Send to

Choose Destination
RNA. 2009 May;15(5):814-22. doi: 10.1261/rna.1565109. Epub 2009 Mar 12.

An expanded seed sequence definition accounts for full regulation of the hid 3' UTR by bantam miRNA.

Author information

Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.


MicroRNAs (miRNAs) are an abundant class of approximately 22 nucleotide (nt) long noncoding RNAs that negatively regulate gene expression post-transcriptionally through imperfect base-pairing interactions with sequences in the target messenger RNA (mRNA). We examined the interactions of the bantam miRNA with the 3' untranslated region (UTR) of the hid mRNA, and a synthetic derivative, in Drosophila S2 cells in order to define the relative contributions of proposed bantam binding sites. The contribution of the bantam miRNA to repression of reporter constructs carrying different 3' UTRs was evaluated by measuring derepression of reporter expression following the transfection of bantam complementary oligoribonucleotides (anti-bantam). Systematic excision of bantam miRNA target sequences in the hid 3' UTR identified by commonly used miRNA target prediction programs failed to relieve repression to the extent predicted by the anti-bantam experiment. However, removal of additional bantam complementary sequences (with a "seed" match to nucleotide 3-9) derepressed the reporter constructs to the full extent, arguing for a less narrow definition of the seed sequence. Further support for the potential contribution of the 3-9 seed register to microRNA-mediated gene regulation is provided by the experimental validation of several novel bantam targets identified with a more relaxed search algorithm.

[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center