Project description: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.
Project description:As early as 24 hours after RNA virus infection, up to 25% of all RNA molecules present in host cells are pathogenic viral RNA (vRNA), i.e. viral messenger RNA (vmRNA), viral genomic RNA (vgRNA), and double stranded replication intermediates (dsRNA). To prevent such a takeover of the host metabolism, the innate immune system of the infected organism must detect threat as soon as possible. When considering RNA viruses recognition, activation of timely proper immune response capable of sensing and neutralizing viral genetic material is crucial for cell survival. Viral nucleic acids are one of the strongest pathogen-associated molecular patterns (PAMPs), molecules causing particular immune system reactions. Human cells are armed with a variety of pattern recognition receptors (PRRs) responsible for PAMPs recognition. The main factors responsible for detecting foreign nucleic acids in mammalian cells have already been identified. For activation of any RNA sensor, detecting an abnormal molecular RNA pattern, not present under normal conditions, is obligatory. These patterns may be some chemical modification of RNA, or the absence of such one, specific secondary or tertiary RNA structure, particular sequence, or dsRNA that can derive from viral genome as it is in the case of dsRNA viruses or from annealed complementary RNA strands, which are generated as RNA virus replication intermediates. However, yet there is still very limited understanding of how different epitranscriptomic marks modulate host immune response. Therefore, we will attempt to comprehensively understand how chemical modifications of viral RNA influence its immunogenic potential and stability in infected cells. Moreover, we will study how epitranscriptomic marks deposited on viral RNAs shield transcripts from being recognized by host antiviral factors.
Project description:ChIP-seq data (H3K4Me3, H3K27Ac histone modifications) of Hodgkin lymphoma cell line L-428. Samples were processed as previously described (Sud et al., 2018). The files are in bam format, aligned to build 37.
