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| Standard Gene Set Name | KASSCHAU_RDR2-DCL3-MUTANT_DIFF |
| Species | Arabidopsis thaliana |
| Brief Description | Significantly upregulated genes in rdr2 and dcl3 mutants (Table S2 PubmedID:17298187) |
| Full Description/Abstract | 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 NAxed, 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 |
| External Pathway ID/Pubmed ID | 17298187 |
| Source | Literature |
| Contributor/Author | Liming Lai and Xijin Ge |
| Organization of contributer | South Dakota State University |
| External URL | http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050057 |