Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids

ABSTRACT: N6-methyladenosine (m6A) is the most abundant mRNA modification, primarily implicated in controlling mRNA stability. The distribution of m6A varies considerably between and within species, and genetic variants associated with differences in m6A levels between humans have been associated with disease. Yet, the determinants governing m6A variability are poorly understood: It is unclear whether it is driven by changes in genetic sequences (‘cis’) or cellular environments (‘trans’) and what its underlying mechanisms are. Here we dissect these determinants via interspecies hybrids in yeast and mammalian systems, allowing us to interrogate methylation at two distinguishable alleles in a shared environment. We find that m6A evolution is driven primarily in ‘cis’, and identify two mechanisms driving m6A changes: (1) Sequence variations leading to formation/disruption of m6A consensus motifs, and (2) Changes in local mRNA secondary structure, whereby RNA structuredness inhibits m6A formation. We demonstrate that secondary structure is causal, and that gain and loss of structure - even when driven by mutations distant from the modified position - are sufficient to abolish and acquire methylation, respectively. Using intra-species hybrids, massively parallel reporter assays and reanalyzing m6A-QTLs among 60 human individuals, we reveal the combined role of sequence and structure in shaping variability in m6A levels also across individuals from the same species. Finally, we demonstrate that differences in m6A levels between homologous genes lead to allele-specific changes in gene expression. Our findings thus define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.

ORGANISM(S): Mus musculus Saccharomyces cerevisiae x Saccharomyces paradoxus Homo sapiens Saccharomyces cerevisiae Saccharomyces paradoxus

PROVIDER: GSE232450 | GEO | 2024/01/24

REPOSITORIES: GEO