How the chromatin states of transposable elements (TEs) are controlled in development and disease is unclear. We present CARGO-BioID, a CRISPR-based proteomic approach to identify TE-associated proteins, and reveal an interplay between RNA N6-methyladenosine (m6A) and DNA methylation that is crucial for regulating TE activation and human embryonic stem cell (hESC) fate.
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References
Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017). A review article that discusses TEs and their gene regulatory roles.
Gu, B. et al. Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements. Science 359, 1050–1055 (2018). This paper reports the CARGO strategy for multiplexed CRISPR targeting.
Michalak, E. M., Burr, M. L., Bannister, A. J. & Dawson, M. A. The roles of DNA, RNA and histone methylation in ageing and cancer. Nat. Rev. Mol. Cell Biol. 20, 573–589 (2019). A review article that covers the topic of RNA and DNA methylation.
Deng, S. et al. RNA m6A regulates transcription via DNA demethylation and chromatin accessibility. Nat. Genet. 54, 1427–1437 (2022). A study that reports crosstalk between RNA m6A methylation and DNA methylation in human cancer cells.
Diao, Y. et al. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat. Methods 14, 629–635 (2017). This paper presents CREST-seq and ‘unmarked enhancers’.
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This is a summary of: Sun, T. et al. Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells. Nat. Genet. https://doi.org/10.1038/s41588-023-01452-5 (2023).
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Regulation of transposable elements and stem cell fate by crosstalk between RNA and DNA methylation. Nat Genet 55, 1259–1260 (2023). https://doi.org/10.1038/s41588-023-01453-4
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DOI: https://doi.org/10.1038/s41588-023-01453-4
