The METTL3-YTHDC1 axis mediates architectural RNA m6A modification to modulate the integrity of chromatin TADs in MLLr + AML genome

Ruishuang Fu; Wenjuan Yu; Rongjie Zhao; Huimin Yang; Beibei Cao; Chunfei Dai; Haoyue Qianjiang; Yujun Xia; Lubo Wang; Jianrong Lu; Ruiqing Zhou; Aiqin Shi; Hanmei Lou; Xiang Zhang; Huacheng Luo

doi:10.1186/s12943-025-02545-x

The METTL3-YTHDC1 axis mediates architectural RNA m⁶A modification to modulate the integrity of chromatin TADs in MLLr + AML genome

Mol Cancer. 2025 Dec 22;25(1):22. doi: 10.1186/s12943-025-02545-x.

Authors

Ruishuang Fu^#¹, Wenjuan Yu^#², Rongjie Zhao^#³, Huimin Yang¹, Beibei Cao¹, Chunfei Dai⁴, Haoyue Qianjiang⁴, Yujun Xia⁴, Lubo Wang⁴, Jianrong Lu⁵, Ruiqing Zhou⁶, Aiqin Shi⁷, Hanmei Lou⁸, Xiang Zhang⁹, Huacheng Luo¹⁰

Affiliations

¹ Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
² Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China.
³ Department of Gynecological Radiotherapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
⁴ College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China.
⁵ Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
⁶ Hematology Department, Guangzhou First People's Hospital, Guangzhou, Guangdong, 510080, China.
⁷ Xianghu Laboratory, Hangzhou, Zhejiang, 311231, China. shiaiqin@xhlab.ac.cn.
⁸ Department of Gynecological Radiotherapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China. louhm@zjcc.org.cn.
⁹ Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China. hillhardaway@zju.edu.cn.
¹⁰ Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China. luohuacheng@him.cas.cn.

^# Contributed equally.

Abstract

Background: The RNA methyltransferase METTL3 as a key regulator of acute myeloid leukemia (AML) contributes to malignant transformation. Chromatin topologically associating domains (TADs) are critical for maintaining AML genome integrity, but the mechanism by which METTL3 facilitates TADs integrity in AML progression remains unclear.

Methods: To determine whether METTL3 is transcriptionally activated by MLL in MLL-rearranged (MLLr+) AML cells, we analyzed MLL ChIP-seq data. Additionally, we performed a multi-omics approach—including RNA-seq, immunoprecipitation-mass spectrometry (IP-MS) for METTL3 and YTHDC1, DNA: RNA hybrid immunoprecipitation sequencing (DRIP-seq), METTL3 ChIP-seq, CTCF ChIP-seq, H3K4me3 and H3K27ac ChIP-seq—to delineate the functional interplay among METTL3-YTHDC1 axis, R-loops, and CTCF in the MLLr + AML genome. Furthermore, METTL3-RIPseq, YTHDC1 RIPseq, CTCF RIPseq, m⁶A-seq, and Hi-C-seq assays were conducted to elucidate the function of the METTL3-YTHDC1 axis-mediated m⁶A modification of architectural RNAs (arcRNAs) in regulating CTCF-dependent TAD boundary activity.

Results: METTL3 is transcriptionally activated by MLL and forms a complex with YTHDC1 and CTCF, colocalizing at promoters and enhancers in MLLr + AML cells. METTL3 depletion disrupts CTCF binding sites (CBSs) and reduces chromatin accessibility at key leukemic genes (e.g. MYB and RUNX1). Hi-C analysis further reveals that YTHDC1 loss compromises CTCF-dependent 3D genome organization. METTL3-mediated m⁶A modification stabilizes arcRNAs and R-loops, which are crucial for maintaining TAD integrity at leukemic loci. Mechanistically, YTHDC1 recognizes m⁶A-modified arcRNAs (e.g. MALAT1) to enhance R-loop formation, thereby sustaining CTCF-mediated TAD activity in the MLLr + AML genome.

Conclusions: Our study identifies the METTL3-YTHDC1-CTCF axis as a critical regulator of AML signature gene expression by orchestrating 3D genome organization. These findings provide novel insights into AML pathogenesis and reveal new therapeutic targets for this kind of aggressive disease.

Graphical Abstract:

Supplementary Information: The online version contains supplementary material available at 10.1186/s12943-025-02545-x.

Keywords: AML; Architectural RNA (arcRNA); CTCF; METTL3; R-loop; YTHDC1; m6A modification.

Abstract

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