Computational evidence for hundreds of non-conserved plant microRNAs
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
Computational evidence for hundreds of non-conserved plant microRNAs. / Lindow, Morten; Krogh, Anders Stærmose.
In: BMC Genomics, Vol. 6, 2005, p. 119.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Computational evidence for hundreds of non-conserved plant microRNAs
AU - Lindow, Morten
AU - Krogh, Anders Stærmose
PY - 2005
Y1 - 2005
N2 - BackgroundMicroRNAs (miRNA) are small (20-25 nt) non-coding RNA molecules that regulate gene expression through interaction with mRNA in plants and metazoans. A few hundred miRNAs are known or predicted, and most of those are evolutionarily conserved. In general plant miRNA are different from their animal counterpart: most plant miRNAs show near perfect complementarity to their targets. Exploiting this complementarity we have developed a method for identification plant miRNAs that does not rely on phylogenetic conservation.ResultsUsing the presumed targets for the known miRNA as positive controls, we list and filter all segments of the genome of length ~20 that are complementary to a target mRNA-transcript. From the positive control we recover 41 (of 92 possible) of the already known miRNA-genes (representing 14 of 16 families) with only four false positives.Applying the procedure to find possible new miRNAs targeting any annotated mRNA, we predict of 592 new miRNA genes, many of which are not conserved in other plant genomes. A subset of our predicted miRNAs is additionally supported by having more than one target that are not homologues.ConclusionThese results indicate that it is possible to reliably predict miRNA-genes without using genome comparisons. Furthermore it suggests that the number of plant miRNAs have been underestimated and points to the existence of recently evolved miRNAs in Arabidopsis.
AB - BackgroundMicroRNAs (miRNA) are small (20-25 nt) non-coding RNA molecules that regulate gene expression through interaction with mRNA in plants and metazoans. A few hundred miRNAs are known or predicted, and most of those are evolutionarily conserved. In general plant miRNA are different from their animal counterpart: most plant miRNAs show near perfect complementarity to their targets. Exploiting this complementarity we have developed a method for identification plant miRNAs that does not rely on phylogenetic conservation.ResultsUsing the presumed targets for the known miRNA as positive controls, we list and filter all segments of the genome of length ~20 that are complementary to a target mRNA-transcript. From the positive control we recover 41 (of 92 possible) of the already known miRNA-genes (representing 14 of 16 families) with only four false positives.Applying the procedure to find possible new miRNAs targeting any annotated mRNA, we predict of 592 new miRNA genes, many of which are not conserved in other plant genomes. A subset of our predicted miRNAs is additionally supported by having more than one target that are not homologues.ConclusionThese results indicate that it is possible to reliably predict miRNA-genes without using genome comparisons. Furthermore it suggests that the number of plant miRNAs have been underestimated and points to the existence of recently evolved miRNAs in Arabidopsis.
U2 - 10.1186/1471-2164-6-119
DO - 10.1186/1471-2164-6-119
M3 - Journal article
C2 - 16159385
VL - 6
SP - 119
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
ER -
ID: 1080097