A Method to Discover Phased siRNA Loci
Author:
- 6 September 2009
- book chapter
- Published by Springer Nature
- Vol. 592, 59-70
Abstract
Short, interfering RNAs (siRNAs) arise from the processing of long double-stranded RNA (dsRNA) by Dicer enzymes. Dicers generate siRNA duplexes by successive hydrolysis of both strands of the dsRNA phosphodiester backbone at positions determined by measuring 21–24 nucleotides from an exposed dsRNA terminus. Therefore, a population of dsRNAs with precisely identical termini will produce siRNA spaced in regular, 21–24-nucleotide intervals. This chapter presents an easily customized and generally applicable strategy for identifying loci which produce the “phased” siRNAs diagnostic of such processing. Given the input of a large set of expressed small RNAs and of the corresponding genome or transcriptome from which the small RNAs are derived, the methodology produces a ranking of user-defined loci with respect to their likely production of phased siRNAs. Top ranked loci are candidates for further computational and biological analyses.Keywords
This publication has 25 references indexed in Scilit:
- Role of RNA polymerase IV in plant small RNA metabolismProceedings of the National Academy of Sciences, 2007
- Genome-Wide Profiling and Analysis of Arabidopsis siRNAsPLOS Biology, 2007
- A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thalianaGenes & Development, 2006
- Elucidation of the Small RNA Component of the TranscriptomeScience, 2005
- A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3 , and ARF4 genesProceedings of the National Academy of Sciences, 2005
- SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in ArabidopsisGenes & Development, 2004
- Endogenous trans-Acting siRNAs Regulate the Accumulation of Arabidopsis mRNAsMolecular Cell, 2004
- CARPEL FACTORY, a Dicer Homolog, and HEN1, a Novel Protein, Act in microRNA Metabolism in Arabidopsis thalianaCurrent Biology, 2002
- MicroRNAs in plantsGenes & Development, 2002
- Endogenous and Silencing-Associated Small RNAs in Plants[W]The Plant Cell, 2002