Endogenous retroviruses (ERVs) are abundant and heterogenous groups of integrated retroviral sequences that affect genome regulation and cell physiology throughout their RNA-centred life cycle¹. Failure to repress ERVs is associated with cancer, infertility, senescence and neurodegenerative diseases^2,3. Here, using an unbiased genome-scale CRISPR knockout screen in mouse embryonic stem cells, we identify m⁶A RNA methylation as a way to restrict ERVs. Methylation of ERV mRNAs is catalysed by the complex of methyltransferase-like METTL3–METTL14⁴ proteins, and we found that depletion of METTL3–METTL14, along with their accessory subunits WTAP and ZC3H13, led to increased mRNA abundance of intracisternal A-particles (IAPs) and related ERVK elements specifically, by targeting their 5′ untranslated region. Using controlled auxin-dependent degradation of the METTL3–METTL14 enzymatic complex, we showed that IAP mRNA and protein abundance is dynamically and inversely correlated with m⁶A catalysis. By monitoring chromatin states and mRNA stability upon METTL3–METTL14 double depletion, we found that m⁶A methylation mainly acts by reducing the half-life of IAP mRNA, and this occurs by the recruitment of the YTHDF family of m⁶A reader proteins⁵. Together, our results indicate that RNA methylation provides a protective effect in maintaining cellular integrity by clearing reactive ERV-derived RNA species, which may be especially important when transcriptional silencing is less stringent.

内源性逆转录病毒 (ERV) 是大量的异源性整合逆转录病毒序列，在整个以 RNA 为中心的生命周期中影响基因组调控和细胞生理学¹。未能抑制 ERV 与癌症、不孕症、衰老和神经退行性疾病有关^2,3。在这里，我们在小鼠胚胎干细胞中使用无偏基因组规模的 CRISPR 敲除筛选，确定 m ⁶ A RNA 甲基化是限制 ERV 的一种方式。ERV mRNA 的甲基化由甲基转移酶样 METTL3–METTL14 复合物催化⁴蛋白质，我们发现 METTL3–METTL14 及其附属亚基 WTAP 和 ZC3H13 的耗尽，通过靶向其 5' 非翻译区，导致脑池内 A 粒子 (IAP) 和相关 ERVK 元件的 mRNA 丰度增加。使用 METTL3–METTL14 酶复合物的受控生长素依赖性降解，我们发现 IAP mRNA 和蛋白质丰度与 m ⁶ A 催化呈动态负相关。通过监测 METTL3–METTL14 双耗尽后的染色质状态和 mRNA 稳定性，我们发现 m ⁶ A 甲基化主要通过缩短 IAP mRNA 的半衰期起作用，这是通过募集 m ⁶ A 阅读蛋白^{5的 YTHDF 家族而发生的}. 总之，我们的结果表明 RNA 甲基化通过清除反应性 ERV 衍生的 RNA 物种在维持细胞完整性方面提供保护作用，这在转录沉默不太严格时可能尤为重要。