A method to discover phased siRNA loci.

Research output: Contribution to journalArticle

4 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)59-70
Number of pages12
JournalMethods in molecular biology (Clifton, N.J.)
Volume592
StatePublished - 2010

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Small Interfering RNA
Double-Stranded RNA
Nucleotides
Ribonuclease III
RNA
Transcriptome
Hydrolysis
Genome
Population

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

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A method to discover phased siRNA loci. / Axtell, Michael J.

In: Methods in molecular biology (Clifton, N.J.), Vol. 592, 2010, p. 59-70.

Research output: Contribution to journalArticle

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