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Scoop.it!
CRISPR-Cas9 is widely used to edit the genome by studying genes of interest and modifying disease-associated genes. 
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Scoop.it!
BigField GEG Tech's insight:
A library of plasmids expressing two gRNAs allows for the mapping of combinatorial genetic interactions with the CRISPR system. Results in cancer cells suggest that cellular context is an important factor for the interaction network.
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Scoop.it!
The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation of on-target gRNA activity data for 10,592 SpCas9 gRNAs. Integrating these with complementary published data, we train a deep learning model, CRISPRon, on 23,902 gRNAs. Compared to existing tools, CRISPRon exhibits significantly higher prediction performances on four test datasets not overlapping with training data used for the development of these tools. Furthermore, we present an interactive gRNA design webserver based on the CRISPRon standalone software, both available via
BigField GEG Tech's insight:
The potential of CRISPR technology is great and ranges from curing genetically engineered diseases to applications in agricultural and industrial biotechnology. However, one of the major challenges is selecting the right gRNA to guide the Cas 9 protein to the right place in the DNA. Researchers at the University of Aarhus and the University of Copenhagen have therefore developed a new method that makes CRISPR gene editing more precise than conventional methods. The new method selects, based on the researchers' new data and implementation of an algorithm, the most suitable gRNAs to help the CRISPR-Cas9 protein with high-precision editing in the right place in our DNA. In their study, they quantified the efficiency of gRNA molecules for more than 10,000 different sites. The work was done using a massive high-throughput library-based method.
Scoop.it!
A tool for genome-wide design of CRISPR guide RNAs reduces off-target effects and facilitates targeting of the non-coding genome.
BigField GEG Tech's insight:
Here, scientists present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. They also show that the trie data structure of GuideScan enables the design of gRNAs that are more specific than those designed by existing tools.
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One of the drawbacks of genome editing is that there are growing concerns about mutations and off-target effects. Researchers then hypothesized that current editing protocols that use Cas9 cause excessive DNA cleavage, resulting in some of the mutations. To test this hypothesis, the researchers built a system called "AIMS" in mouse cells, which assessed Cas9 activity separately for each chromosome. Their results showed that the commonly used method was associated with very high editing activity. They determined that this high activity caused some of the undesirable side effects, so they looked for gRNA editing methods that could suppress it. They found that an additional cytosine extension at the 5' end of the gRNA was effective as a "safeguard" against overactivity and controlled DNA cleavage. As a result of this study, the first mathematical model of the correlation between various genome editing patterns and Cas9 activity was created that can maximize the desired editing efficiency by developing activity-regulating gRNAs with appropriate Cas9 activity.