Genomics

Dataset Information

0

Lmx1b ChIP-seq dataset in embryonic day 12.5 (e12.5) wild type mouse limb buds


ABSTRACT: Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct downstream gene targets in the limb have been confirmed. To determine direct targets of Lmx1b during limb dorsalization (E12.5), we performed chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Nearly 84% (n=617) of the Lmx1b-bound genomic fragments or intervals (LBIs) identified by two Lmx1b-ChIP-seqs overlap with chromatin regulatory marks indicative of potential cis-regulatory modules (PCRMs). In addition, 73 LBIs mapped to known cis-regulatory modules (CRMs) active during limb development. We compared Lmx1b-bound PCRMs to genes differentially expressed by Lmx1b at E12.5 and found 292 PCRMs within 1 Mb of 254 Lmx1b-regulated genes. Gene ontology analysis of these associated genes suggests that Lmx1b mediates dorsalization through the regulation of extracellular matrix production, bone/joint formation, axonal guidance, vascular development, cell proliferation and cell movement. We validated the functional activity of 2 PCRMs associated to Lmx1b-regulated genes, demonstrating activity and overlap with the associated gene during limb development. This is the first report to describe the genome-wide distribution of Lmx1b binding during limb development, directly linking Lmx1b to targets that accomplish limb dorsalization.

ORGANISM(S): Mus musculus

PROVIDER: GSE84064 | GEO | 2017/05/06

SECONDARY ACCESSION(S): PRJNA327925

REPOSITORIES: GEO

Similar Datasets

| E-GEOD-21446 | biostudies-arrayexpress
2008-02-15 | GSE10516 | GEO
2010-07-06 | GSE21446 | GEO
| E-GEOD-10516 | biostudies-arrayexpress
2012-05-22 | GSE34732 | GEO
| E-GEOD-34732 | biostudies-arrayexpress
2022-12-02 | GSE202223 | GEO
| E-GEOD-12008 | biostudies-arrayexpress
2008-12-04 | GSE12008 | GEO
| E-GEOD-81897 | biostudies-arrayexpress