Ontology highlight
ABSTRACT:
PROVIDER: PRJNA796822 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17601566.fastq.gz | Fastqsanger.gz | |||
| SRR17601567.fastq.gz | Fastqsanger.gz | |||
| SRR17601568.fastq.gz | Fastqsanger.gz | |||
| SRR17601569.fastq.gz | Fastqsanger.gz | |||
| SRR17601570.fastq.gz | Fastqsanger.gz |
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Project description:Soybean is a critical source of vegetable protein, yet its proteome remains under-characterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D-data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity, with significant differences in protein-transcript abundance across organs. We also map N6-methyladenosine (m6A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of proteome and m6A methylome identifies novel regulator in m6A methylation. This comprehensive proteomic and m6A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.
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Project description:N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (âm6A levelsâ), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3â untranslated regions (3â-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications. m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates
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