MOTIVATION: Small interfering RNAs (siRNAs) are produced from much longer sequences of double-stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterization of the precursors from which they are derived. RESULTS: High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated datasets. AVAILABILITY: Our methods are available as the Bioconductor (www.bioconductor.org) package segmentSeq (version 1.5.6 and above).
MOTIVATION: Small interfering RNAs (siRNAs) are produced from much longer sequences of double-stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterization of the precursors from which they are derived. RESULTS: High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated datasets. AVAILABILITY: Our methods are available as the Bioconductor (www.bioconductor.org) package segmentSeq (version 1.5.6 and above).
Authors: José Roberto Bermúdez-Barrientos; Obed Ramírez-Sánchez; Franklin Wang-Ngai Chow; Amy H Buck; Cei Abreu-Goodger Journal: Nucleic Acids Res Date: 2020-02-28 Impact factor: 16.971
Authors: Jiayu Wen; Jaaved Mohammed; Diane Bortolamiol-Becet; Harrison Tsai; Nicolas Robine; Jakub O Westholm; Erik Ladewig; Qi Dai; Katsutomo Okamura; Alex S Flynt; Dayu Zhang; Justen Andrews; Lucy Cherbas; Thomas C Kaufman; Peter Cherbas; Adam Siepel; Eric C Lai Journal: Genome Res Date: 2014-07 Impact factor: 9.043
Authors: Adrian A Valli; Bruno A C M Santos; Silvia Hnatova; Andrew R Bassett; Attila Molnar; Betty Y Chung; David C Baulcombe Journal: Genome Res Date: 2016-03-11 Impact factor: 9.043