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| Status |
Public on Sep 08, 2006 |
| Title |
Small RNA identification in Arabidopsis thaliana using 454 data |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Expression profiling by MPSS
|
| Summary |
The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. By analyzing an rdr2 loss-of-function mutant using two different parallel sequencing technologies, MPSS and 454, we characterized the complement of miRNAs expressed in Arabidopsis inflorescence to considerable depth. Nearly all known miRNAs were enriched in this mutant and we identified 13 new miRNAs, all of which were relatively low abundance and constitute new families. Trans-acting siRNAs (ta-siRNAs) were even more highly enriched. Computational and gel blot analyses suggested that the minimal number of miRNAs in Arabidopsis is approximately 155. The size profile of small RNAs in rdr2 reflected enrichment of 21-nt miRNAs and other classes of siRNAs like ta-siRNAs, and a significant reduction in 24-nt heterochromatic siRNAs. Other classes of small RNAs were found to be RDR2-independent, particularly those derived from long inverted repeats and a subset of tandem repeats. The small RNA populations in other Arabidopsis small RNA biogenesis mutants were also examined; a dcl2/3/4 triple mutant showed a similar pattern to rdr2, whereas dcl1-7 and rdr6 showed reductions in miRNAs and ta-siRNAs consistent with their activities in the biogenesis of these types of small RNAs. Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs.
Keywords: small RNA sequences generated by 454 sequencing
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| Overall design |
Small RNAs identified from inflorescence tissues.
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| |
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| Contributor(s) |
Lu C, Meyers BC, Green PJ |
| Citation(s) |
16954541 |
| |
| Submission date |
Jul 18, 2006 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
bmeyers@danforthcenter.org
|
| Phone |
314-587-1422
|
| Organization name |
Donald Danforth Plant Science Center
|
| Lab |
Meyers lab
|
| Street address |
975 N Warson Road
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL2675 |
Small RNA identification in Arabidopsis thaliana using modified MPSS |
| GPL4011 |
Small RNAs identified using 454 sequencing |
|
| Samples (6)
|
| GSM120717 |
rdr2, mixed stage inflorescence small RNA MPSS set |
| GSM121453 |
rdr2, mixed stage inflorescence small RNA 454 set |
| GSM121454 |
rdr6, mixed stage inflorescence small RNA 454 set |
| GSM121455 |
Col-0, mixed stage inflorescence small RNA 454 set |
| GSM121456 |
dcl1-7, mixed stage inflorescence small RNA 454 set |
| GSM121457 |
dcl234, mixed stage inflorescence small RNA 454 set |
|
| Relations |
| BioProject |
PRJNA96199 |
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