The molecular basis underlying the interaction between retrotransposable elements (RTEs) and the human genome remains poorly understood. Here, we profiled N⁶-methyladenosine (m⁶A) deposition on nascent RNAs in human cells by developing a new method MINT-Seq, which revealed that many classes of RTE RNAs, particularly intronic LINE-1s (L1s), are strongly methylated. These m⁶A-marked intronic L1s (MILs) are evolutionarily young, sense-oriented to hosting genes, and are bound by a dozen RNA binding proteins (RBPs) that are putative novel readers of m⁶A-modified RNAs, including a nuclear matrix protein SAFB. Notably, m⁶A positively controls the expression of both autonomous L1s and co-transcribed L1 relics, promoting L1 retrotransposition. We showed that MILs preferentially reside in long genes with critical roles in DNA damage repair and sometimes in L1 suppression per se, where they act as transcriptional “roadblocks” to impede the hosting gene expression, revealing a novel host-weakening strategy by the L1s. In counteraction, the host uses the SAFB reader complex to bind m⁶A-L1s to reduce their levels, and to safeguard hosting gene transcription. Remarkably, our analysis identified thousands of MILs in multiple human fetal tissues, enlisting them as a novel category of cell-type-specific regulatory elements that often compromise transcription of long genes and confer their vulnerability in neurodevelopmental disorders. We propose that this m⁶A-orchestrated L1–host interaction plays widespread roles in gene regulation, genome integrity, human development and diseases.

逆转录转座因子 (RTE) 与人类基因组之间相互作用的分子基础仍然知之甚少。在这里，我们通过开发一种新方法 MINT-Seq 分析了N ⁶ -甲基腺苷 (m ⁶ A) 在人类细胞中新生 RNA 上的沉积，该方法表明许多类别的 RTE RNA，特别是内含子 LINE-1 (L1)，被强烈甲基化. 这些m ⁶ A 标记的电子L 1 ( MIL) 在进化上很年轻，面向宿主基因，并被十几种 RNA 结合蛋白 (RBP) 结合，这些蛋白是 m ⁶ A 修饰的 RNA 的推定新读者，包括核基质蛋白 SAFB。值得注意的是，m ⁶A 正向控制自主 L1 和共转录 L1 遗迹的表达，促进 L1 逆转录转座。我们表明，MIL 优先驻留在长基因中，这些长基因在 DNA 损伤修复中起着关键作用，有时在 L1 抑制本身中起着关键作用，它们充当转录“障碍”以阻碍宿主基因表达，揭示了 L1 的一种新的宿主弱化策略。作为对抗，宿主使用 SAFB 阅读器复合体来绑定 m ⁶A-L1s 以降低它们的水平，并保护宿主基因转录。值得注意的是，我们的分析在多个人类胎儿组织中发现了数千个 MIL，将它们列为一类新的细胞类型特异性调控元件，这些元件通常会损害长基因的转录并赋予它们在神经发育障碍中的脆弱性。我们提出，这种 m ⁶ A 编排的 L1-宿主相互作用在基因调控、基因组完整性、人类发育和疾病中发挥着广泛的作用。