Reference Report

Reference
Citation	Ruby, J.G., Stark, A., Johnston, W.K., Kellis, M., Bartel, D.P., Lai, E.C. (2007). Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17(12): 1850--1864. (Export to RIS)
FlyBase ID	FBrf0202916
Publication Type	Research paper
PubMed ID	17989254
PubMed Abstract	MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these predictions. In addition to validating 20 of our top 45 predictions for novel miRNA loci, the large-scale sequencing identified many miRNAs that had not been predicted. In total, 59 novel genes were identified, increasing our tally of confirmed fly miRNAs to 148. The large-scale sequencing also refined the identities of previously known miRNAs and provided insights into their biogenesis and expression. Many miRNAs were expressed in particular developmental contexts, with a large cohort of miRNAs expressed primarily in imaginal discs. Conserved miRNAs typically were expressed more broadly and robustly than were nonconserved miRNAs, and those conserved miRNAs with more restricted expression tended to have fewer predicted targets than those expressed more broadly. Predicted targets for the expanded set of microRNAs substantially increased and revised the miRNA-target relationships that appear conserved among the fly species. Insights were also provided into miRNA gene evolution, including evidence for emergent regulatory function deriving from the opposite arm of the miRNA hairpin, exemplified by mir-10, and even the opposite strand of the DNA, exemplified by mir-iab-4.
DOI	10.1101/gr.6597907
Related Publication(s)
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Associated Information
Comments
Associated Files
Other Information
Secondary IDs
Language of Publication	English
Additional Languages of Abstract
Also Published As
Parent Publication
Publication Type	Journal
Abbreviation	Genome Res.
Title	Genome Research
Publication Year	1995-
ISBN/ISSN	1088-9051
Data from Reference
Genes (139)
	ban bft CR31044 Grip84 let-7 mir-1 mir-2a-1 mir-2a-2 mir-2b-1 mir-2b-2 mir-2c mir-3 mir-4 mir-5 mir-6-1 mir-6-2 mir-6-3 mir-7 mir-8 mir-9a mir-9b mir-9c mir-10 mir-11 mir-12 mir-13a mir-13b-1 mir-13b-2 mir-14 mir-31a mir-31b mir-33 mir-34 mir-79 mir-87 mir-92a mir-92b mir-100 mir-124 mir-125 mir-133 mir-137 mir-184 mir-190 mir-193 mir-210 mir-219 mir-252 mir-263b mir-274 mir-275 mir-276a mir-276b mir-277 mir-278 mir-279 mir-280 mir-281-1 mir-281-2 mir-282 mir-283 mir-284 mir-285 mir-286 mir-287 mir-288 mir-289 mir-303 mir-304 mir-305 mir-306 mir-307a mir-308 mir-309 mir-310 mir-311 mir-312 mir-313 mir-314 mir-315 mir-316 mir-317 mir-318 mir-375 mir-927 mir-929 mir-932 mir-954 mir-955 mir-956 mir-957 mir-958 mir-959 mir-960 mir-961 mir-963 mir-964 mir-965 mir-966 mir-967 mir-968 mir-969 mir-970 mir-971 mir-972 mir-973 mir-974 mir-975 mir-976 mir-977 mir-978 mir-979 mir-980 mir-981 mir-982 mir-983-1 mir-983-2 mir-984 mir-985 mir-986 mir-987 mir-988 mir-989 mir-990 mir-991 mir-992 mir-993 mir-994 mir-995 mir-996 mir-997 mir-998 mir-999 mir-1000 mir-1001 mir-1002 mir-iab-4 Nnf1a qsm