CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes) is an adaptive immune system found in a wide range of prokaryotes, from commensal bacteria to exotic extremophilic archaea. The development of CRISPR-Cas into a genome editing tool has revolutionized biology and it serves to highlight how efficient and sequence-specific this system is. In the native hosts, that efficiency and sequence specificity allow bacteria and archaea to quickly recognize and degrade DNA of invaders like phages. But before a prokaryote can mount a targeted defense, it must first have a memory of that invader. While the mechanics of invader targeting have been well studied, the process of CRISPR memory formation, termed adaptation, is relatively unexplored. My research is focused on this aspect of CRISPR biology.
There are many classes and subtypes of CRISPR-Cas found in a diverse range of prokaryotes, and it follows that there are many functional variations. However, there are key common features. First there is the CRISPR array, which acts as the repository for sequence information about invaders. A stretch of regulatory DNA is followed by a series of short, directed repeats, and in between those repeats lie the "spacers" which are short sequences with homology to invader DNA. The array is transcribed to produce the guide RNAs that allow for sequence specific targeting. Second, there are the proteins that work with and are encoded near the CRISPR array. These Cas proteins are involved in adaptation (acquisition of new spacers), processing the guide RNAs, and pairing with guide RNAs to carry out invader degradation. For my research, I apply the tools and strategies of high throughput sequencing and analysis to learn how new spacers are selected, processed, and incorporated into the CRISPR array. Long term, I aim to take what we learn and use it to better understand the genetics, population dynamics, and gene transfer capabilities of microbes.