| 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. |
Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium. Unlocking the secrets of the genome. Nature. 2009 Jun 18;459(7249):927-30. PMID: 19536255.
Bell O, Wirbelauer C, Hild M, Scharf AN, Schwaiger M, MacAlpine DM, Zilbermann F, van Leeuwen F, Bell SP, Imhof A, Garza D, Peters AH, Schübeler D. Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila. EMBO J. 2007 Dec 12;26(24):4974-84. Epub 2007 Nov 15. PMID: 18007591.
Georlette D, Ahn S, MacAlpine DM, Cheung E, Lewis PW, Beall EL, Bell SP, Speed T, Manak JR, Botchan MR. Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells. Genes Dev. 2007 Nov 15;21(22):2880-96. Epub 2007 Oct 31. PMID: 17978103.
Park EA, Macalpine DM, Orr-Weaver TL. Drosophila follicle cell amplicons as models for metazoan DNA replication: a cyclinE mutant exhibits increased replication fork elongation. Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16739-46. Epub 2007 Oct 11. 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. Epub 2006 Mar 8. PMID: 16525018.
MacAlpine DM, Bell SP. A genomic view of eukaryotic DNA replication. Chromosome Res. 2005;13(3):309-26. Review. PMID: 15868424.
MacAlpine DM, Rodríguez HK, Bell SP. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev. 2004 Dec 15;18(24):3094-105. PMID: 15601823.
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