Frederick W. Alt
Department of Genetics
Karp Family Research Building, Rm. 09216
One Blackfan Circle
Boston, MA 02115
Lab Members: 8 postdoctoral fellows, 5 graduate students, 4 instructors/Lecuturers
The broad focus of the Alt lab is the elucidation of 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 (SHM) 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/SHM. 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. Functionally, we showed IGCR1 to employ CTCF binding elements and to be involved in the formation of large IgH loops that contain distant enhancer elements. Other studies employ genetic and cytogenetic approaches to study 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. For such studies, the lab developed several new models for B and T cell lymphomas and brain tumors. 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 universe of translocations (the translocatome) that arise from a fixed DSB. This approach also is useful for defining genomic DSBs. 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 in various mouse and human cells.
Recent Graduate Student Rotation Projects:
1. Analysis of the mechanisms of the synergy between 53BP1 and XLF in DNA end-joining through studies that employ metaphase telomere FISH and biochemical assays of end stability and processing during V(D)J recombination.
2. Elucidating of a newly discovered B cell developmental program within the gut with respect to B cell tolerance and dietary commensal antigens and development of a quantitative LM-PCR technique to measure DNA breaks within immunoglobulin genes.
3. Analysis of the role of XLF and DNA ligase 3 in end-joining and immunoglobulin IgH class switch recombination through cellular and biochemical assays of end joining.
4. Use of high through put translocation cloning to assay for translocations and DSBs in neuronal stem cells.
5. Introducing DNA DSB sites into the N-myc gene to study mechanisms that influence it's translocation.
6. Studies of cis elements that regulate IgH V(D)J rearrangement in progenitor B cells
Please see the electronic album of Alt Lab alumni, compiled by HHMI in 2010, titled: "FREDERICK W. ALT: A SUPPORTIVE MENTOR AND HARD-DRIVING SCIENTIST"
Chiarle, R., Zhang, Y., Frock, R.L., Lewis, S.M., Molinie, B., Ho, Y-J., Myers, D.R., Choi, V.W., Compagno, M., Malkin, D.J., Neuberg, D., Monti, S., Giallourakis, C.C., Gostissa, M. and Alt, F.W. (2011) Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 147, 107-119. PMC3186939 [Available on 2012/9/30]
Guo, C., Yoon, H.S., Franklin, A., Jain, S., Ebert, A., Cheng, H-L. Hansen, E., Despo, O., Bossen, C., Vettermann, C., Bates, J.G., Richards, N., Myers, D., Patel, H., Gallagher, M., Schlissel, M.S., Murre, C., Busslinger, M., Giallourakis, C.C. and Alt, F.W. (2011) CTCF binding elements mediate control of V(D)J recombination. Nature 477, 424-430. Epub 2011 Sept 11 PMC3342812
Zhang, Y., McCord, R.P., Ho, Y-J., Lajoie, B.R., Hildebrand, D.G., Simon, A.C., Becker, M.S., Alt, F.W. and Dekker, J. (2012) Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148, 908-921. Epub 2012 Feb. 16, PMC3320767
Wesemann, D.R., Portuguese, A.J., Magee, J.M., Gallagher, M.P., Zhou, X., Panchakshari, R.A. and Alt, F.W. Reprogramming IgH isotype-switched B cells to functional-grade induced pluripotent stem cells. Proc. Natl. Acad. Sci. USA In Press.
For a complete listing of publications click here.
Last Update: 7/26/2012