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| Status |
Public on Jun 25, 2010 |
| Title |
Expanding the MicroRNA Targeting Code: A Novel Type of Site with Centered Pairing |
| Organisms |
Danio rerio; Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
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| Summary |
We present “centered sites,” a class of microRNA target sites that lacks both perfect seed pairing and 3'-compensatory pairing and instead has 11–12 contiguous Watson–Crick pairs to the center of the microRNA. In elevated Mg2+, centered sites impart mRNA cleavage, but in cells, centered sites repress protein output without consequential Agronaute-catalyzed cleavage. Our study also identified novel extensively paired sites that are cleavage substrates in cultured cells and human brain. This expanded repertoire of cleavage targets and the identification of the centered site type help explain why central regions of many microRNAs are evolutionarily conserved.
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| Overall design |
To study centered sites and identify miRNA cleavage targets, mRNA degradomes were sequenced from human brain and HeLa cells, and smallRNAs were sequenced from human brain and zebrafish embryo at 24 hours post fertilization (hpf). Replicates were combined before the analysis. Fastq files are not available for GSM548638 and GSM548639.
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| Contributor(s) |
Shin C, Nam J, Farh KH, Chiang HR, Shkumatava A, Bartel DP |
| Citation(s) |
20620952 |
| |
| Submission date |
Jun 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin-Wu Nam |
| E-mail(s) |
jwnam@wi.mit.edu
|
| Organization name |
Whitehead Institute
|
| Lab |
Bartel lab
|
| Street address |
Nine Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
| GPL10164 |
Illumina Genome Analyzer (Danio rerio) |
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| Samples (11)
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| Relations |
| SRA |
SRP002640 |
| BioProject |
PRJNA128943 |
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