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. RNA-seq of MuSC

DNA G-四链体（G-quadruplexes，G4s）是一类在富含鸟嘌呤的DNA序列中形成的非经典二级结构。近期研究表明，G4s可通过多种基因调控机制参与调控多种生物学过程，发挥关键作用。新兴的G4谱型分析技术可实现内源性G4形成的全基因组定位。本研究中，我们对骨骼肌干细胞（skeletal muscle stem cells，MuSCs）中的G4景观进行了定位，这类细胞对于损伤诱导的肌肉再生至关重要。在MuSCs从静息态到激活态再到分化态的肌源性谱系发育进程中，我们发现内源性G4的形成呈现动态变化特征：当MuSCs进入激活状态并增殖时，G4的形成会出现显著诱导。我们进一步证实，G4诱导可促进MuSCs激活，进而推动肌肉再生过程。从机制层面来看，启动子相关G4s可通过促进DNA环化调控基因转录。此外，我们发现，在激活态MuSCs中，G4位点富集转录因子（transcription factor，TF）结合事件；MAX蛋白可结合G4结构，以促进E-P环化与基因转录。上述所揭示的全局调控功能与机制，还以CCNE1启动子为研究范式进行了深入解析，证实CCNE1是激活态MuSCs中确凿的G4/MAX调控靶基因。综上，我们的研究首次证实了G4s在MuSCs中广泛且动态的形成模式，并阐明了G4s在促进基因表达以及MuSCs激活与增殖过程中的机制性作用。本研究包含MuSCs的RNA测序（RNA-seq）数据集。