Flexible guide-RNA design for CRISPR applications using Protospacer Workbench

2015 ◽  
Vol 33 (8) ◽  
pp. 805-806 ◽  
Author(s):  
Cameron Ross MacPherson ◽  
Artur Scherf
Keyword(s):  
Guide Rna ◽  
Rna Design

Guide RNA Design for CRISPR/Cas9-Mediated Potato Genome Editing

2018 ◽  
Vol 479 (1) ◽  
pp. 90-94 ◽  
Author(s):  
A. V. Khromov ◽  
V. A. Gushchin ◽  
V. I. Timerbaev ◽  
N. O. Kalinina ◽  
M. E. Taliansky ◽  
...  
Keyword(s):  
Genome Editing ◽  
Potato Genome ◽  
Guide Rna ◽  
Rna Design

scholarly journals DeepCRISPR: optimized CRISPR guide RNA design by deep learning

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Guohui Chuai ◽  
Hanhui Ma ◽  
Jifang Yan ◽  
Ming Chen ◽  
Nanfang Hong ◽  
...  
Keyword(s):  
Deep Learning ◽  
Guide Rna ◽  
Rna Design

scholarly journals CRISPR-offinder: a CRISPR guide RNA design and off-target searching tool for user-defined protospacer adjacent motif

2017 ◽  
Vol 13 (12) ◽  
pp. 1470-1478 ◽  
Author(s):  
Changzhi Zhao ◽  
Xiaoguo Zheng ◽  
Wubin Qu ◽  
Guanglei Li ◽  
Xinyun Li ◽  
...  
Keyword(s):  
Guide Rna ◽  
Protospacer Adjacent Motif ◽  
Target Searching ◽  
Rna Design

scholarly journals GuideScan software for improved single and paired CRISPR guide RNA design

2017 ◽  
Vol 35 (4) ◽  
pp. 347-349 ◽  
Author(s):  
Alexendar R Perez ◽  
Yuri Pritykin ◽  
Joana A Vidigal ◽  
Sagar Chhangawala ◽  
Lee Zamparo ◽  
...  
Keyword(s):  
Guide Rna ◽  
Rna Design

scholarly journals Complete guide RNA design for CRISPR-mediated regulation of human long noncoding RNA transcription

2018 ◽  
Author(s):  
Amir Saberi ◽  
Renjun Zhu ◽  
Chulan Kwon
Keyword(s):  
Noncoding Rna ◽  
Large Fraction ◽  
Guide Rna ◽  
Transcription Start Sites ◽  
Common Reference ◽  
Functional Studies ◽  
Short Palindromic Repeat ◽  
Genome Annotations ◽  
Rna Design ◽  
Genome Scale

AbstractTranscription inhibition and activation of long noncoding RNAs (lncRNAs) mediated by clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technology provides potential advantages in high-throughput functional genomics studies over RNA interference or overexpression platforms. In this work, we identify over 90,000 lncRNA transcription start sites (TSSs) based on the MiTranscriptome human genome annotation and design single guide RNA (sgRNA) libraries with strong predicted activities and low off-target effects for CRISPR-mediated inhibition and activation (CRISPRi/a) of their transcription. A large fraction of these TSSs correspond to putative genes that are not annotated in common reference genome annotations and have never been functionally studied. Our CRISPRi/a libraries, or their context-dependent subsets, are potentially useful in genome-scale functional studies of human lncRNAs.

scholarly journals kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9

2019 ◽  
Author(s):  
Mahmudur Rahman Hera ◽  
Amatur Rahman ◽  
Atif Rahman
Keyword(s):  
Genome Editing ◽  
Design Tool ◽  
Target Region ◽  
Guide Rna ◽  
Guide Rnas ◽  
Rna Design ◽  
Reference Genomes ◽  
Target Effects

AbstractGenome editing using the CRISPR/Cas9 system requires designing guide RNAs (sgRNA) that are efficient and specific. Guide RNAs are usually designed using reference genomes which limits their use in organisms with no or incomplete reference genomes. Here, we present kRISP-meR, a reference free method to design sgRNAs for CRISPR/Cas9 system. kRISP-meR takes as input a target region and sequenced reads from the organism to be edited and generates sgRNAs that are likely to minimize off-target effects. Our analysis indicates that kRISP-meR is able to identify majority of the guides identified by a widely used sgRNA designing tool, without any knowledge of the reference, while retaining specificity.

scholarly journals Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens

2020 ◽  
Author(s):  
Xinyi Guo ◽  
Hans-Hermann Wessels ◽  
Alejandro Méndez-Mancilla ◽  
Daniel Haro ◽  
Neville E. Sanjana
Keyword(s):  
Rna Virus ◽  
H1n1 Influenza ◽  
Model Organisms ◽  
Messenger Rnas ◽  
Protein Coding ◽  
Guide Rna ◽  
Knock Down ◽  
Guide Rnas ◽  
Rna Targeting ◽  
Rna Design

AbstractCRISPR-Cas13 mediates robust transcript knockdown in human cells through direct RNA targeting. Compared to DNA-targeting CRISPR enzymes like Cas9, RNA targeting by Cas13 is transcript- and strand-specific: It can distinguish and specifically knock-down processed transcripts, alternatively spliced isoforms and overlapping genes, all of which frequently serve different functions. Previously, we identified optimal design rules for RfxCas13d guide RNAs (gRNAs), and developed a computational model to predict gRNA efficacy for all human protein-coding genes. However, there is a growing interest to target other types of transcripts, such as noncoding RNAs (ncRNAs) or viral RNAs, and to target transcripts in other commonly-used organisms. Here, we predicted relative Cas13-driven knock-down for gRNAs targeting messenger RNAs and ncRNAs in six model organisms (human, mouse, zebrafish, fly, nematode and flowering plants) and four abundant RNA virus families (SARS-CoV-2, HIV-1, H1N1 influenza and MERS). To allow for more flexible gRNA efficacy prediction, we also developed a web-based application to predict optimal gRNAs for any RNA target entered by the user. Given the lack of Cas13 guide design tools, we anticipate this resource will facilitate CRISPR-Cas13 RNA targeting in common model organisms, emerging viral threats to human health, and novel RNA targets.

scholarly journals Enhanced guide-RNA Design and Targeting Analysis for Precise CRISPR Genome Editing of Single and Consortia of Industrially Relevant and Non-Model Organisms

2017 ◽  
Author(s):  
Brian J. Mendoza ◽  
Cong T. Trinh
Keyword(s):  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Genome Editing ◽  
Population Analysis ◽  
Strain Engineering ◽  
Pathway Engineering ◽  
Model Organisms ◽  
Guide Rna ◽  
Novel Applications ◽  
Rna Design

AbstractMotivationGenetic diversity of non-model organisms offers a repertoire of unique phenotypic features for exploration and cultivation for synthetic biology and metabolic engineering applications. To realize this enormous potential, it is critical to have an efficient genome editing tool for rapid strain engineering of these organisms to perform novel programmed functions.ResultsTo accommodate the use of CRISPR/Cas systems for genome editing across organisms, we have developed a novel method, named CASPER (CRISPR Associated Software for Pathway Engineering and Research), for identifying on- and off-targets with enhanced predictability coupled with an analysis of non-unique (repeated) targets to assist in editing any organism with various endonucleases. Utilizing CASPER, we demonstrated a modest 2.4% and significant 30.2% improvement (F-test, p<0.05) over the conventional methods for predicting on- and off-target activities, respectively. Further we used CASPER to develop novel applications in genome editing: multitargeting analysis (i.e. simultaneous multiple-site modification on a target genome with a sole guide-RNA (gRNA) requirement) and multispecies population analysis (i.e. gRNA design for genome editing across a consortium of organisms). Our analysis on a selection of industrially relevant organisms revealed a number of non-unique target sites associated with genes and transposable elements that can be used as potential sites for multitargeting. The analysis also identified shared and unshared targets that enable genome editing of single or multiple genomes in a consortium of interest. We envision CASPER as a useful platform to enhance the precise CRISPR genome editing for metabolic engineering and synthetic biology applications.

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