DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights [RNA-seq]

DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in Guanine-rich DNA sequences and recent studies demonstrate G4s play important roles in modulating multiple biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling permit global mapping of endogenous G4 formation. Here in this study, we map the G4 landscapes in skeletal muscle stem cells (MuSCs) which are essential for injury induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs from quiescent to activated to differentiated cells, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter associated G4s regulate gene transcription in through facilitating DNA looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs and MAX binds to G4 structures to promote E-P looping and gene transcription. The above uncovered global regulatory function/mechanism are further dissected on the paradigm of CCNE1 promoter demonstrating CCNE1 is a bona fid G4/MAX regulatory target in activated MuSCs. Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in MuSCs and the mechanistic role of G4s in promoting gene expression and MuSC activation/proliferation.