Correction: CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences

Prykhozhij, Sergey V.; Rajan, Vinothkumar; Gaston, Daniel; Berman, Jason N.

doi:10.1371/journal.pone.0138634

Cited by 20 publications

(4 citation statements)

References 1 publication

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“…Conserved regions in exon 1 for BnMLP6 loci and exons 3 and 4 for BnNPF5.12 loci were targeted by single-guide RNAs (sgRNAs) ( Supplementary Table S5 ). CRISPys ( Hyams et al ., 2018 ) and CRISPR MultiTargeter ( Prykhozhij et al , 2015 ) were used to locate suitable sgRNAs, and off-targets were predicted by Cas-OFFinder ( Bae et al , 2014 ). Four mutant combinations were created: two independent lines of quadruple BnNPF5.12 , two independent lines of 14-fold BnMLP6 and one quadruple BnNPF5.12 /octuple BnMLP6 line and a quadruple BnNPF5.12 /14-fold BnMLP6 line.…”

Section: Methodsmentioning

confidence: 99%

Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum

Dölfors,

Ilbäck,

Bejai

et al. 2024

Journal of Experimental Botany

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Plant defense responses to the soil-borne fungus Verticillium longisporum causing stem stripe disease on oilseed rape (Brassica napus) are poorly understood. In this study, a population of recombinant inbred lines (RILs) using the Arabidopsis thaliana accessions Sei-0 and Can-0 was established. Composite interval mapping, transcriptome data and T-DNA mutant screening identified the NITRATE/PEPTIDE TRANSPORTER FAMILY 5.12 gene (AtNPF5.12) as being associated with disease susceptibility in Can-0. Coimmunoprecipitation revealed interaction between AtNPF5.12 and the MAJOR LATEX PROTEIN family member AtMLP6, and fluorescence microscopy confirmed interaction in the plasma membrane and endoplasmic reticulum. CRISPR/Cas9 technology was applied to mutate the NPF5.12 and MLP6 genes in B. napus. Elevated fungal growth in the npf5.12 mlp6 double mutant of both oilseed rape and Arabidopsis demonstrated their importance in defense against V. longisporum. Colonization of this fungus depends also on available nitrates in the host root. Accordingly, the negative effect of nitrate depletion on fungal growth was less pronounced in Atnpf5.12 plants with impaired nitrate transport. In addition, suberin staining revealed involvement of the NPF5.12 and MLP6 genes in suberin barrier formation. Together, these results demonstrate a dependency of multiple plant factors that lead to successful V. longisporum root infection.

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Section: Methodsmentioning

confidence: 99%

Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum

Dölfors,

Ilbäck,

Bejai

et al. 2024

Journal of Experimental Botany

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“…Being a pair of molecular scissors, the Cas-9 protein needs an indicator as to which portion of the DNA sequence to cleave and this is where the usage of single guide RNA (SgRNA) falls in. As the Cas9 cuts and stores the viral DNA for repeated CRISPR, it removes the PAM sequence to ensure that the bacterial genome is not viewed as a target [7]. This is really relevant for scientists to learn while developing the RNA guide.…”

Section: B Single Guide Rna (Sgrna) and Its Needmentioning

confidence: 99%

Elucidative PAM/Target Sequence for CRISPR/Cas- 9 Activity in Breast Cancer Using a Computational Approach

De¹,

Biswas²

2020

IJISRT

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Directed genomic area for release and modification are indicated by the nearness of nuclease explicit PAM sequence. By hindering the signs, Herceptin can slow or stop bosom malignant growth development. The outcomes show 4 top of the line direct RNAs for altering HER2 quality, the objective arrangements that are pertinent for cleavage by that gRNA, likewise 4. The central clarification for the terrible sign of cockeyed cleavage is accepted to be in the arranging of the single guide RNA for the Cas-9 protein. This is extremely basic for researchers to know while planning guide RNA. Albeit the two guys and females are inclined to bosom malignant growth, it is more probable for females to build up this sort of disease. Be that as it may, with such a large number of HER2 receptors, bosom malignant growth cells can assemble an excessive number of development signals. The most widely recognized qualities engaged with bosom malignancy incorporate HER2, BRCA1, and BRCA2. In this manner, we propose the genomic approach of controlling the HER2 quality guided by CRISPR/Cas-9 to guarantee lesser symptoms and increasingly powerful treatment.

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“…In addition, there are several other approaches to increase the efficiency of genome editing and reduce off-target rates, such as improved design tools for single guide RNA sequences (Moreno-Mateos et al, 2015 ; Prykhozhij et al, 2015 ; Haeussler et al, 2016 ) and high-throughput functional genomics workflows (Varshney et al, 2016 ). Additionally, Kelly A. Smith et al found that single nucleotide polymorphisms (SNPs) within the target site insulate genome editing.…”

Section: Optimization Of the Crispr-cas9 System In Zebrafish Genome Ementioning

confidence: 99%

Versatile Genome Engineering Techniques Advance Human Ocular Disease Researches in Zebrafish

Zheng

Han

Xiang

et al. 2018

Front. Cell Dev. Biol.

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Over recent decades, zebrafish has been established as a sophisticated vertebrate model for studying human ocular diseases due to its high fecundity, short generation time and genetic tractability. With the invention of morpholino (MO) technology, it became possible to study the genetic basis and relevant genes of ocular diseases in vivo. Many genes have been shown to be related to ocular diseases. However, the issue of specificity is the major concern in defining gene functions with MO technology. The emergence of the first- and second-generation genetic modification tools zinc-finger nucleases (ZFNs) and TAL effector nucleases (TALENs), respectively, eliminated the potential phenotypic risk induced by MOs. Nevertheless, the efficiency of these nucleases remained relatively low until the third technique, the clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, was discovered. This review highlights the application of multiple genome engineering techniques, especially the CRISPR/Cas9 system, in the study of human ocular diseases in zebrafish.

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Correction: CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences

Cited by 20 publications

References 1 publication

Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum

Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum

Elucidative PAM/Target Sequence for CRISPR/Cas- 9 Activity in Breast Cancer Using a Computational Approach

Versatile Genome Engineering Techniques Advance Human Ocular Disease Researches in Zebrafish

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