Intensive “Analyzing the properties of novel genomic editors”
On July 10-11, 2023, another bioinformatics intensive was held at Skoltech. The intensive was devoted to the study of genome editing systems.
At the introductory lecture, Matvey Kolesnik, a member of the laboratory, spoke about genome editing technologies and ways of their application. Despite the fact that such technologies (e.g. CRISPR-Cas9) are actively used nowadays, scientists continue to search for new, more optimal editing systems.
After the lecture, the participants started the practical part of the intensive, which included working on the server and writing a small script in Python.
We worked with data shared with us by colleagues from St. Petersburg Polytechnic University. They investigated Cas9 proteins from the bacteria Clostridium cellulolyticum, Capnocytophaga ochracea and Pasteurella pneumotropica.
Using bioinformatics methods, we tried to understand what targets these Cas9 enzymes are able to recognize and how new genome editing systems can be developed based on them.
The approach used to analyze Cas9 proteins (sequencing of amplicon libraries containing targets with different PAMs) is very broad - it can be applied to solve a wide variety of problems. For example, a fundamentally similar approach has recently been successfully applied to search for genes required for bacterial cell survival and phage reproduction [1], and for antidotes to amanitotoxin poisoning [2]. We hope that the new knowledge and skills that the participants acquired at the intensives will prove useful in their work and inspire them to dive deeper into the field of bioinformatics and microbial biology.
[1] F. Rousset, L. Cui, E. Siouve, C. Becavin, F. Depardieu, and D. Bikard, “Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors,” PLoS Genet, vol. 14, no. 11, p. e1007749, Nov. 2018, doi: 10.1371/journal.pgen.1007749. [2] B. Wang et al, “Identification of indocyanine green as an STT3B inhibitor against mushroom α-amanitin cytotoxicity,” Nat Commun, vol. 14, no. 1, p. 2241, May 2023, doi: 10.1038/s41467-023-37714-3.