Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel.
Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, 1090, Austria.
Genome Biol. 2024 Feb 15;25(1):48. doi: 10.1186/s13059-024-03182-1.
N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability is driven by changes in genetic sequences ('cis') or cellular environments ('trans') and via which mechanisms.
Here we dissect the determinants governing RNA methylation via interspecies and intraspecies hybrids in yeast and mammalian systems, coupled with massively parallel reporter assays and m6A-QTL reanalysis. We find that m6A evolution and variability is driven primarily in 'cis', via two mechanisms: (1) variations altering m6A consensus motifs, and (2) variation impacting mRNA secondary structure. We establish that mutations impacting RNA structure - even when distant from an m6A consensus motif - causally dictate methylation propensity. Finally, we demonstrate that allele-specific differences in m6A levels lead to allele-specific changes in gene expression.
Our findings define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.
N6-甲基腺苷（m6A）是最丰富的 mRNA 修饰物，可控制 mRNA 的稳定性。m6A 在物种之间和物种内部的分布差异很大。然而，尚不清楚这种可变性在多大程度上是由遗传序列（“顺式”）或细胞环境（“反式”）变化以及通过哪些机制驱动的。
在这里，我们通过酵母和哺乳动物系统中的种间和种内杂种，结合大规模平行报告基因检测和 m6A-QTL 再分析，剖析了控制 RNA 甲基化的决定因素。我们发现 m6A 的进化和可变性主要是通过两种机制在“顺式”中驱动的：（1）改变 m6A 共识基序的变异；（2）影响 mRNA 二级结构的变异。我们确定，即使影响 RNA 结构的突变远离 m6A 共识基序，也会导致甲基化倾向发生因果变化。最后，我们证明了 m6A 水平的等位基因特异性差异会导致基因表达的等位基因特异性变化。
我们的研究结果定义了控制 m6A 进化和多样性的决定因素，并描述了其对基因表达调控的影响。
