Abstract
Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.
Highlights
Small RNAs are approximately 20–30 nucleotide non-coding RNA molecules that play a key role in the regulation of genome function[1]
LC8 is distinguished amongst the polymerase IV (PolIV)-dependent locus classes in containing significant numbers of RDR2-independent loci (31% of the LC8 loci are identified as RDR2-independent), of loci with a high ratio of 21/22 to 23/24 sRNAs (16% of the LC8 loci), and loci associated with mRNA expression (28% of the LC8 loci)
We have generated a detailed map of sRNA loci in Arabidopsis based on large volumes of sequencing data
Summary
Small RNAs (sRNAs) are approximately 20–30 nucleotide non-coding RNA molecules that play a key role in the regulation of genome function[1]. The set of small RNA loci identified within LC1-3 is unique in significantly associating with genes, with 79.2% of the loci overlapping genes falling in one of the three locus classes.
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