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Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes.

Virology 392, 203-214 (2009)
DOI
Open Access Green as soon as Postprint is submitted to ZB.
Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the data set. We present evidence to Suggest that every genomic position could be a putative cleavage site for vsRNA formation, although viral genomes contain specific regions that serve as preferential sources of vsRNA production. Hotspots for vsRNAs of 21-, 22-, and 24-nt usually coincide in the same genomic regions, indicating similar target affinities among Dicer-like (DCL) enzymes. In the light Of Our results, the overall contribution of perfectly base paired (double-stranded RNA and imperfectly base paired structures within single-stranded RNA to vsRNA formation is discussed. Our census of vsRNAs extends the Current view of the distribution and composition of vsRNAs in virus-infected plants, and contributes to a better understanding of vsRNA biogenesis.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Plant-virus interactions; Plant virus; Vital small RNAs; RNA silencing; small interfering rnas; dicer-like proteins; trans-acting sirnas; arabidopsis-thaliana; silencing suppressor; argonaute proteins; antiviral defense; virus; biogenesis; micrornas
Reviewing status