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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 59-70 |
| Number of pages | 12 |
| Journal | Methods in molecular biology (Clifton, N.J.) |
| Volume | 592 |
| DOIs | |
| State | Published - 2010 |
All Science Journal Classification (ASJC) codes
- Molecular Biology
- Genetics
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