Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

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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 Dicer-like (DCL) genes. The profiling involved direct analysis using a multiplexed, parallel-sequencing strategy. Small RNA-generating 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 siRNA-generating 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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  • 5
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  • 3
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  • Work was supported by grants 1R01GM085318, 1P01HL048546, and 2R01RR020833 from NIH to JHP; by a grant from the Schroeder-Kurth Fund to JHP; by grant BFU2010-14875 from the Ministerio de Ciencia e Innovacion (MICINN) to CC; and by grants from the Fanconi Anemia Research Fund to JPK and JHP.



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