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

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

PROVIDER: PRJNA972002 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24529900_1.fastq.gz	Fastqsanger.gz
	SRR24529900_2.fastq.gz	Fastqsanger.gz
	SRR24529901_1.fastq.gz	Fastqsanger.gz
	SRR24529901_2.fastq.gz	Fastqsanger.gz
	SRR24529802_1.fastq.gz	Fastqsanger.gz

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

Project description: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.

2024-01-24 | GSE232450 | GEO

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

Project description:BackgroundN6-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.ResultsHere 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.ConclusionsOur findings define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.

| S-EPMC10870504 | biostudies-literature

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA]

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Project description:We present SIGNAL-seq (Split-pool Indexing siGNalling AnaLysis by sequencing): a multiplexed split-pool combinatorial barcoding method that simultaneously measures RNA and post-translational modifications (PTMs) in fixed single cells from 3D models. SIGNAL-seq PTM measurements are equivalent to mass cytometry and RNA gene detection is analogous to split-pool barcoding scRNA-seq. By measuring both mRNA ligand-receptor pairs and PTMs in single cells, SIGNAL-seq can simultaneously un- cover inter- and intra-cellular regulation of tumour microenvironment plasticity. This SuperSeries is composed of the SubSeries listed below.

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