Genome-Wide Profiling and Analysis of Arabidopsis siRNAs Export

@article{citeulike:1237036, 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.}, author = {Kasschau, Kristin D. and Fahlgren, Noah and Chapman, Elisabeth J. and Sullivan, Christopher M. and Cumbie, Jason S. and Givan, Scott A. and Carrington, James C.}, citeulike-article-id = {1237036}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pbio.0050057}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17298187}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17298187}, day = {1}, doi = {10.1371/journal.pbio.0050057}, journal = {PLoS Biology}, keywords = {profiling, smrna}, month = {March}, number = {3}, pages = {e57+}, posted-at = {2008-11-21 21:58:42}, priority = {2}, title = {Genome-Wide Profiling and Analysis of Arabidopsis siRNAs}, url = {http://dx.doi.org/10.1371/journal.pbio.0050057}, volume = {5}, year = {2007} }

TY - JOUR ID - citeulike:1237036 L3 - citeulike-article-id:1237036 N2 - 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. IS - 3 JF - PLoS Biology TI - Genome-Wide Profiling and Analysis of Arabidopsis siRNAs VL - 5 SP - e57 KW - profiling KW - smrna AU - Kasschau, Kristin AU - Fahlgren, Noah AU - Chapman, Elisabeth AU - Sullivan, Christopher AU - Cumbie, Jason AU - Givan, Scott AU - Carrington, James PY - 2007/03/01/ UR - http://dx.doi.org/10.1371/journal.pbio.0050057 ER -