|
| Status |
Public on Dec 22, 2012 |
| Title |
C. elegans piRNAs are processed from capped-small RNAs transcribed at promoters throughout the genome |
| Organisms |
Caenorhabditis elegans; Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Piwi-interacting (pi) RNAs are a class of germline-expressed small RNAs that have been linked to epigenetic programming in metazoa. C. elegans piRNAs known as 21U-RNAs are defined by more than 15,000 genome-encoded species. To explore the origin of 21U-RNAs we employed methods to enrich the 5' ends of Pol II transcripts. We show that a species of capped-short (cs) RNA is frequently expressed bidirectionally at Pol II loci in C. elegans. Interestingly, at annotated 21U-RNA loci, csRNAs originate precisely 2 nt upstream of the mature piRNA species suggesting that csRNAs are piRNA precursors. In addition, we show that csRNAs associated with TS sites genome-wide define a previously overlooked class of 21U-RNA loci, and nearly double the number of piRNA species available for genome surveillance. Our methods should be of general utility in TS site identification and 5' anchored RNA-expression profiling.
|
| |
|
| Overall design |
Identification of capped RNA including capped small RNA and long capped RNA in C. elegans. The mouse data are independent data to test the CapSeq sequencing protocol.
|
| |
|
| Contributor(s) |
Lee H, Chaves D, Conte D |
| Citation(s) |
23260138 |
| Submission date |
Aug 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Craig Mello |
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Craig Mello
|
| Street address |
368 Plantatoin Street, Suite AS5-2047
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL9269 |
Illumina Genome Analyzer II (Caenorhabditis elegans) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
|
| Samples (11)
|
| GSM984429 |
CapSeq, insert size 20-100 nt YA |
| GSM984430 |
CapSeq, insert size 100-130 nt mutation, adult stage |
| GSM984431 |
CapSeq, insert size 100-130 nt 4wk |
| GSM984432 |
CapSeq, insert size 100-130 nt 6m |
| GSM984433 |
PRG1 IP, insert size 18-40 nt adult |
| GSM984434 |
PRG1 IP input, insert size 18-40 nt adult |
| GSM984435 |
CIP-PNK, insert size 18-40 nt adult |
| GSM984436 |
CIP-TAP, insert 18-40 nt adult |
|
| Relations |
| BioProject |
PRJNA172751 |
| SRA |
SRP014826 |
Less...
More...