N6-methyladenosine (m6A) is a reversible and dynamic RNA modification in eukaryotes. However, how cells establish cell-specific m6A methylomes is still poorly understood. Here, we developed a computational framework to systematically identify cell-specific trans regulators of m6A through integrating gene expressions, binding targets and binding motifs of large number of RNA binding proteins (RBPs) with a co-methylation network constructed using large-scale m6A methylomes across diverse cell states. We applied the framework and successfully identified 32 high-confidence m6A regulators that modulated the variable m6A sites away from stop codons in a cell-specific manner. To validate them, we knocked down three regulators respectively and found two of them (TRA2A and CAPRIN1) selectively promoted the methylations of the m6A sites co-localized with their binding targets on RNAs through physical interactions with the m6A writers. Knockdown of TRA2A increased the stabilities of the RNAs with TRA2A bound near the m6A sites and decreased the viability of cells. The successful identification of m6A regulators demonstrates a powerful and widely applicable strategy to elucidate the cell-specific m6A regulators. Additionally, our discovery of pervasive trans-acting regulating of m6A provides novel insights into the mechanisms by which spatial and temporal dynamics of m6A methylomes are established.

中文翻译：

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综合网络分析确定了 m6A 的细胞特异性反式调节因子。

N6-甲基腺苷 (m6A) 是真核生物中可逆的动态 RNA 修饰。然而，细胞如何建立细胞特异性 m6A 甲基化组仍然知之甚少。在这里，我们开发了一个计算框架，通过将大量 RNA 结合蛋白 (RBP) 的基因表达、结合靶标和结合基序与使用大规模 m6A 甲基化组构建的共甲基化网络整合，系统地识别 m6A 的细胞特异性反式调节因子跨越不同的细胞状态。我们应用了该框架并成功鉴定了 32 个高可信度的 m6A 调节因子，它们以细胞特异性方式将可变 m6A 位点调节为远离终止密码子。为了验证它们，我们分别击倒了三个调节器，发现其中两个（TRA2A 和 CAPRIN1）通过与 m6A 编写器的物理相互作用选择性地促进了 m6A 位点的甲基化，这些位点与其在 RNA 上的结合靶点共定位。敲除 TRA2A 增加了 RNA 的稳定性，TRA2A 结合在 m6A 位点附近，并降低了细胞的活力。m6A 调节剂的成功鉴定证明了一种强大且广泛适用的策略来阐明细胞特异性 m6A 调节剂。此外，我们发现对 m6A 的普遍反式作用调节提供了对 m6A 甲基化组时空动态建立机制的新见解。敲低 TRA2A 增加了 RNA 的稳定性，TRA2A 结合在 m6A 位点附近，并降低了细胞的活力。m6A 调节剂的成功鉴定证明了一种强大且广泛适用的策略来阐明细胞特异性 m6A 调节剂。此外，我们发现对 m6A 的普遍反式作用调节提供了对 m6A 甲基化组时空动态建立机制的新见解。敲除 TRA2A 增加了 RNA 的稳定性，TRA2A 结合在 m6A 位点附近，并降低了细胞的活力。m6A 调节剂的成功鉴定证明了一种强大且广泛适用的策略来阐明细胞特异性 m6A 调节剂。此外，我们发现对 m6A 的普遍反式作用调节提供了对 m6A 甲基化组时空动态建立机制的新见解。