Clustered regularly interspaced short palindromic repeats (CRISPR) are arrays of short (ca. 30bp) DNA direct repeats (DR) arranged in an alternating fashion with spacers, which are instead different oligos, of ca. 25-70bp. CRISPR arrays have so far been reported in ca. 50% of bacteria and most archaea. The spacers in the array are mobile genetic elements (MGE) acquired upon bacteriophage invasions and, therefore, represent a historical record of previous infections. Upstream of the CRISPR array sits a CRISPR-associate (Cas) gene: when a phage injects its DNA through the membrane, Cas genes recruit the appropriate transcribed spacer sequence from the CRISPR array. Such a sequence acts as a guide to binding the complex to the viral genome and allows the Cas nuclease to produce a double-strand break, neutralizing the viral threat. CRISPR-Cas is a formidable example of the acquired immune response.
In the context of genome sequencing, CRISPR research efforts have been based on short reads, and, to date, the potential of long-read sequencing technologies for CRISPR-Cas applications has not been thoroughly assessed.
Our research group, established in September 2021 and led by Dr. Giancarlo Russo, focuses on two aspects associated with CRISPR-Cas systems. On the one hand, we investigate the long-term co-evolution of bacteria and phages in vivo, both in isolation and embedded in their natural microbial communities. On the other hand, we explore epigenetic and post-transcriptional changes in cancer cells and their regulating effects on preferential isoforms’ usage, as well as how such phenotypes are affected by epigenetic editing. The common thread is to leverage the potential of long-read sequencing technologies to identify DNA and RNA modifications and dissect alternative splicing in the context of CRISPR-Cas research.