Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology

Using Hi-C, promoter-capture Hi-C (pCHi-C), and other genome-wide approaches in skeletal muscle progenitors that inducibly express a master transcription factor, Pax7, we systematically characterize at high-resolution the spatio-temporal re-organization of compartments and promoter-anchored interactions as a consequence of myogenic commitment and differentiation. We identify key promoter-enhancer interaction motifs, namely, cliques and networks, and interactions that are dependent on Pax7 binding. Remarkably, Pax7 binds to a majority of super-enhancers, and together with a cadre of interacting transcription factors, assembles feed-forward regulatory loops. During differentiation, epigenetic memory and persistent looping are maintained at a subset of Pax7 enhancers in the absence of Pax7. We also identify and functionally validate a previously uncharacterized Pax7-bound enhancer hub that regulates the essential myosin heavy chain cluster during skeletal muscle cell differentiation. Our studies lay the groundwork for understanding the role of Pax7 in orchestrating changes in the three-dimensional chromatin conformation in muscle progenitors.This work was supported by funding to B.D.D. from the NIH (1R21AR068786-01A1 and 1R01GM122395) and funding to R.C.R.P. from the NIH (1R01AR055299-01A1 and 1R01AR071439-01). The mass spectrometric work is supported in part by NYU Grossman School of Medicine and the Laura and Isaac Perlmutter Cancer Center Support grant P30CA016087 from the National Cancer Institute. B.D.D. would also like to thank the NYU Center for Skeletal and Craniofacial Biology for generously providing a pilot grant. This research was partially funded by the European Union’s H2020 Framework Programme through the ERC (grant agreement 609989 to M.A.M-R.). We also acknowledge the support of Spanish Ministerio de Ciencia, Innovación y Universidades through BFU2017-85926-P to M.A.M-R. CRG thanks the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Progra