Impact of gut microbiota on the m6A epitranscriptome in mouse cecum and liver tissues

The intestinal microbiota modulates host physiology and gene expression via mechanisms that are not fully understood. A recently discovered layer of gene expression regulation is N6-methyladenosine (m6A) and N6,2′ -O-dimethyladenosine (m6Am) modifications of mRNA. To unveil if these epitranscriptomic marks are affected by the gut microbiota, we performed methylated RNA-immunoprecipitation and sequencing (MeRIP-seq) to examine m6A-modifications in transcripts of mice displaying either a conventional, or a modified, or no gut microbiota and discovered that the microbiota has a strong influence on m6A- modifications in the cecum, and also, albeit to a lesser extent, in the liver, affecting pathways related to metabolism, inflammatory and antimicrobial responses . We furthermore analysed expression levels of several known writer and eraser enzymes and found the methyltransferase Mettl16 to be downregulated in absence of a microbiota. As a consequence, one of its targets, the S-adenosyl methionine synthase Mat2a was less expressed in mice without gut flora. We furthermore show that distinct commensal bacteria, Akkermansia muciniphila, Lactobacillus plantarum can affect specific m6A modifications. Together, we report here epitranscriptomic modifications as an additional level of interaction in the complex interplay between commensal bacteria and their host.

肠道菌群通过尚未完全阐明的机制调控宿主生理状态与基因表达。近来发现的一类全新基因表达调控层级为信使RNA（mRNA）的N6-甲基腺嘌呤（N6-methyladenosine, m6A）与N6,2′-O-二甲基腺嘌呤（N6,2′-O-dimethyladenosine, m6Am）修饰。为探明此类表观转录组标记是否受肠道菌群影响，我们开展了甲基化RNA免疫沉淀测序（methylated RNA-immunoprecipitation and sequencing, MeRIP-seq）实验，以检测具有正常肠道菌群、改造菌群或无菌状态的小鼠转录本中的m6A修饰情况。研究发现，肠道菌群对小鼠盲肠中的m6A修饰具有显著调控作用，在肝脏中也存在一定程度的影响（尽管强度较弱），并会调控代谢、炎症应答与抗菌应答相关的通路。我们还对多种已报道的m6A修饰写入酶（writer）与擦除酶（eraser）的表达水平进行了分析，发现甲基转移酶Mettl16在无菌小鼠体内的表达量显著下调。受其调控的靶标之一——S-腺苷甲硫氨酸合酶Mat2a，在肠道菌群缺失的小鼠中表达量同样降低。此外我们证实，特定的共生细菌——嗜黏蛋白阿克曼氏菌（Akkermansia muciniphila）与植物乳杆菌（Lactobacillus plantarum）可调控特定的m6A修饰。综上，本研究揭示表观转录组修饰是共生细菌与宿主之间复杂互作网络中的又一层调控机制。