TOPOLOGICAL MECHANISMS OF DNA BREAK REPAIR IN LYMPHOCYTES

Summary Mammalian genomes are subject to a constant barrage of damage from metabolites, external agents, or physiologic processes, including transcription and replication. Developing lymphocytes also target double- strand breaks (DSBs) to antigen receptor loci during V(D)J recombination. To maintain genomic stability, DSBs must be repaired with high fidelity, minimizing oncogenic alterations such as chromosomal deletions and translocations. The DSB response extensively revises flanking chromatin via ATM-mediated phosphorylation of the histone variant H2Ax, producing γH2Ax, which spreads for 100s of kb around a DSB. In somatic cells, most of which are non-cycling, γH2Ax domains serve as chromatin-based platforms to facilitate repair by the non- homologous end joining (NHEJ) and, likely, as adherent surfaces to hold broken chromosome ends together. Indeed, ends are destabilized in cells lacking ATM or H2Ax, which have elevated levels of translocations. Thus, a deeper understanding of mechanisms that coordinate DSB repair and sequester ends from the rest of the genome remains an important goal. In this regard, links between repair, transcription, and epigenetic landscapes around DSBs are emerging. A feature that bridges many of these processes is the 3D conformation of chromatin, which determines the range of chromosomal contacts made by a persistent DSB. The applicant has shown that the topological “environment” of a DSB in non-cycling lymphocytes determines the spread and contours of γH2Ax domains, paralleling chromosome contacts of the break site. In addition, transcription of genes within γH2Ax domains was repressed, perhaps minimizing introduction of new breaks associated with RNA polymerase readthrough. A key finding from the prior funding period was that DSBs near the border of topologically-associated domains (TADs) produce highly asymmetric γH2Ax platforms on each chromosome end – one of which is very short – which may enhance disassociation of chromosome ends when the break persists. Indeed, genomic alterations, including those associated with cancer, are enriched near topological borders. Launching from these discoveries, the applicant now proposes to define the functional relationships between chromosome topology and DSB repair outcomes. Overarching hypotheses for three aims of the project are: (i) persistent DSBs adjacent to TAD borders will generate distinct profiles of repair products due to unstable association of chromosome ends, promoting extensive deletions and translocations, (ii) the mechanism of TAD formation, called loop extrusion, is required for generation of DDR platforms; impairment of this process will deleteriously affect repair outcomes, and (iii) transcription within a γH2Ax domain harboring a persistent DSB will enhance the probability of its deletional repair to an expressed gene with which it contacts. Together, the proposed project will fill fundamental knowledge gaps about how DSB responses integrate spatial, transcriptional, and chromatin-based mechanisms to sequester chromosome ends for efficient repair, minimizing their oncogenic potential in somatic cells.