|
| Status |
Public on Jun 24, 2016 |
| Title |
m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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 (“m6A levels”), 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 3’ untranslated regions (3’-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.
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| |
|
| Overall design |
m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates
|
| |
|
| Contributor(s) |
Wang J, Molinie B, Xing Y, Giallourakis CC |
| Citation(s) |
27376769 |
| |
| Submission date |
Feb 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinkai Wang |
| Organization name |
University of California, Los Angeles
|
| Street address |
650 Charles E. Young Drive South, CHS 33-228
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7278 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA275864 |
| SRA |
SRP055176 |
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