cis-regulation of Grem1 during limb development [ChIP-seq]

Chromatin immunoprecipitation in combination with sequencing (ChIP-seq) was used to identify the interactions of CRMs with key regulators of Grem1 expression, namely SMAD4 (mediating response to BMP signal transduction) and GLI3 (SHH signal transduction). This analysis revealed the presence of a single significantly enriched SMAD4 ChIP-seq peak in CRM2 during initiation of forelimb bud development, when BMP4 is required to initiate/upregulate the Grem1 transcription. During progression of limb development, GLI3 chromatin complexes interact with all enhancers except CRM5. which agrees with the predominant role of SHH-mediated Grem1 regulation during outgrowth and/or GLI3R-mediated repression during termination. Thus, the Grem1 TAD encodes an array of CRM enhancers that integrate inputs from BMP and SHH signaling into the dynamic regulation of Grem1 during limb bud outgrowth. Overall design: ChIP-Seq of Smad4 and Gli3 on whole embryo and embryonic limb bud.