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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  • description.provenance : Submitted by Mary Phan (mpscanner@gmail.com) on 2011-02-04T18:48:27Z No. of bitstreams: 1 pbio.0050057.pdf: 9818104 bytes, checksum: edd83e4c01a20fdc589e03d818a54c45 (MD5)
  • description.provenance : Approved for entry into archive by Sue Kunda(sue.kunda@oregonstate.edu) on 2011-02-10T22:11:23Z (GMT) No. of bitstreams: 1 pbio.0050057.pdf: 9818104 bytes, checksum: edd83e4c01a20fdc589e03d818a54c45 (MD5)
  • description.provenance : Made available in DSpace on 2011-02-10T22:11:23Z (GMT). No. of bitstreams: 1 pbio.0050057.pdf: 9818104 bytes, checksum: edd83e4c01a20fdc589e03d818a54c45 (MD5) Previous issue date: 2007-03

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