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      siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction

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          Abstract

          RNA interference (RNAi) is a technique used for transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS). PTGS is an ubiquitous basic biological phenomenon involved in the regulation of transcript abundance and plants’ immune response to viruses. PTGS also mediates genomic stability by silencing of retroelements. RNAi has become an important research tool for studying gene function by strong and selective suppression of target genes. Here, we present si-Fi, a software tool for design optimization of RNAi constructs necessary for specific target gene knock-down. It offers efficiency prediction of RNAi sequences and off-target search, required for the practical application of RNAi. si-Fi is an open-source (CC BY-SA license) desktop software that works in Microsoft Windows environment and can use custom sequence databases in standard FASTA format.

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          RNA interference is mediated by 21- and 22-nucleotide RNAs.

          S. Elbashir (2001)
          Double-stranded RNA (dsRNA) induces sequence-specific posttranscriptional gene silencing in many organisms by a process known as RNA interference (RNAi). Using a Drosophila in vitro system, we demonstrate that 21- and 22-nt RNA fragments are the sequence-specific mediators of RNAi. The short interfering RNAs (siRNAs) are generated by an RNase III-like processing reaction from long dsRNA. Chemically synthesized siRNA duplexes with overhanging 3' ends mediate efficient target RNA cleavage in the lysate, and the cleavage site is located near the center of the region spanned by the guiding siRNA. Furthermore, we provide evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the siRNA-protein complex.
          Article 0 comments Cited 535 times – based on 0 reviews     Review now
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            Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism.

            Pietro D Spanu, James C. Abbott, Joëlle Amselem … (2010)
            Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.
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              The barley Mlo gene: a novel control element of plant pathogen resistance.

              Rainer Büschges, Karin Hollricher, Ralph Panstruga … (1997)
              Mutation-induced recessive alleles (mlo) of the barley Mlo locus confer a leaf lesion phenotype and broad spectrum resistance to the fungal pathogen, Erysiphe graminis f. sp. hordei. The gene has been isolated using a positional cloning approach. Analysis of 11 mutagen-induced mlo alleles revealed mutations leading in each case to alterations of the deduced Mlo wild-type amino acid sequence. Susceptible intragenic recombinants, isolated from mlo heteroallelic crosses, show restored Mlo wild-type sequences. The deduced 60 kDa protein is predicted to be membrane-anchored by at least six membrane-spanning helices. The findings are compatible with a dual negative control function of the Mlo protein in leaf cell death and in the onset of pathogen defense; absence of Mlo primes the responsiveness for the onset of multiple defense functions.
              Article 0 comments Cited 251 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Journal
                Journal ID (nlm-ta): Front Plant Sci
                Journal ID (iso-abbrev): Front Plant Sci
                Journal ID (publisher-id): Front. Plant Sci.
                Title: Frontiers in Plant Science
                Publisher: Frontiers Media S.A.
                ISSN (Electronic): 1664-462X
                Publication date (Electronic): 15 August 2019
                Publication date Collection: 2019
                Volume: 10
                Electronic Location Identifier: 1023
                Affiliations
                [1] 1Leibniz Institute of Plant Genetics and Crop Plant Research , Seeland, Germany
                [2] 2Institute of Cellular and Molecular Botany, University of Bonn , Bonn, Germany
                [3] 3Physics II Institute, University of Giessen , Giessen, Germany
                Author notes

                Edited by: Dapeng Wang, University of Leeds, United Kingdom

                Reviewed by: Firoz Ahmed, Jeddah University, Saudi Arabia; Shaoli Das, National Institutes of Health (NIH), United States

                *Correspondence: Dimitar Douchkov, douchkov@ 123456ipk-gatersleben.de

                This article was submitted to Bioinformatics and Computational Biology, a section of the journal Frontiers in Plant Science

                †In memoriam: Patrick Schweizer passed away last 09 March 2018.

                Article
                DOI: 10.3389/fpls.2019.01023
                PMC ID: 6704232
                PubMed ID: 31475020
                SO-VID: 94ed2acd-34ae-438d-9c48-61171f2ad047
                Copyright © Copyright © 2019 Lück, Kreszies, Strickert, Schweizer, Kuhlmann and Douchkov
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                Date received : 14 February 2019
                Date accepted : 22 July 2019
                Page count
                Figures: 6, Tables: 3, Equations: 0, References: 64, Pages: 12, Words: 5607
                Categories
                Subject: Plant Science
                Subject: Methods

                ScienceOpen disciplines: Plant science & Botany
                Keywords: si-fi,rna interface,off-target,rnai design,rnai efficiency prediction,posttranscriptional gene silencing
                Data availability:
                ScienceOpen disciplines: Plant science & Botany
                Keywords: si-fi, rna interface, off-target, rnai design, rnai efficiency prediction, posttranscriptional gene silencing

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