Cargando…

MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing

RNA interference (RNAi) is mediated by small (20–30 nucleotide) RNAs that are produced by complex processing pathways. In animals, three main classes are recognized: microRNAs (miRNAs), small-interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs). Understanding of small RNA pathways has benefi...

Descripción completa

Detalles Bibliográficos
Autores principales: Jarva, Taiya, Zhang, Jialin, Flynt, Alex
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10197562/
https://www.ncbi.nlm.nih.gov/pubmed/37214880
http://dx.doi.org/10.1101/2023.05.07.539760
_version_ 1785044575948111872
author Jarva, Taiya
Zhang, Jialin
Flynt, Alex
author_facet Jarva, Taiya
Zhang, Jialin
Flynt, Alex
author_sort Jarva, Taiya
collection PubMed
description RNA interference (RNAi) is mediated by small (20–30 nucleotide) RNAs that are produced by complex processing pathways. In animals, three main classes are recognized: microRNAs (miRNAs), small-interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs). Understanding of small RNA pathways has benefited from genetic models where key enzymatic events were identified that lead to stereotypical positioning of small RNAs relative to precursor transcripts. Increasingly there is interest in using RNAi in non-model systems due to ease of generating synthetic small RNA precursors for research and biotechnology. Unfortunately, small RNAs are often rapidly evolving, requiring investigation of a species’ endogenous small RNAs prior to deploying an RNAi approach. This can be accomplished through small non-coding RNA sequencing followed by applying various computational tools; however, the complexity and separately maintained packages lead to significant challenges for annotating global small RNA populations. To address this need, we developed a simple and efficient R package (MiSiPi-Rna) which can be used to characterize pre-selected loci with plots and statistics, aiding researchers understanding RNAi biology specific to their target species. Additionally, MiSiPi-Rna pioneers several computational approaches to identifying Dicer processing to assist annotation of miRNA and siRNA.
format Online
Article
Text
id pubmed-10197562
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Cold Spring Harbor Laboratory
record_format MEDLINE/PubMed
spelling pubmed-101975622023-05-20 MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing Jarva, Taiya Zhang, Jialin Flynt, Alex bioRxiv Article RNA interference (RNAi) is mediated by small (20–30 nucleotide) RNAs that are produced by complex processing pathways. In animals, three main classes are recognized: microRNAs (miRNAs), small-interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs). Understanding of small RNA pathways has benefited from genetic models where key enzymatic events were identified that lead to stereotypical positioning of small RNAs relative to precursor transcripts. Increasingly there is interest in using RNAi in non-model systems due to ease of generating synthetic small RNA precursors for research and biotechnology. Unfortunately, small RNAs are often rapidly evolving, requiring investigation of a species’ endogenous small RNAs prior to deploying an RNAi approach. This can be accomplished through small non-coding RNA sequencing followed by applying various computational tools; however, the complexity and separately maintained packages lead to significant challenges for annotating global small RNA populations. To address this need, we developed a simple and efficient R package (MiSiPi-Rna) which can be used to characterize pre-selected loci with plots and statistics, aiding researchers understanding RNAi biology specific to their target species. Additionally, MiSiPi-Rna pioneers several computational approaches to identifying Dicer processing to assist annotation of miRNA and siRNA. Cold Spring Harbor Laboratory 2023-05-09 /pmc/articles/PMC10197562/ /pubmed/37214880 http://dx.doi.org/10.1101/2023.05.07.539760 Text en https://creativecommons.org/licenses/by-nc/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (https://creativecommons.org/licenses/by-nc/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Jarva, Taiya
Zhang, Jialin
Flynt, Alex
MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing
title MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing
title_full MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing
title_fullStr MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing
title_full_unstemmed MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing
title_short MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing
title_sort misipi-rna: an integrated tool for characterizing small regulatory rna processing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10197562/
https://www.ncbi.nlm.nih.gov/pubmed/37214880
http://dx.doi.org/10.1101/2023.05.07.539760
work_keys_str_mv AT jarvataiya misipirnaanintegratedtoolforcharacterizingsmallregulatoryrnaprocessing
AT zhangjialin misipirnaanintegratedtoolforcharacterizingsmallregulatoryrnaprocessing
AT flyntalex misipirnaanintegratedtoolforcharacterizingsmallregulatoryrnaprocessing