Chromatin looping allows enhancer-bound regulatory factors to influence transcription. Large domains, referred to as topologically associated domains, participate in genome organization. However, the mechanisms underlining interactions within these domains, which control gene expression, are not fully understood. 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 identify 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 transcription factors can promote formation of sub-topologically associated domain interactions involved in lineage specification.
Bibliographical noteFunding Information:
This project was supported by NIH grants R01 AR055299 and AR071439 (R.C.R.P.), U01 HL100407R01 (R.C.R.P. and D.J.G.), R21 AR068786 (B.D.D.), R01 GM122395 (B.D.D.), and by Regenerative Medicine Minnesota (A.M.). C.O.C. was supported by PINN MICITT Costa Rica. The authors thank the continuous support of Dr. James Thomson, Dr. Ron Stewart and Scott Swanson from the Morgridge Institute for Research (Madison, WI). We also thank the help from: Dr. Gabriel Starrett (computational analyses); Yi Ren (Lillehei Heart Institute FACS core); the staff of the University of Minnesota Genomic Center (technical support); Bridget Dillon, Asma Redwan, and Bayardo Garay (technical assistance). The authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper. URL: http://www.msi.umn.edu. In addition, the authors would like to thank Dr. Michael Kyba and Dr. Daryl Gohl for critical reading of the manuscript and Cynthia Faraday for assistance with artwork.