News from CRG
CRISPR-Cas9 is a molecular tool composed of two simple components: a molecular barcode, called «sgRNA», which is designed by the researcher to recognise one precise location in the genome; and a protein, Cas9, that binds to a structured loop in the sgRNA. Until recently most studies employing CRISPR-Cas9 were aimed at silencing protein-coding genes. Until recently, the experimental tools to study «non-coding DNA» have not been available.
Prof Rory Johnson, former Staff Scientist at the Computational Biology of RNA Processing laboratory of the CRG and now group leader at the University of Bern, recently created a tool based on CRISPR-Cas9, called «DECKO», which can be used to delete any desired piece of non-coding DNA. While working on DECKO, Johnson and colleagues at the Guigo’s laboratory realised that no software was available for designing the pairs of sgRNAs that are required, meaning that designing deletion experiments was time-consuming. To overcome this, the Masters student Carlos Pulido designed a software pipeline called CRISPETa.
CRISPETa is a powerful and flexible solution for designing CRISPR deletion experiments. The user tells CRISPETa what region they wish to delete, and the software returns a set of optimised pairs of sgRNAs that can directly be used by experimental researchers. Importantly, CRISPETa is designed for use by non-experts, and is available in a user friendly website, making CRISPR deletion available to the widest possible number of scientific and biomedical researchers.
Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, et al. (2017) Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PLoS Comput Biol 13(3): e1005341. doi: 10.1371/journal.pcbi.1005341