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| Status |
Public on Jun 23, 2017 |
| Title |
m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
HeLa cell chromatin associated nascent pre-mRNA (CA-RNA) contains many unspliced introns and m6A in exons, but very rarely in introns. m6A methylation of exons in CA-RNA frequently occur before splicing of exons and is essentially completed upon the release of mRNA into the nucleoplasm. m6A modifications are virtually the same in the newly synthesized CA-RNA, nucleoplasmic mRNA in transit and in the steady state cytoplasmic mRNA. This result suggests quantitatively little cytoplasmic methylation or demethylation. Only ~10% of m6As in CA-RNA are within 50 nucleotides of 5' or 3' splice sites arguing against a common splicing function of methylation. Both HeLa and mouse embryonic stem cell mRNAs showed a distinct increase of m6As, some in clusters, in short-lived mRNAs. Thus there is an unanticipated observation that m6A is added to exons presumably coincident with or soon after exon definition in nascent pre-mRNA, linking nuclear methylation to cytoplasmic mRNA stability.
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| Overall design |
Precise mapping m6A sites in human HeLa cells (CA-RNA, nucleoplasmic RNA and cytoplasmic RNAs) and mouse embryonic stem (ES) cells by m6A-CLIP/IP (briefly m6A-CLIP); mRNA half-life quantification by Actinomycin-D treatment and followed with RNA-Seq at different time points with biological replicates in mouse ES cells; RNAseq of HeLa CA-RNA (Ribo 0), nucleoplasmic RNA (Ribo 0), cytoplasmic RNA (Ribo 0) and cytoplasmic RNA (polyA+)
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| Contributor(s) |
Darnell JE Jr, Darnell RB |
| Citation(s) |
28637692 |
| |
| Submission date |
Sep 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shengdong Ke |
| E-mail(s) |
sk2410@caa.columbia.edu
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| Organization name |
The Jackson Laboratory
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| Lab |
The Ke Lab of Quantitative RNA Biology
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| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA341466 |
| SRA |
SRP083953 |
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