DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights

Xiaona Chen; Feng Yang; Suyang Zhang; Xiaofan Guo; Jieyu ZHAO; Yulong Qiao; Liangqiang He; Yang Li; Qin Zhou; Michael Tim-Yun Ong; Chun Kit KWOK; Hao Sun; Huating Wang

doi:10.1186/s13059-025-03753-w

DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights

Xiaona Chen^* (Co-first Author), Feng Yang (Co-first Author), Suyang Zhang (Co-first Author), Xiaofan Guo, Jieyu ZHAO, Yulong Qiao, Liangqiang He, Yang Li, Qin Zhou, Michael Tim-Yun Ong, Chun Kit KWOK, Hao Sun^*, Huating Wang^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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Abstract

Background: DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in guanine-rich DNA sequences and play important roles in modulating biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling allows global mapping of endogenous G4 formation.

Results: Here in this study, we map the G4 landscapes in adult skeletal muscle stem cells (MuSCs), which are essential for injury-induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that the G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter-associated G4s regulate gene transcription through facilitating chromatin looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs; MAX binds to G4 structures to synergistically facilitate chromatin looping and gene transcription, thus promoting MuSC activation and regeneration. The above uncovered global regulatory functions/mechanisms are further dissected on the paradigm of Ccne1 promoter, demonstrating that Ccne1 is a bona fide G4/MAX regulatory target in activated MuSCs.

Conclusions: Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in adult MuSCs and the mechanistic role of G4s in modulating gene expression and MuSC activation/proliferation.

© The Author(s) 2025

Original language	English
Article number	269
Number of pages	33
Journal	Genome Biology
Volume	26
Online published	5 Sept 2025
DOIs	https://doi.org/10.1186/s13059-025-03753-w
Publication status	Published - 2025

Funding

This work was supported by the National Key R&D Program of China to H.W. (project code: 2022YFA0806003); National Natural Science Foundation of China (NSFC) (project code: 32300703) to X.C.; Natural Science Foundation of Guangdong Province, China (project code: 2024A1515030291) to X.C.; Non-Communicable Chronic Disease-National Science and Technology Major Project of China to H. W. (project code: 2024ZD0530400); The InnoHK initiative of the Innovation and Technology Commission of the Hong Kong Special Administrative Region Government to H.W.; Health and Medical Research Fund (HMRF) from Health Bureau of HK to H.W. (project codes: 10210906 and 08190626); Theme-based Research Scheme (TRS) from RGC to H.W. (project code:T13-602/21-N); General Research Fund (GRF) from Research Grants Council (RGC) of the Hong Kong Special Administrative Region, China, to H.W. (project codes: 14108225, 14106521, 14105123, 14103522, and 14105823 to H.W.); the National Natural Science Foundation of China (NSFC) to H.W. (project codes: 82172436); and Area of Excellence Scheme (AoE) from RGC to H.W. (project code: AoE/M-402/20). The Chinese University of Hong Kong (CUHK) Strategic Seed Funding for Collaborative Research Scheme (SSFCRS) to H.W.; National Natural Science Foundation of China (NSFC) Project (project code: 32471343, 32222089) to C.K.K.; Research Grants Council (RGC) of the Hong Kong Special Administrative Region (project code: RFS2425-1S02, CityU 11100123, CityU 11100222, CityU 11100421) to C.K.K.; Croucher Foundation Project (project code: 9509003) to C.K.K.; State Key Laboratory of Marine Pollution Seed Collaborative Research Fund (project code: SCRF/0070) to C.K.K.; City University of Hong Kong projects (project code: 9680376, 7030001, 9678302) to C.K.K.

Research Keywords

DNA G-quadruplex
Skeletal muscle stem cells
Muscle regeneration
Chromatin looping
MAX

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This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

RGC Funding Information

RGC-funded

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10.1186/s13059-025-03753-w

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title = "DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights",

abstract = "Background: DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in guanine-rich DNA sequences and play important roles in modulating biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling allows global mapping of endogenous G4 formation.Results: Here in this study, we map the G4 landscapes in adult skeletal muscle stem cells (MuSCs), which are essential for injury-induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that the G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter-associated G4s regulate gene transcription through facilitating chromatin looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs; MAX binds to G4 structures to synergistically facilitate chromatin looping and gene transcription, thus promoting MuSC activation and regeneration. The above uncovered global regulatory functions/mechanisms are further dissected on the paradigm of Ccne1 promoter, demonstrating that Ccne1 is a bona fide G4/MAX regulatory target in activated MuSCs.Conclusions: Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in adult MuSCs and the mechanistic role of G4s in modulating gene expression and MuSC activation/proliferation.{\textcopyright} The Author(s) 2025",

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author = "Xiaona Chen and Feng Yang and Suyang Zhang and Xiaofan Guo and Jieyu ZHAO and Yulong Qiao and Liangqiang He and Yang Li and Qin Zhou and Ong, {Michael Tim-Yun} and KWOK, {Chun Kit} and Hao Sun and Huating Wang",

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AU - Chen, Xiaona

AU - Yang, Feng

AU - Zhang, Suyang

AU - Guo, Xiaofan

AU - ZHAO, Jieyu

AU - Qiao, Yulong

AU - He, Liangqiang

AU - Li, Yang

AU - Zhou, Qin

AU - Ong, Michael Tim-Yun

AU - KWOK, Chun Kit

AU - Sun, Hao

AU - Wang, Huating

PY - 2025

Y1 - 2025

N2 - Background: DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in guanine-rich DNA sequences and play important roles in modulating biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling allows global mapping of endogenous G4 formation.Results: Here in this study, we map the G4 landscapes in adult skeletal muscle stem cells (MuSCs), which are essential for injury-induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that the G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter-associated G4s regulate gene transcription through facilitating chromatin looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs; MAX binds to G4 structures to synergistically facilitate chromatin looping and gene transcription, thus promoting MuSC activation and regeneration. The above uncovered global regulatory functions/mechanisms are further dissected on the paradigm of Ccne1 promoter, demonstrating that Ccne1 is a bona fide G4/MAX regulatory target in activated MuSCs.Conclusions: Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in adult MuSCs and the mechanistic role of G4s in modulating gene expression and MuSC activation/proliferation.© The Author(s) 2025

AB - Background: DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in guanine-rich DNA sequences and play important roles in modulating biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling allows global mapping of endogenous G4 formation.Results: Here in this study, we map the G4 landscapes in adult skeletal muscle stem cells (MuSCs), which are essential for injury-induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that the G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter-associated G4s regulate gene transcription through facilitating chromatin looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs; MAX binds to G4 structures to synergistically facilitate chromatin looping and gene transcription, thus promoting MuSC activation and regeneration. The above uncovered global regulatory functions/mechanisms are further dissected on the paradigm of Ccne1 promoter, demonstrating that Ccne1 is a bona fide G4/MAX regulatory target in activated MuSCs.Conclusions: Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in adult MuSCs and the mechanistic role of G4s in modulating gene expression and MuSC activation/proliferation.© The Author(s) 2025

KW - DNA G-quadruplex

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JO - Genome Biology

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ER -

DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights

Abstract

Funding

Research Keywords

Publisher's Copyright Statement

RGC Funding Information

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RFS: Developing RNA Structure-Targeting Bi-/Multi-Functional Laptamer-Based Chimeras for Gene Regulation

GRF: Developing Novel Short Peptides to Target G-quadruplex Structure and Modulate Gene Function

GRF: Evolving New L-RNA Aptamers and Developing L-RNA aptamer-peptide Conjugates to Control G-quadruplex Structure-associated Gene Activity

Cite this

DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights

Abstract

Funding

Research Keywords

Publisher's Copyright Statement

RGC Funding Information

Access Output

Other Access Options

Permanent Link

Other Files and Links

Fingerprint

Projects

RFS: Developing RNA Structure-Targeting Bi-/Multi-Functional Laptamer-Based Chimeras for Gene Regulation

GRF: Developing Novel Short Peptides to Target G-quadruplex Structure and Modulate Gene Function

GRF: Evolving New L-RNA Aptamers and Developing L-RNA aptamer-peptide Conjugates to Control G-quadruplex Structure-associated Gene Activity

Cite this