scholarly journals CRISPR‐Cereal: A Guide RNA Design Tool Integrating Regulome and Genomic Variation for Wheat, Maize and Rice

Author(s):  
Chao He ◽  
Hao Liu ◽  
Dijun Chen ◽  
Wen‐Zhao Xie ◽  
Mengxin Wang ◽  
...  
2019 ◽  
Author(s):  
Mahmudur Rahman Hera ◽  
Amatur Rahman ◽  
Atif Rahman

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.


2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Hidemi Zamora ◽  
Javier Cornejo

As suicide is the nineteenth leading cause of death worldwide, it is important to focus on discovering ways to reduce the risk of suicide-related death as much as possible. With CRISPR starting to become increasingly popular over the past few years, this gene editing technique has been used to study how to edit, turn off, or knock out multiple parts of the genome. However, research on genes related to diseases as cystic fibrosis or Alzheimer’s disease has been mainly prioritized and, even though they are of high importance as well, important issues such as suicide have been left into oblivion. Four genes have been proven to be key in influencing suicide risk, showing that not only environmental factors account for an increased possibility of death by this cause. Therefore, gene editing techniques such as CRISPR could be applied in order to knock out those genes and reduce this risk. This research used Synthego’s guide RNA design tool to predict how the use of CRISPR can be helpful in knocking out those four suicide-related genes and, consequently, in preventing suicide. The top-ranked guide RNAs for each gene were used, showing the best results possible and with the least number of off-targets, which, in turn, demonstrates the effectiveness of CRISPR as a potential technique to reduce the number of suicide-related deaths worldwide.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Daqi Wang ◽  
Chengdong Zhang ◽  
Bei Wang ◽  
Bin Li ◽  
Qiang Wang ◽  
...  

Abstract Highly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA activity for two highly specific SpCas9 variants (eSpCas9(1.1) and SpCas9-HF1) and wild-type SpCas9 (WT-SpCas9) in human cells, and obtain indel rates of over 50,000 gRNAs for each nuclease, covering ~20,000 genes. We evaluate the contribution of 1,031 features to gRNA activity and develope models for activity prediction. Our data reveals that a combination of RNN with important biological features outperforms other models for activity prediction. We further demonstrate that our model outperforms other popular gRNA design tools. Finally, we develop an online design tool DeepHF for the three Cas9 nucleases. The database, as well as the designer tool, is freely accessible via a web server, http://www.DeepHF.com/.


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

2018 ◽  
Vol 479 (1) ◽  
pp. 90-94 ◽  
Author(s):  
A. V. Khromov ◽  
V. A. Gushchin ◽  
V. I. Timerbaev ◽  
N. O. Kalinina ◽  
M. E. Taliansky ◽  
...  

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

2017 ◽  
Vol 13 (12) ◽  
pp. 1470-1478 ◽  
Author(s):  
Changzhi Zhao ◽  
Xiaoguo Zheng ◽  
Wubin Qu ◽  
Guanglei Li ◽  
Xinyun Li ◽  
...  

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

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