Regulated Distributed
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More Great Information on Regulated Distributed:
Plant cis-NAT siRNAs (Genomebiology)
Background: Many eukaryotic genomes encode cis-natural antisense transcripts
(cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that
are processed by the RNAi machinery into small interfering RNAs (siRNAs). A
few so-called nat-siRNAs have been reported in plants, mammals, Drosophila,
and yeasts. However, many questions remain regarding the features and
biogenesis of nat-siRNAs. Results: Through deep sequencing, we identified more
than 17,000 unique siRNAs corresponding to cis-NATs from biotic and abiotic
stress-challenged Arabidopsis thaliana and 56,000 from abiotic stress-treated
rice. These siRNAs were enriched in the overlapping regions of NATs and
exhibited either site-specific or distributed patterns, often with strand
bias. Out of 1,439 and 767 cis-NAT pairs identified in Arabidopsis and rice,
respectively, 84 and 119 could generate at least 10 siRNAs per million reads
from the overlapping regions. Among them, 16 cis-NAT pairs from Arabidopsis
and 34 from rice gave rise to nat-siRNAs exclusively in the overlap regions.
Genetic analysis showed that the overlapping double-stranded RNAs could be
processed by Dicer-like 1 (DCL1) and/or DCL3. The DCL3-dependent nat-siRNAs
were also dependent on RNA-dependent RNA polymerase 2 (RDR2) and plant-
specific RNA Polymerase IV (PolIV), whereas only a fraction of DCL1- dependent
nat-siRNAs was RDR- and PolIV-dependent. ...