ARTICLE https://doi.org/10.1038/s41467-020-19999-w OPEN Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology Nan Zhang1, Julen Mendieta-Esteban 2, Alessandro Magli 3,4, Karin C. Lilja1, Rita C. R. Perlingeiro 3,4, ✉ Marc A. Marti-Renom 2,5,6,7, Aristotelis Tsirigos 1 & Brian David Dynlacht1 1234567890():,; 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 system- atically characterize at high-resolution the spatio-temporal re-organization of compartments and promoter-anchored interactions as a consequence of myogenic commitment and dif- ferentiation. 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 differ- entiation. Our studies lay the groundwork for understanding the role of Pax7 in orchestrating changes in the three-dimensional chromatin conformation in muscle progenitors. 1 Department of Pathology and Perlmutter Cancer Institute, New York University School of Medicine, New York, NY 10016, USA. 2 CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. 3 Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA. 4 Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA. 5 Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. 6 Universitat Pompeu Fabra (UPF), Barcelona, Spain. 7 ICREA, ✉ Barcelona, Spain. email: [email protected] NATURE COMMUNICATIONS | (2020) 11:6222 | https://doi.org/10.1038/s41467-020-19999-w | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-19999-w hromatin structure and topology play important roles in and after its withdrawal, cells differentiate and display the mor- Cthe regulation of gene expression. Although it is well phology and gene expression profiles of myocytes (Fig. 1a)11,19. established that enhancers can activate or repress gene To characterize how chromatin structure is globally re-organized expression through looping to promoters1–5, the extent to which during skeletal muscle progenitor specification and differentia- this phenomenon directs specification of myogenic precursors tion, we generated chromosomal conformation maps using in situ and differentiation of skeletal muscle has not been extensively Hi-C and pCHi-C and performed chromatin immunoprecipita- investigated. Mammalian adult skeletal muscle has a robust tion (ChIP)-seq to detect CTCF and cohesin (Smc3) recruitment ability to regenerate, a process that depends on muscle stem cells, in both progenitor (+Dox) and differentiated (−Dox) iPax7 cells termed satellite cells. Satellite cells are characterized by expression (Fig. 1b) and compared our results to published data from mouse of the transcription factor (TF) paired-box 7 (Pax7), which plays ESCs22 (Supplementary Data 1). We identified between 2755 and a central role in satellite cell specification, maintenance, and 2841 topologically associated domains (TADs) in undifferentiated function6–8. Previous studies have shown that Pax7 can act as a ESCs, progenitor, and differentiated iPax7 cells (Supplementary pioneer factor to open local chromatin regions and preferentially Fig. 1A, B), and >85% of TAD boundaries were bound by CTCF bind to enhancers in skeletal muscle progenitors and the and cohesin (Smc3). As previously reported22, TAD boundaries pituitary9–11. However, it remains unclear whether and how Pax7 remained largely stable across different cell populations (Fig. 1c). can control gene expression through local chromatin remodeling, However, we found that promoter-anchored inter-TAD interac- enhancer activation, and long-range interactions. tions (detected by pCHi-C) occurred more frequently in Whereas topological changes in chromatin have been exten- ESCs than in iPax7 skeletal muscle progenitors, and the sively investigated in diverse tissue and cell types12–18, technical number of interactions and average interaction distance did not obstacles have hindered similar discoveries in skeletal muscle further decrease during iPax7 cell differentiation (Fig. 1d, e progenitors. For example, satellite cells represent a low- and Supplementary Fig. 1C–E). These restrictions on inter-TAD abundance population in muscle tissue, and these cells sponta- interactions could result from changes in chromatin condensation neously differentiate once isolated. We sought to overcome this during the process of lineage specification and cell obstacle through the induced expression of Pax7 in mouse differentiation23. embryonic stem cells (ESCs), from which skeletal muscle pro- We also used our Hi-C data to explore genome compartmen- genitors, termed iPax7 cells, were derived. Upon transplantation talization, wherein active (A) and repressed (B) chromatin can be into dystrophic mice, iPax7 muscle progenitors functionally segregated into two compartments24. Notably, we observed mimic satellite cells and are able to seed the stem cell niche and striking compartmental switching from ESCs to iPax7 progeni- ameliorate muscle wasting19,20. Importantly, iPax7 progenitors tors, altering ~20% of the genome. In contrast, during iPax7 cell also recapitulate the transcriptomic and epigenetic features of differentiation, the scale of compartment reorganization was satellite cells11. Thus, iPax7 myogenic cells represent a good considerably dampened and comprised only ~6.5% of genomic model for investigating how this TF regulates genomic archi- regions (Fig. 1f, g). Overall, changes in the enrichment of active tecture in muscle progenitor cells. histone modifications and accessible chromatin were consistent To assess genome-wide changes during progenitor specifica- with the activity of switched compartments (Supplementary tion and differentiation in iPax7 cells, we performed Hi-C and Fig. 1F, G). Notably, genes within compartments undergoing promoter capture Hi-C (pCHi-C), which revealed an extensive switching were enriched for skeletal muscle development- and three-dimensional (3D) reorganization of chromatin. By com- cell identity-related annotations (Fig. 1h). Taken together, our paring our results with data from mouse ESCs21, and aided by 3D results suggest that chromatin conformational changes primarily modeling of pCHi-C interactions and proteome-wide capture of occur at an early stage during skeletal muscle lineage specifica- Pax7-interacting proteins, we identified enhancer hubs (EnHs) tion, with additional conformational changes occurring less and elucidated key promoter–enhancer (P–En) interaction frequently during myogenic differentiation. motifs, spatio-temporal rewiring of P–En interactions, and the corresponding impact on gene expression in each cell population during myogenesis. We identified two classes of Pax7-associated Demarcating stable and transient P–En interactions during P–En contacts, the maintenance of which was either Pax7- skeletal muscle specification and differentiation. To understand dependent or independent. Enhancers from the latter group were how cis-regulatory elements regulate myogenic differentiation associated with recruitment of additional myogenic TFs and and gene expression in adult skeletal muscle cells, we generated epigenetic memory during differentiation, and they retained their high-resolution pCHi-C maps capturing genome-wide, long- long-range interactions and an open and active state upon the range interactions with a curated set of 25,747 Ensembl annotated loss of Pax7. Furthermore, we show that Pax7 binds most super- promoters in iPax7 mouse skeletal muscle progenitors (+Dox) enhancers (SEs) that interact with target promoters in iPax7 and differentiating myocytes after Dox withdrawal (−Dox) muscle progenitors and that it establishes feed-forward loops with (Fig. 1b). We also compared our results with published data from a cohort of TFs with which it physically interacts, providing an mouse ESCs21, from which iPax7 cells originate. After merging explanation for the pivotal role of this factor in skeletal muscle data from replicates, we used CHiCAGO25 to identify 107,330 to stem cell specification and maintenance. Lastly, using epigenome 121,802 high-confidence interactions between annotated pro- editing, we show that a previously uncharacterized Pax7-bound moters and distal promoter-interacting DNA fragments in ESCs, EnH within the myosin heavy chain (Myh) cluster can activate Dox-treated, and differentiated conditions (Supplementary three Myh genes needed to build muscle. Fig. 2A and Supplementary Data 1). The majority (>99%) of captured interactions were found in cis (Supplementary Data 1), and >65% of them linked promoter to non-promoter regions in Results all three cell populations, with median distances between 131 and Global chromatin conformational changes during muscle cell 155 kb (Supplementary