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New plant study reveals a 'deeply hidden' layer of the transcriptome
Date:12/27/2007

for homing in on its RNA targets, explains Dmitry A. Belostotsky of the University of Missouri-Kansas City. On the other hand, genome-wide analyses of permanent genetic mutations often produce a complex mixture of direct and indirect effects, making it very hard to untangle. Thus, we think our strategy has a broadly-applicable value.

From a genomics perspective it really allowed us to visualize what information from the genome is actually expressed, adds co-first author Brian D. Gregory, Ph.D., a postdoctoral researcher in Eckers lab. When you knock down exosome activity, you see changes in the transcriptome that are not visible under any other circumstance.

Since the common notion is that the exosome plays a central role in bulk RNA turnover, the researchers say, they expected to find the levels of all transcripts increasing when they inactivated the exosome complex. But not everything is going up, instead the exosome mechanism seems to be very tightly regulated, says Ecker. We didnt see regions that are known to be silenced to go up, instead we found a very specific group of transcripts that are regulated in this way.

Among them are regular protein-coding RNAs, RNA processing intermediates and hundreds of non-coding RNAs, the vast majority of which hadnt been described before. These strange transcripts are associated with small RNA-producing loci as well as with repetitive sequence elements, says Gregory. They are under very tight regulation by the exosome, but we still dont know exactly what this means.

It is likely that these RNAs that are usually deeply hidden become important for genome function or stability under some circumstances, adds co-first author Julia Chekanova, an assistant at the University of Missouri-Kansas City. We need to do more work to figure out what these circumstances are.


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Contact: Gina Kirchweger
kirchweger@salk.edu
858-453-4100 x1340
Salk Institute  
Source:Eurekalert

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