Exosome is not related to small RNA or RdDM based silencing in plants

DOI: 10.1371/journal.pgen.1003411   PMID:  23555312

I looked at the paper The Role of the Arabidopsis Exosome in siRNA– Independent Silencing of Heterochromatic Loci.  This was an interesting topic for me, as it connected some aspects of RNA metabolism and use I hadn’t originally thought as interacting.  The paper is examining the premise that the exosome might be indirectly involved in the regulation of small RNA production and RdDM in plants, as has been reported in yeast.  This effect was previously examined in Bühler M et al. 2008, in the yeast model organism S. pombe, where exosome deficient mutants were found to have vastly altered levels of siRNAs.  This is thought to be caused by a buildup of aberrant non-degraded ncRNAs interacting with small RNAs and siRNA machinery.

The authors used small RNA sequencing to determine the global make-up of annotated small RNAs in Arabidopsis, looking for a difference in exosome deficient plants.  The authors couldn’t find an effect in small RNA quantity or distribution, considering both the type of small RNA (miRNA, genic RNA, ncRNA…) as well as the possible target location (TEs, inverted/tandem/double repeats..)

Despite the apparent lack of exosome mutation on small RNAs, the authors did find a downstream effect, where mutant plants had an increase in the quantities of RdDM-regulated heterochromatic loci.  They examined this in the context of POL IV and V mutants, in which exosome deficiency lead to a dramatic loss of regulation in these (2) loci.  Following data shows that this is not from a decrease in methylation of these sites.  Histone association is seen to be lower in these loci in exosome deficient plants, as well as an association between exosome and flanking scaffold regions, leading the group to speculate that there is a cooperative effect between these structures, acting independently of RdDM.

Looking at the data in this paper, there are still several enigmatic results that are poorly explained by their model.  Their data indicate that there is a combinatorial effect between the exosome and RNA pol V in silencing heterochromatin loci, but later data contradicts this, showing that mutant plants containing mutations in both have higher enrichment when pulled down by histone (figure 6a).  I struggled to find reasoning for this observation in the paper, but perhaps I missed it in my readings.  Despite some of these confusing points, I thought the results presented provided an interesting context for alternative forms of heterochromatin regulation, rather than RdDM. Overall a broad and interesting read.  My take-away points are 1) that the exosome in plants (as opposed to yeasts) must have some layer of insulation between RNA degradation and RdDM machinery and 2)  there are alternative forms of RNA directed heterochromatin regulation.

Hope this isn’t too far off topic, just thought it was interesting.

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