Study: Software Technology for CRISPR Deletion Experiments

A study published on March 2, 2017 in PLOS Computational Biology describes a new software technology for CRISPR deletion experiments. The software, called CRISPR Paired Excision Tool (CRISPETa), selects single guide RNAs (sgRNAs) to assist in the deletion of non-protein coding sections of DNA.

“CRISPETa is a design software that is intended for use with experimental methods. The user tells CRISPETa the target in the genome which should be deleted. CRISPETa will then return to the user the identified ideal cutting sites,” said Rory Johnson, study author and assistant professor at the National Centers of Competence in Research (NCCR) RNA & Disease, in an email to Pharmaceutical Technology. “The user then uses that information to create vectors to perform the cutting experiment. More specifically, CRISPETa provides pairs of cutting sites. These sequences are used with a system we previously designed, called ‘DECKO.’”

Double Excision CRISPR Knockout (DECKO), a technology also developed by researchers from Johnson’s laboratory, uses two sgRNAs to excise pieces of non-coding DNA. CRISPETa is designed to work in tandem with DECKO, by selecting “optimal sgRNAs for deletion of user-defined target sites,” the PLOS study noted. CRISPETa is available via a webserver or a standalone platform, and could potentially be valuable for therapeutic purposes-including the deletion of sections of non-coding DNA that may cause disease, the researchers noted in a press release.

CRISPETa is also highly scalable, making it suitable for large or small experiments, Johnson told this publication. “The scalability is one of the key advantages of CRISPETa. Present methods are manual, making them rather painstaking. CRISPETa, in contrast, is fully automated. This will be valuable for researchers who want to use this approach for high-throughput screening in the future,” Johnson noted.

In the PLOS study the researchers said that CRISPETa reliably produced deletion efficiencies targeting the enhancer and exonic fragment of the MALAT1 oncogene of greater than or equal to 50%. Johnson said the research team did not directly compare CRISPETa to other methods; however, the technologies efficiency “looks comparable to the small number of previous studies that have been published.” But still, the researchers hope to improve CRISPETa in the future.

“On the other hand, improving this to 100% efficiency is a key objective in future,” said Johnson. “However, it is likely that experimental conditions, rather than bioinformatic considerations, is where much of the improvement will be made.”

Source: Eureka Alert, PLOS Computational Biology