title: Genome-wide profiling and analysis of Arabidopsis siRNAs.
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 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.
authors.affiliation: Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Kristin D
authors.initials: KD
authors.lastname: Kasschau
authors.forename: Noah
authors.initials: N
authors.lastname: Fahlgren
authors.forename: Elisabeth J
authors.initials: EJ
authors.lastname: Chapman
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Sullivan
authors.forename: Jason S
authors.initials: JS
authors.lastname: Cumbie
authors.forename: Scott A
authors.initials: SA
authors.lastname: Givan
authors.forename: James C
authors.initials: JC
authors.lastname: Carrington
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D017931:DNA Primers; D020869:Gene Expression Profiling; D018745:Genome, Plant; D034741:RNA, Small Interfering
chemical_list: D017931:DNA Primers; D034741:RNA, Small Interfering