2. Academic Validation
  3. FOCAS: Transcriptome-wide screening of individual m6A sites functionally dissects epitranscriptomic control of gene expression in cancer

FOCAS: Transcriptome-wide screening of individual m6A sites functionally dissects epitranscriptomic control of gene expression in cancer

  • Cell. 2025 Dec 31:S0092-8674(25)01372-8. doi: 10.1016/j.cell.2025.11.037.
Xinning Zhang 1,  Yifan Zhang 1,  Xinyu Liu 1,  Chang Liu 2,  Ying Liu 3,  Yuan He 4,  Yuhang Qiu 5,  Lida Sun 5,  Jing Hu 5,  Yawei Gao 6,  Wensheng Wei 7,  Jun Liu 8
Affiliations

Affiliations

  • 1 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.
  • 2 Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
  • 3 Changping Laboratory, Beijing 102206, China.
  • 4 Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
  • 5 State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
  • 6 State Key Laboratory of Cardiology, Medical Innovation Center, Department of Reproductive Medicine Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, 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.
  • 7 Changping Laboratory, Beijing 102206, China; Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
  • 8 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: [email protected].
PMID: 41478283 DOI: 10.1016/j.cell.2025.11.037
Abstract

Although N6-methyladenosine (m6A) is a pervasive RNA modification essential for gene regulation, dissecting the functions of individual m6A sites remains technically challenging. To overcome this, we developed functional m6A sites detection by CRISPR-dCas13b-FTO screening (FOCAS), a CRISPR-dCas13b-based platform enabling high-throughput, site-specific functional screening of m6A. Applying FOCAS to four human Cancer cell lines identified 4,475 m6A-regulated genes influencing cell fitness via both mRNAs and non-coding RNAs (ncRNAs), many of which are newly linked to Cancer and exhibit dynamic developmental expression. FOCAS uncovered context-dependent and reader-specific effects of m6A within the same gene, revealing its intricate regulatory logic. We further uncovered universal and cell-type-specific m6A patterns, with unique sites enriched in ncRNAs and universal ones in transcription-related genes. In SMMC-7721 cells, we identified m6A-regulated transcriptional networks that demonstrated extensive epitranscriptome-transcriptome crosstalk. Overall, this study established a powerful, unbiased approach for the functional dissection of m6A, advancing the understanding of its complexity and therapeutic relevance in cancers.

Keywords

FOCAS; RNA m(6)A modification; cell fitness; transcriptional-related network; universal and unique FiGenes.

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