Our long-term objective is to elucidate networks of eukaryotic small RNAs and their regulatory targets. We are motivated in this endeavor by the growing body of evidence that demonstrates fundamental cellular activities for diverse classes of RNAs in the 20-30 nucleotide range. One class that has received particular attention are the microRNAs, an abundant family of -22 nucleotide inhibitory RNAs that derive from hairpin precursor transcripts. It is estimated that there at least one thousand human microRNAs, which collectively regulate at least 30% of human genes. Additional classes of processed small RNAs include endogenous small interfering RNAs (siRNAs), repeat associated siRNAs, and Piwi-associated RNAs. We propose herein a focused set of experimental and computational experiments to characterize the small RNA component of the Drosophila melanogaster genome. (1) We will perform high-throughput pyrosequencing of a broad variety of libraries to obtain comprehensive coverage of expressed Drosophila small RNAs. (2) We will exploit the recent availability of a dozen sequenced fly genomes to make highly specific computational predictions of microRNA genes and microRNA targets in silico. (3) We will use microarray profiling and other molecular techniques to validate the endogenous expression of microRNAs and other novel small RNA genes. We will also perform in vivo phenotypic assays to demonstrate their biological activity. (4) We will elucidate the structures of primary microRNA transcripts by genetically stabilizing these transient species, followed by genome tiling microarray analysis. This work will culminate in a thorough annotation of the different classes of processed small RNAs and their associated precursor transcripts in Drosophila. Going beyond Drosophila, it is well documented that misregulation of small RNA pathways has tremendous adverse consequences for the development and physiology of all eukaryotic species. This comprehensive effort to uncover small RNA genes in flies will not only inform the annotation of small RNA genes in the human genome, but also lay the foundation for future studies of their normal and pathological roles. Insights gained from this genetically tractable model organism will be relevant for understanding the functional contributions of small RNAs to human disease.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01HG004261-03
Application #
7691802
Study Section
Special Emphasis Panel (ZHG1-HGR-P (J1))
Program Officer
Good, Peter J
Project Start
2007-05-04
Project End
2011-03-31
Budget Start
2009-04-01
Budget End
2010-03-31
Support Year
3
Fiscal Year
2009
Total Cost
$458,688
Indirect Cost
Name
Sloan-Kettering Institute for Cancer Research
Department
Type
DUNS #
064931884
City
New York
State
NY
Country
United States
Zip Code
10065
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Chung, Wei-Jen; Agius, Phaedra; Westholm, Jakub O et al. (2011) Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res 21:286-300

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