Identifications of conserved 7-mers in 3-UTRs and microRNAs in Drosophila

@article{gu07, abstract = {BACKGROUND: MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing between the 5'-end of miRNA and the target mRNA 3'-UTRs is essential for the miRNA:mRNA recognition. Recent studies show that many seed matches in 3'-UTRs, which are fully complementary to miRNA 5'-ends, are highly conserved. Based on these features, a two-stage strategy can be implemented to achieve the de novo identification of miRNAs by requiring the complete base-pairing between the 5'-end of miRNA candidates and the potential seed matches in 3'-UTRs. RESULTS: We presented a new method, which combined multiple pairwise conservation information, to identify the frequently-occurred and conserved 7-mers in 3'-UTRs. A pairwise conservation score (PCS) was introduced to describe the conservation of all 7-mers in 3'-UTRs between any two Drosophila species. Using PCSs computed from 6 pairs of flies, we developed a support vector machine (SVM) classifier ensemble, named Cons-SVM and identified 689 conserved 7-mers including 63 seed matches covering 32 out of 38 known miRNA families in the reference dataset. In the second stage, we searched for 90 nt conserved stem-loop regions containing the complementary sequences to the identified 7-mers and used the previously published miRNA prediction software to analyze these stem-loops. We predicted 47 miRNA candidates in the genome-wide screen. CONCLUSION: Cons-SVM takes advantage of the independent evolutionary information from the 6 pairs of flies and shows high sensitivity in identifying seed matches in 3'-UTRs. Combining the multiple pairwise conservation information by the machine learning approach, we finally identified 47 miRNA candidates in D. melanogaster.}, author = {Gu, Jin and Fu, Hu and Zhang, Xuegong and Li, Yanda }, citeulike-article-id = {1888813}, doi = {http://dx.doi.org/10.1186/1471-2105-8-432}, issn = {1471-2105}, journal = {BMC Bioinformatics}, keywords = {microrna}, month = {November}, pages = {432+}, posted-at = {2007-11-09 09:56:36}, priority = {3}, publisher = {BioMed Central}, title = {Identifications of conserved 7-mers in 3-UTRs and microRNAs in Drosophila}, url = {http://dx.doi.org/10.1186/1471-2105-8-432}, volume = {8}, year = {2007} }

TY - JOUR ID - gu07 L3 - citeulike-article-id:1888813 TI - Identifications of conserved 7-mers in 3-UTRs and microRNAs in Drosophila JF - BMC Bioinformatics VL - 8 SP - 432 PB - BioMed Central SN - 1471-2105 N2 - BACKGROUND: MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing between the 5'-end of miRNA and the target mRNA 3'-UTRs is essential for the miRNA:mRNA recognition. Recent studies show that many seed matches in 3'-UTRs, which are fully complementary to miRNA 5'-ends, are highly conserved. Based on these features, a two-stage strategy can be implemented to achieve the de novo identification of miRNAs by requiring the complete base-pairing between the 5'-end of miRNA candidates and the potential seed matches in 3'-UTRs. RESULTS: We presented a new method, which combined multiple pairwise conservation information, to identify the frequently-occurred and conserved 7-mers in 3'-UTRs. A pairwise conservation score (PCS) was introduced to describe the conservation of all 7-mers in 3'-UTRs between any two Drosophila species. Using PCSs computed from 6 pairs of flies, we developed a support vector machine (SVM) classifier ensemble, named Cons-SVM and identified 689 conserved 7-mers including 63 seed matches covering 32 out of 38 known miRNA families in the reference dataset. In the second stage, we searched for 90 nt conserved stem-loop regions containing the complementary sequences to the identified 7-mers and used the previously published miRNA prediction software to analyze these stem-loops. We predicted 47 miRNA candidates in the genome-wide screen. CONCLUSION: Cons-SVM takes advantage of the independent evolutionary information from the 6 pairs of flies and shows high sensitivity in identifying seed matches in 3'-UTRs. Combining the multiple pairwise conservation information by the machine learning approach, we finally identified 47 miRNA candidates in D. melanogaster. KW - microrna AU - Gu, Jin AU - Fu, Hu AU - Zhang, Xuegong AU - Li, Yanda PY - 2007/11/08/ UR - http://dx.doi.org/10.1186/1471-2105-8-432 ER -