N6-methyladenosine on L1PA governs the trans-silencing of LTRs and restrains totipotency in naive human embryonic stem cells

Xuehao Zhu; Zhanhe Chang; Weide Xiao; Xinbao Zhang; Mingli Ma; Jiang Wu; Jindian Hu; Yan Bi; Xiaochen Kou; Yanhong Zhao; Yifan Sheng; Baoxing Dong; Jiaxing Sun; Che Chen; You Wu; Xuelian Liu; Wenqing Ding; Kaiyuan Jia; Yingfan Yao; Lihua Sun; Xianbin Yu; Hong Wang; Jun Liu; Yixuan Wang; Shaorong Gao; Yawei Gao

doi:10.1016/j.stem.2025.10.003

N6-methyladenosine on L1PA governs the trans-silencing of LTRs and restrains totipotency in naive human embryonic stem cells

Cell Stem Cell. 2025 Nov 6;32(11):1773-1791.e13. doi: 10.1016/j.stem.2025.10.003. Epub 2025 Oct 29.

Authors

Xuehao Zhu¹, Zhanhe Chang¹, Weide Xiao², Xinbao Zhang¹, Mingli Ma¹, Jiang Wu¹, Jindian Hu¹, Yan Bi¹, Xiaochen Kou³, Yanhong Zhao³, Yifan Sheng¹, Baoxing Dong¹, Jiaxing Sun³, Che Chen¹, You Wu¹, Xuelian Liu⁴, Wenqing Ding², Kaiyuan Jia², Yingfan Yao¹, Lihua Sun⁵, Xianbin Yu³, Hong Wang¹, Jun Liu⁶, Yixuan Wang⁷, Shaorong Gao⁸, Yawei Gao⁹

Affiliations

¹ Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Department of Reproductive Medicine Center, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
² State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
³ Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
⁴ Department of Reproductive Medicine Center, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
⁵ Department of Reproductive Medicine Center, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
⁶ State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing 100871, China; Sycamore Research Institute of Life Sciences, Shanghai 201203, China. Electronic address: junliu1223@pku.edu.cn.
⁷ Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Department of Reproductive Medicine Center, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China. Electronic address: wangyixuan@tongji.edu.cn.
⁸ Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Department of Reproductive Medicine Center, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China. Electronic address: gaoshaorong@tongji.edu.cn.
⁹ Department of Reproductive Medicine Center, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Sycamore Research Institute of Life Sciences, Shanghai 201203, China. Electronic address: gaoyawei@tongji.edu.cn.

PMID: 41167193
DOI: 10.1016/j.stem.2025.10.003

Abstract

Transposable elements (TEs) occupy nearly half of the genome and drive developmental innovation, yet the mechanisms of silencing long terminal repeats (LTRs) remain incompletely understood. We demonstrate that methyltransferase-like 3 deficiency reverts naive human embryonic stem cells (hESCs) to a totipotent-like state with reactivation and chromatin resetting of 8C-associated genes, eRNAs, and LTRs, particularly ERV1 and ERVL-MaLR. Moreover, m⁶A on primate-specific L1PA is found to be essential. Mechanistically, L1PA binds 8C-associated LTRs and eRNAs and regulates chromatin through RNA-scaffold complexes with chromatin regulators, where m⁶A directs protein-binding preference. In naive hESCs, m⁶A on L1PA suppresses EP300 binding to ERV1 and enhances KAP1 binding to ERVL-MaLR, thereby restricting LTR activity. In parallel, the m⁶A-L1PA axis or m⁶A on eRNAs limits EP300/H3K27ac occupancy at 8C enhancers. Our findings reveal a conserved mechanism in which humans and mice employ species-specific long interspersed nuclear element-1 subfamilies with m⁶A to regulate LTR activity, underscoring the crucial role of transposons in RNA-chromatin crosstalk during cell fate transitions.

Keywords: RNA m(6)A methylation; human embryonic stem cells; pluripotency; totipotency; transposable elements.

MeSH terms

Adenosine* / analogs & derivatives
Adenosine* / metabolism
Animals
Chromatin / metabolism
Gene Silencing*
Human Embryonic Stem Cells* / cytology
Human Embryonic Stem Cells* / metabolism
Humans
Long Interspersed Nucleotide Elements* / genetics
Methyltransferases / metabolism
Mice
Terminal Repeat Sequences* / genetics

Substances

Adenosine
N-methyladenosine
Chromatin
Methyltransferases