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Are the current gRNA ranking prediction algorithms useful for genome editing in plants?
Introducing a new trait into a crop through conventional breeding commonly takes decades, but recently developed genome sequence modification technology has the potential to accelerate this process. One of these new breeding technologies relies on an RNA-directed DNA nuclease (CRISPR/Cas9) to cut th...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980586/ https://www.ncbi.nlm.nih.gov/pubmed/31978124 http://dx.doi.org/10.1371/journal.pone.0227994 |
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author | Naim, Fatima Shand, Kylie Hayashi, Satomi O’Brien, Martin McGree, James Johnson, Alexander A. T. Dugdale, Benjamin Waterhouse, Peter M. |
author_facet | Naim, Fatima Shand, Kylie Hayashi, Satomi O’Brien, Martin McGree, James Johnson, Alexander A. T. Dugdale, Benjamin Waterhouse, Peter M. |
author_sort | Naim, Fatima |
collection | PubMed |
description | Introducing a new trait into a crop through conventional breeding commonly takes decades, but recently developed genome sequence modification technology has the potential to accelerate this process. One of these new breeding technologies relies on an RNA-directed DNA nuclease (CRISPR/Cas9) to cut the genomic DNA, in vivo, to facilitate the deletion or insertion of sequences. This sequence specific targeting is determined by guide RNAs (gRNAs). However, choosing an optimum gRNA sequence has its challenges. Almost all current gRNA design tools for use in plants are based on data from experiments in animals, although many allow the use of plant genomes to identify potential off-target sites. Here, we examine the predictive uniformity and performance of eight different online gRNA-site tools. Unfortunately, there was little consensus among the rankings by the different algorithms, nor a statistically significant correlation between rankings and in vivo effectiveness. This suggests that important factors affecting gRNA performance and/or target site accessibility, in plants, are yet to be elucidated and incorporated into gRNA-site prediction tools. |
format | Online Article Text |
id | pubmed-6980586 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-69805862020-02-04 Are the current gRNA ranking prediction algorithms useful for genome editing in plants? Naim, Fatima Shand, Kylie Hayashi, Satomi O’Brien, Martin McGree, James Johnson, Alexander A. T. Dugdale, Benjamin Waterhouse, Peter M. PLoS One Research Article Introducing a new trait into a crop through conventional breeding commonly takes decades, but recently developed genome sequence modification technology has the potential to accelerate this process. One of these new breeding technologies relies on an RNA-directed DNA nuclease (CRISPR/Cas9) to cut the genomic DNA, in vivo, to facilitate the deletion or insertion of sequences. This sequence specific targeting is determined by guide RNAs (gRNAs). However, choosing an optimum gRNA sequence has its challenges. Almost all current gRNA design tools for use in plants are based on data from experiments in animals, although many allow the use of plant genomes to identify potential off-target sites. Here, we examine the predictive uniformity and performance of eight different online gRNA-site tools. Unfortunately, there was little consensus among the rankings by the different algorithms, nor a statistically significant correlation between rankings and in vivo effectiveness. This suggests that important factors affecting gRNA performance and/or target site accessibility, in plants, are yet to be elucidated and incorporated into gRNA-site prediction tools. Public Library of Science 2020-01-24 /pmc/articles/PMC6980586/ /pubmed/31978124 http://dx.doi.org/10.1371/journal.pone.0227994 Text en © 2020 Naim et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Naim, Fatima Shand, Kylie Hayashi, Satomi O’Brien, Martin McGree, James Johnson, Alexander A. T. Dugdale, Benjamin Waterhouse, Peter M. Are the current gRNA ranking prediction algorithms useful for genome editing in plants? |
title | Are the current gRNA ranking prediction algorithms useful for genome editing in plants? |
title_full | Are the current gRNA ranking prediction algorithms useful for genome editing in plants? |
title_fullStr | Are the current gRNA ranking prediction algorithms useful for genome editing in plants? |
title_full_unstemmed | Are the current gRNA ranking prediction algorithms useful for genome editing in plants? |
title_short | Are the current gRNA ranking prediction algorithms useful for genome editing in plants? |
title_sort | are the current grna ranking prediction algorithms useful for genome editing in plants? |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980586/ https://www.ncbi.nlm.nih.gov/pubmed/31978124 http://dx.doi.org/10.1371/journal.pone.0227994 |
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