Table 5. cont. miRNA Group ID D.melanogaster miRNA miR-964 miR-967 miR-977 dme-miR-964 dme-miR-967 dme-miR-977 miR-980 miR-983 miR-984 dme-miR-980 dme-miR-983 dme-miR-984 miR-986 miR-987 miR-990 miR-993 dme-miR-986 dme-miR-987 dme-miR-990 dme-miR-993 miR-995 dme-miR-995 miR-996 dme-miR-996 miR-998 dme-miR-998 miR-1001 miR-1002 dme-miR-1001 dme-miR-1002 Human Sequence-Related miRNAs 59 Sequence Full Sequence hsa-let-7g hsa-let-7i hsa-miR-98 hsa-miR-651 hsa-miR-620 hsa-let-7a hsa-let-7b hsa-let-7c hsa-let-7e hsa-let-7f hsa-let-7g hsa-let-7i hsa-miR-98 hsa-miR-202 hsa-miR-22 hsa-miR-655 hsa-let-7a hsa-let-7b hsa-let-7c hsa-let-7d hsa-let-7e hsa-let-7f hsa-let-7g hsa-let-7i hsa-miR-98 hsa-miR-513c hsa-miR-545* hsa-miR-559 hsa-miR-197 hsa-miR-99a* hsa-miR-99b* hsa-miR-556-5p hsa-miR-21* hsa-miR-29a hsa-miR-29b hsa-miR-29c hsa-miR-593* hsa-miR-28-3p hsa-miR-134 hsa-miR-708* hsa-miR-21* hsa-miR-29a hsa-miR-29b hsa-miR-29c hsa-miR-593* hsa-miR-555 hsa-miR-26a hsa-let-7a hsa-let-7d hsa-let-7f hsa-let-7g hsa-miR-100* hsa-miR-29a hsa-miR-29c Table 5. cont. miRNA Group ID D.melanogaster miRNA miR-1003 miR-1010 miR-1016 dme-miR-1003 dme-miR-1010 dme-miR-1016 MicroRNAs of Worms and Flies 59 Sequence hsa-miR-26b hsa-miR-342-3p hsa-miR-412 hsa-miR-412 Human Sequence-Related miRNAs Full Sequence 82 D. melanogaster miRNAs have homology at the 59 end with 117 human miRNAs (Dataset S13), and 40 D. melanogaster miRNAs are $70% identical with 56 human miRNAs (Dataset S14). Please refer to Dataset S15 for fly-human miRNAs with 60–69.9% overall similarity. Group IDs correspond to D. melanogaster miRNAs with human related sequences. doi:10.1371/journal.pone.0002818.t005 described—extensive 39 pairing has been suggested to act as a determinant of target specificity or regulatory sensitivity within miRNA families [41], but it is the 59 end sequences that are thought to drive target selection and major regulation. Nonethe- less, we were curious as to whether miRNAs could share significant sequence similarity at the 39 end but negligible or weak 59 similarity. We therefore probed relationships among 39 end sequences of mature C. elegans miRNAs by multiple alignments of the 39 sequence of each miRNA against 39 sequences of all the remaining miRNAs. About half of C. elegans miRNAs are $60% similar to another at their 39 end (67/139); one quarter of these are .70% identical. In general, however, the more nucleotide similarity at the 39 end, the more identical the miRNAs are at the 59 end. It may be noteworthy that within the group of miRNAs with 50–70% 39 similarity, we could identify some with extensive sequence identity at the 39 end and low 59 similarity (Figure S3). These groups are: 1) cel-lin-4, cel-miR-87; 2) cel-miR-90, cel-miR- 124 (39 region of identity also conserved to some extent in cel-miR- 80, cel-miR-81, cel-miR-82 and cel-miR-234); 3) cel-miR-81, cel- miR-799 (39 region of identity also conserved to some extent in cel- miR-80 and cel-miR-82); and 4) cel-miR-52, cel-mir-53, cel-miR- 70, cel-miR-229 and cel-miR-272. Although no data are yet available to address the potential functions of these 39-related miRNAs, their conservation suggests these 39 motifs could be important for miRNA function. For example, a hexanucleotide 39 terminal motif has recently been shown to direct hsa-miR-29b to the nucleus [77]. Searches of the C. elegans 39 miRNA motifs in Drosophila and humans identified 39 relationships of cel-miR-80 and cel-miR-799 with hsa-miR-208a, and interestingly revealed 39 relationships of hsa-miR-208a with hsa-miR-129-3p and hsa-miR-129* and of hsa-miR-124 with hsa-miR-377* (Figure S3). Thus, 39 homolo- gous sequences might reveal functional similarities among miRNAs in nematodes, flies and humans. Overall, although some 39 end similarities can be distinguished among miRNAs (even for miRNAs placed into different families), our overview of 39 end homologies among miRNAs strongly supports the current idea that 59 end miRNA sequences are much more highly conserved than 39 ends. Clustering of mir genes in C. elegans and D. melanogaster genomes miRNAs can derive from their own transcription units or from exons or introns of other genes [78]. Consecutive mir genes with PLoS ONE | www.plosone.org 12 July 2008 | Volume 3 | Issue 7 | e2818