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| Status |
Public on Oct 09, 2014 |
| Title |
Genome-wide quantification of microRNA processing efficiency from RNA-seq data |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Microprocessor is responsible for conversion of pri-miRNA transcripts into pre-miRNA hairpins in miRNA biogenesis. The in vivo properties of this process remain enigmatic. Here, we present the first study of in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile, from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. Based on differential processing efficiencies we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression.
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| Overall design |
We performed polyA independent deep sequencing of the chromatin-isolated RNA fraction for 5 samples: 2 replicates in HeLa cells, 1 Drosha knock down in HeLa cells, 1 sample for A549 cells and 1 sample for HEK293 cells. We also performed deep sequencing of the small RNA fraction in the same cell lines.
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| Contributor(s) |
Conrad T, Marsico A, Gehre M, Orom UA |
| Citation(s) |
25310978, 28250203 |
| Submission date |
Apr 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Annalisa Marsico |
| E-mail(s) |
marsico@molgen.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Department |
Computational Biology
|
| Street address |
Ihnestraße 63-73
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA244784 |
| SRA |
SRP041228 |
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