 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 07, 2012 |
| Title |
Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals |
| Organisms |
Drosophila melanogaster; Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Drosophila Dicer-1 produces microRNAs (miRNAs) from pre-miRNA, whereas Dicer-2 generates small interfering RNAs (siRNAs) from long dsRNA. loquacious (loqs) encodes three Dicer partner proteins, Loqs-PA, Loqs-PB, and, Loqs-PD, generated by alternative splicing. To understand the function of each Loqs isoform, we constructed loqs isoform-specific rescue flies. Loqs-PD promotes siRNA production in vivo by Dicer-2. Loqs-PA or Loqs-PB is required for viability, but the proteins are not fully redundant: Loqs-PB is required to produce a specific subset of miRNAs. Surprisingly, Loqs-PB tunes the product size cleaved by Dicer-1 from pre-miR-307a, generating a longer miRNA isoform with a distinct seed sequence and target specificity. The mouse and human Dicer-binding partner TRBP, a homolog of Loqs-PB, similarly tunes the site of pre-miR-132 cleavage by mammalian Dicer. Thus, Dicer-binding partner proteins can change the choice of cleavage site by Dicer, producing miRNAs with different target specificities than those that would be made by Dicer alone.
|
| |
|
| Overall design |
Examination of Dicer-binding proteins on small RNA profiles of female fly heads, fly ovaries, mouse embryonic fibroblasts, and mouse tail fibroblasts.
|
| |
|
| Contributor(s) |
Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD |
| Citation(s) |
23063653 |
| Submission date |
Apr 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryuya Fukunaga |
| E-mail(s) |
fukunaga@jhmi.edu
|
| Phone |
5088561220
|
| Organization name |
Umass Medical School
|
| Department |
BMP
|
| Lab |
Zamore
|
| Street address |
364 Plantation st.
|
| City |
Worcester |
| State/province |
Ma |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
|
| Samples (24)
|
| GSM919400 |
Small RNA from female fly head of wIR |
| GSM919401 |
Small RNA from female fly head of wIR: loqsKO; loqs-PA/TM3 |
| GSM919402 |
Small RNA from female fly head of wIR: loqsKO; loqs-PB/TM3 |
| GSM919403 |
Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PB/TM3 |
| GSM919404 |
Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PD/TM3 |
| GSM919405 |
Small RNA from female fly head of wIR: loqsKO; loqs-PB, loqs-PD/TM3 |
| GSM919406 |
Small RNA from female fly head of wIR: loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3 |
| GSM919407 |
Small RNA from female fly head of wIR: loqsKO/CyO |
| GSM919408 |
Small RNA from female fly head of wIR: loqsf00791 |
| GSM919409 |
Small RNA from female fly head of wIR: loqsf00791/CyO |
| GSM919410 |
Small RNA from fly ovary of w1118 |
| GSM919411 |
Small RNA from fly ovary of w1118: loqsKO; loqs-PA/TM3 |
| GSM919412 |
Small RNA from fly ovary of w1118: loqsKO; loqs-PB/TM3 |
| GSM919413 |
Small RNA from fly ovary of w1118: loqsKO; loqs-PA, loqs-PB/TM3 |
| GSM919414 |
Small RNA from fly ovary of w1118: loqsKO; loqs-PA, loqs-PD/TM3 |
| GSM919415 |
Small RNA from fly ovary of w1118: loqsKO; loqs-PB, loqs-PD/TM3 |
| GSM919416 |
Small RNA from fly ovary of w1118: loqsKO; loqs-PA, loqs-PB, loqs-PD/TM3 |
| GSM919417 |
Small RNA from fly ovary of w1118: loqsKO/CyO |
| GSM919418 |
Small RNA from fly ovary of w1118: loqsf00791 |
| GSM919419 |
Small RNA from fly ovary of w1118: loqsf00791/CyO |
| GSM919420 |
Small RNA from wild-type mouse embryonic fibroblast |
| GSM919421 |
Small RNA from PACT-/- mouse embryonic fibroblast |
| GSM919422 |
Small RNA from TRBP-/+ mouse tail fibroblast |
| GSM919423 |
Small RNA from TRBP-/- mouse tail fibroblast |
|
| Relations |
| BioProject |
PRJNA159933 |
| SRA |
SRP012343 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37443_RAW.tar |
2.1 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...