Alt Laboratory

The broad focus of the Alt lab is the elucidation of mechanisms that generate antigen receptor diversity in the Immune system and mechanisms that maintain genomic stability in mammalian cells. More specifically, the lab studies V(D)J recombination in developing B and T lymphocytes and IgH heavy chain class switch recombination (CSR) and somatic hypermutation in mature B lymphocytes. Studies of these processes employ biochemical approaches to elucidate molecular mechanisms by which the RAG endonuclease and Activation Induced Cytidine Deaminase function on DNA to initiate, respectively, VDJ recombination and CSR. As one example, our recent studies showed a role for the RNA exosome in targeting AID to both strands of duplex DNA. Other studies focus on the elucidation of genetic and epigenetic chromosomal processes that regulate how RAG and AID are targeted to their specific chromosomal DNA substrates. In this regard, our recent work defined a control region, termed IGCR1, in the IgH locus that regulates proximal versus distal VH usage, lineage-specificity, ordered assembly of VH, D, and JH segments and feedback regulation/allelic exclusion.

Alt Lab research projects

New studies focus on the use of novel mouse models and various types of high throughput genomic studies to elucidate how AID is targeted during CSR versus SHM in germinal center B cells and to define factors (e.g. sequence motifs, transcription patterns) that generate off-target AID activity during these processes. Other studies are aimed at elucidating roles of general DNA double strand break (DSB) repair and response pathways in VDJ recombination and CSR, and the interplay of DSB repair and response pathways in suppressing genomic instability and cancer. A major new lab research area focuses on how organization of the genome in the nucleus influences programmed gene rearrangements and chromosomal translocations. For this purpose, we have developed high throughput genomic translocation sequencing strategies to identify the translocations genome wide that can arise from fixed DSBs. This approach also identifies sites of endogenous genomic DSBs including RAG or AID off-target sequences and transcription start sites. Our goal is to establish the contribution of mechanistic elements (three dimensional genome organization, DSBs, transcription, epigenetic modifications, repair pathways, etc.) that contribute to the formation of translocations and other forms of genomic instability in mouse and human cells.

Mechanism and control of V(D)J recombination

The Alt lab continues to elucidate many new aspects of the mechanism and control of V(D)J recombination including discovering that this reaction is regulating by a process that allows the initiating RAG endonuclease V(D)J recombination factors to explore directionally within chromosomal loop domains for target substrates. His lab also continues to discover new aspects of the mechanism and regulation IgH CSR and the related process of Ig variable region exon somatic hypermutation. The lab's recent work, based on their development of high through-put methods to study DSBs and chromosomal translocations, have provided major new insights into the mechanisms that contribute to chromosomal rearrangements within the 3D genome of developing lymphocytes and cancer cells or their progenitors. The lab also has used their new approaches to identify a set of genes that recurrently break in neuronal stem and progenitor cells and, thereby, which may contribute to brain diversification and neuropsychiatric diseases and cancer. Most recently, the lab has built on their more basic molecular immunology discoveries on antibody gene assembly to generate innovative new mouse models for testing immunization strategies for eliciting HIV-1 broadly neutralizing antibodies.