Adaptive immunity: from CRISPR to CRIHSP?

Clustered regularly interspaced short palindromic repeats (CRISPR) confer adaptive immunity in prokaryotes against viral infection and plasmid transformation. Here, we identified abundant clustered regularly interspaced homologous stem-loop pairs (CRIHSP) within human adaptive immunity-related genes, such as antigen receptor germline genes. By examining genomic stability under activation-induced cytidine deaminase (AID) overexpression, we found that CRIHSP structures are preferred targets for AID. Through collecting and analyzing cancer cell genomic mutation databases, we discovered that these mutation sites tend to cluster toward stem-loop structures. Importantly, the frequency of stem-loop sequences within immunoglobulin heavy chain variable (IGHV) gene segments was over 3-fold higher compared to that within other regions. We concurrently observed stem-loop structures frequently flanking RSS motifs. Conservative estimates indicate a 74.07% probability of immunoglobulin heavy chain diversity (IGHD) gene segment enclosure within stem-loop. These RSS-proximal stem-loops may assemble into homologous stem-loop pair (HSP)-like intermediates and subsequent CRIHSP arrays. Our results implicate CRIHSP architectures as critical enhancer of antigen receptor gene recombination and diversification. Further molecular dissection of these processes could potentially elucidate mechanisms underlying cancer cell genomic instability, chromatin folding and dynamic regulation, gene expression control, etc.