| Our laboratory is interested in understanding the mechanisms by which the molecular architecture of the chromosome regulates fundamental biological processes such as replication and transcription. Specifically, how are replication, transcription and chromatin modification coordinated on a genomic scale to maintain genomic stability? We are addressing this question by using genomic, computational and biochemical approaches in the model organism Drosophila melanogaster.
DNA replication is an essential cell cycle event required for the timely and accurate duplication of chromosomes. Replication initiates at multiple sites (called origins of replication) distributed across each chromosome. The failure to properly regulate origin selection and activation may result in catastrophic genomic instability and potentially tumorigenesis. Recent metazoan genomic studies have demonstrated a correlation between time of DNA replication and transcriptional activity, with actively transcribed regions of the genome being replicated early. However, the underlying mechanism of this correlation remains unclear. By systematically
characterizing the replication dynamics of multiple cell types, each with distinct transcriptional programs, we will be in a position to understand how these processes are coordinated.
Another goal of the laboratory is to identify the chromosomal features that direct and regulate metazoan DNA replication. Origins of DNA replication are marked by the formation of multi-protein complex, called the preRC. Despite conservation of the proteins that comprise the preRC in all eukaryotes, very little is known about the sequence elements required for the selection and regulation of metazoan origins. We are using genomic tiling microarrays to systematically map all the sites of preRC assembly in the Drosophila genome. The high resolution mapping of thousands of replication origins will provide an unprecedented opportunity to use both computational approaches and comparative genomics to identify cis-acting elements that may regulate replication. |
| Georlette D, Ahn S, MacAlpine D, Cheung E, Lewis P, Beall E, Speed T, Manak J, and Botchan M. Genomic profiling and expression studies reveal both positive and negative roles for the Drosophila Myb-MuvB/dREAM complex in proliferating cells. 2007. Genes Dev. In Press. PMID 17978103
Bell O, Wirbelauer C, Hild M, Scharf A, Schwaiger M, MacAlpine D, Zilberman F, van Leeuwen F, Bell S, Imhof A, Garza D, Peters A, Schubeler D. Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila. 2007. EMBO
J. In Press.
Park E, MacAlpd Orr-Weaver T.ine D, an Drosophila follicle cell amplicons as models for metazoan DNA replication: A cyclinE mutant exhibits increased replication fork elongation. 2007. PNAS. PMID 17940024 Tanny RE, MacAlpine DM, Blitzblau HG, Bell SP. Genome-wide analysis of re-replication reveals inhibitory controls that target multiple stages of replication initiation. Mol Biol Cell. 2006 May;17(5):2415-23. PMID: 16525018
MacAlpine DM, Bell SP. A genomic view of eukaryotic DNA replication. Chromosome Res. 2005;13(3):309-26. Review. PMID: 15868424
Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A. 2005 May 3;102(18):6419-24. PMID: 15845769
MacAlpine DM, Rodriguez HK, Bell SP. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev. 2004 Dec 15;18(24):3094-105. PMID: 15601823
Schubeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O'Neill LP, Turner BM, Delrow J, Bell SP, Groudine M. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 2004 Jun 1;18(11):1263-71. PMID: 15175259
Claycomb JM, MacAlpine DM, Evans JG, Bell SP, Orr-Weaver TL. Visualization of replication initiation and elongation in Drosophila. J Cell Biol. 2002 Oct 28;159(2):225-36. PMID: 12403810
MacAlpine DM, Kolesar J, Okamoto K, Butow RA, Perlman PS. Replication and preferential inheritance of hypersuppressive petite mitochondrial DNA. EMBO J. 2001 Apr 2;20(7):1807-17. PMID: 11285243
MacAlpine DM, Perlman PS, Butow RA. The numbers of individual mitochondrial DNA molecules and mitochondrial DNA nucleoids in yeast are co-regulated by the general amino acid control pathway. EMBO J. 2000 Feb 15;19(4):767-75. PMID: 10675346
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