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Genome-Wide Profiling and Analysis of Arabidopsis siRNAs Public Deposited

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  • Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants with defects in three RNA-dependent RNA polymerase (RDR) and four Dicerlike (DCL) genes. The profiling involved direct analysis using a multiplexed, parallel-sequencing strategy. Small RNAgenerating loci, especially those producing predominantly 24-nt siRNAs, were found to be highly correlated with repetitive elements across the genome. These were found to be largely RDR2- and DCL3-dependent, although alternative DCL activities were detected on a widespread level in the absence of DCL3. In contrast, no evidence for RDR2-alternative activities was detected. Analysis of RDR2- and DCL3-dependent small RNA accumulation patterns in and around protein-coding genes revealed that upstream gene regulatory sequences systematically lack siRNAgenerating activities. Further, expression profiling suggested that relatively few genes, proximal to abundant 24-nt siRNAs, are regulated directly by RDR2- and DCL3-dependent silencing. We conclude that the widespread accumulation patterns for RDR2- and DCL3-dependent siRNAs throughout the Arabidopsis genome largely reflect mechanisms to silence highly repeated sequences
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  • Kasschau, K. D., Fahlgren, N., Chapman, E. J., Sullivan, C. M., Cumbie, J. S., Givan, S. A., Carrington, J. C. (2007). Genome-Wide Profiling and Analysis of Arabidopsis siRNAs. PLoS Biology, 5(3), 0479-0493
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  • We thank Sarah Grant and Jeff Dangl for providing Col-0 leaf RNA; Heather Sweet for excellent plant management and care; Amy Shatswell for genotyping and seed preparation; and Erin McWhorter for media preparation. Author contributions. KDK, NF, EJC, and JCC conceived and designed the experiments. KDK, NF, EJC, CMS, and JSC performed the experiments. KDK, NF, CMS, JSC, SAG, and JCC analyzed the data and contributed reagents/materials/analysis tools. KDK, NF, EJC, and JCC wrote the paper. Funding. This work was supported by grants from the National Science Foundation 2010 Project (MCB-0209836), the National Institutes of Health (AI43288), and the United States Department of Agriculture (2005-35319-15280)
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