborating regulatory networks in the developing limb. This SuperSeries is composed of the SubSeries listed below.

OTHER RELATED OMICS DATASETS IN: PRJNA108815PRJNA107069PRJNA108817

ORGANISM(S): Mus musculus

PROVIDER: GSE11077 | GEO | 2008/09/15

SECONDARY ACCESSION(S): PRJNA107069

REPOSITORIES: GEO

Similar Datasets

2008-09-15 | GSE11062 | GEO
| E-GEOD-11063 | biostudies-arrayexpress
2020-01-21 | GSE133712 | GEO
2014-11-11 | GSE55707 | GEO
2008-09-15 | GSE11063 | GEO
2017-03-10 | GSE86478 | GEO
2020-01-21 | GSE133710 | GEO
2022-01-21 | GSE178838 | GEO
2024-02-03 | GSE224508 | GEO
| E-GEOD-42132 | biostudies-arrayexpress