A survey of fly and nematode small RNAs by deep sequencing

Small RNAs of -22 nt length play a variety of roles in the biology of animals by repressing the translation or stimulating the degradation of complementary messenger RNAs. Depending on the structure of their precursors, they can be categorized as either microRNAs (miRNAs) or small interfering RNAs (siRNAs). In animals, miRNAs derive from characteristic hairpins in primary transcripts through two sequential RNase III-mediated cleavages; Drosha cleaves near the base of the stem to liberate a pre-miRNA hairpin, then Dicer cleaves near the loop to generate a miRNA:miRNA* duplex. Large-scale sequencing of cDNAs derived from endogenously expressed small RNAs is used here to examine the small RNAs of the nematode Caenorhabditis elegans and the fly Drosophila melanogaster, revealing a number of previously unidentified miRNA genes from each organism. These data also revealed a novel miRNA biogenesis pathway, the mirtron pathway, in which debranched introns mimic the structural features of pre-miRNAs to enter the miRNA-processing pathway without Drosha-mediated cleavage. Mirtrons were identified in both D. melanogaster and C. elegans, some of which exhibit patterns of sequence conservation suggesting important regulatory functions. Sequencing was performed across a time-course of D. melanogaster development, permitting refinement of preexisting miRNA annotations and providing insights into miRNA biogenesis and expression. Conserved miRNAs were typically expressed more broadly and robustly than non conserved miRNAs, and miRNAs with more restricted expression tended to have fewer predicted targets. Insights were also provided into miRNA gene evolution.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Biology.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2008

Author dc:creator

• Ruby, J. Graham (James Graham)

Advisor dc:contributor.advisor

• David P. Bartel.

• Biology.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/43230

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/43230