| dc.description.abstract |
<p>Small noncoding RNAs (ncRNAs) are key regulators of plant development through modulation
of the processing, stability and translation of larger RNAs. I generated small RNA
datasets comprising over 200 million aligned Illumina sequence reads covering all
major cell types of the root as well as four distinct developmental zones. These
data were analyzed for three major types of small RNAs, namely microRNAs (miRNAs),
repeat associated small interfering RNAs (ra-siRNAs), and trans-acting siRNAs (ta-siRNAs).
133 of the 243 known miRNAs were found to be expressed in the root, and most showed
tissue- or zone-specific expression patterns. My collaborators and I identified 70
new high-confidence miRNAs, and knockdown of three of the newly identified miRNAs
resulted in altered root growth phenotypes. Ra-siRNAs specify methylation by the
RNA directed DNA methylation (RdRM) pathway, requiring the generation of additional
methylation datasets. Preliminary analysis shows cell-type specific methylation patterns
that correlate with small RNA and mRNA expression. Analysis of ta-siRNAs revealed
new ta-siRNA generating loci, and a novel triggering miRNA for TAS1 loci. In summary,
our study demonstrates the power of isolating individual cell types and developmental
zones in combination with deep sequencing and computational analyses to obtain detailed
profiles of ncRNAs, as well as to significantly extend the compendium of known functional
RNAs.</p>
|
|
