Genome binding/occupancy profiling by high throughput sequencing Other
Chromatin looping allows enhancer-bound regulatory factors to influence transcription. Large domains, referred to as Topologically Associated Domains (TADs), participate in genome organization but the mechanisms underlining interactions within TADs, that actually control gene expression, are largely unknown. Here we report that activation of embryonic myogenesis is associated with establishment of long-range chromatin interactions centered on Pax3-bound loci. Using mass spectrometry and genomic studies, we identified the ubiquitously expressed LIM-domain binding protein 1 (Ldb1) as the mediator of looping interactions at a subset of Pax3 binding sites. Ldb1 is recruited to Pax3-bound elements independently of CTCF-Cohesin, and is necessary for efficient deposition of H3K4me1 at these sites and chromatin looping. When Ldb1 is deleted in Pax3-expressing cells in vivo, specification of migratory myogenic progenitors is severely impaired. These results highlight Ldb1 requirement for Pax3 myogenic activity and demonstrate how a transcription factor promotes formation of sub-TAD interactions associated with lineage specification.
Pax3 doxycycline-inducible murine embryonic stem cells (iPax3) were used to investigate Pax3 function during myogenic lineage specification. ChIP-seq for histone marks was used to characterize the Pax3-bound loci and define enhancers. ChIP-seq for Ldb1, Smc1 and Ctcf was performed to test/validate Pax3-dependent recruitment of these proteins at Pax3-bound sites. HiChIP was used to study chromatin looping at Pax3 bound sites.