Department of Microbiology and Molecular Genetics, College of Biological Sciences
DNA replication and repair: mapping and characterizing replication-induced fragile sites.
Accurate cell division requires complete duplication of nuclear DNA, providing the daughter cell with a precise copy of the encoded genomic information. For faithful replication, the replication phases of initiation, elongation and termination must be coordinated to copy the nuclear DNA once and only once per cell cycle. Faithful replication must also retain higher order epigenetic components of chromatin that confer transcriptional regulation, three-dimensional organization, and cell identity.
DNA damage can arise as a consequence of replicative stress, a phenomenon that encompasses a wide array of conditions leading to replication fork stalling or collapse. Defects in replication can lead to DNA damage and inappropriate repair can result in heritable mutations—including point mutations, deletion or duplication events, or chromosomal translocations—all of which are hallmarks of cancer. DNA replication begins with the coordinated association of over 100 proteins onto DNA at starting points -- called origins -- at tens of thousands of distinct genomic sites in mammals. Replication fork collapse results in a double-strand break (DSB) in the DNA, which requires proteins involved in homologous recombination (HR) for repair of the lesion and subsequent fork restart. By examining HR protein recruitment using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), we identified genomic loci that associated with multiple DNA replication and repair factors in response to the replication poison hydroxyurea (HU), and termed these regions early replicating fragile sites or ERFS.
The Barlow lab uses a combination of molecular biology, microscopy and genome-wide sequencing techniques to investigate the molecular and genetic factors that predispose replicating cells DNA damage and genome instability using the mouse immune system as our model. Activated B lymphocytes can have a doubling time as short as 8 hours, suggesting that these rapidly proliferating cells are particularly vulnerable to replicative stress, and may contribute to lymphomagenesis.
Grad Group Affiliations
- Biochemistry, Molecular, Cellular and Developmental Biology
- Integrative Genetics and Genomics
Specialties / Focus
- Cancer Biology
- Chromosome Biology
- Chromosome Dynamics and Nuclear Function
- Computational Biology
- DNA Repair
- Model Organism Genetics
- Molecular Genetics
- MIC 102 General Microbiology
- MIC 175 Cancer Biology
Honors and Awards
- 2008 Samuel W. Rover and Lewis Rover Award for Genetics and Development, Columbia University
- 2013 NIH Fellows Award for Research Excellence
- 2014 National Institutes of Health Career Development Award
- 2000 BA Biology Rice University
- 2008 PhD Genetics and Development Columbia Univeristy
Waisertreiger I, Popovich K, Block M, Anderson KR, and Barlow JH. Visualizing locus-specific sister chromatid exchange reveals differential patterns of replication stress-induced fragile site breakage. Oncogene. 39(6):1260-1272. 2020.
Lopes-Contreras, A.J., Specks, J., Barlow, J.H., Ambrogio, C., Desler, C., Vikinsson, S., Rodrigo-Perez, S., Green, H., Rasmussen, L.J., Murga, M., Nussenzweig, A., and Fernandez-Capetillo, O. Increased Rrm2 dosage reduces fragile site breakage and prolongs survival of ATR mutant mice. Genes Dev. 29(7):690-5. 2015.
Barlow, J. H. and Nussenzweig, A. replication initiation and genome instability: a crossroads for DNA and RNA synthesis. Cell Mol Life Sci. 71(23): 4545-59. 2014.
Barlow, J.H.*, Faryabi, R. B.*, Callen, E., Wong, N., Malhowski, A., Chen, H.T., Gutierrez-Cruz, G., Sun, H., McKinnon, P., Wright, G., Casellas, R., Robbiani, D.F., Staudt, L., Fernandez-Capetillo, O., and Nussenzweig, A. A novel class of early replicating fragile sites that contribute to genome instability in B cell lymphomas. Cell.152: 620-632, 2013.
Bothmer, A., Robbiani, D.F., Di Virgilio, M., Bunting, S.F., Klein, I.A., Feldhahn, N.A., Barlow, J.H., Chen, H., Bosque, D., Callen, E., Nussenzweig, A., and Nussenzweig, M.C. Regulation of DNA End Joining, Resection, and Immunoglobulin Class Switch Recombination by 53BP1. Molecular Cell. 42(3):319-329, 2011.
Barlow, J.H. and Rothstein, R. Timing is everything: cell cycle control of Rad52. Cell Division. 5:7, 2010.
Barlow, J.H. and Rothstein, R. The B-type cyclins and Mec1 kinase activity regulate Rad52 recruitment in S phase. EMBO Journal. 28(8):1121-30, 2009.
Barlow, J.H., Lisby, M. and Rothstein, R. Differential regulation of the cellular response to DNA double-strand breaks in G1. Molecular Cell. 30:73-85, 2008.
Lisby, M., Barlow, J.H., Burgess, R.C., and Rothstein, R. Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell. 118:699-713, 2004.