Loss of genetic control causing inappropriate and excessive proliferation is a hallmark of cancer cells. Many of the defective regulatory pathways that lead to aberrant proliferation converge on molecular events that facilitate DNA replication. Replication regulatory pathways can provide good targets for synthetic lethality approaches that specifically kill cancer cells, but replication problems that go undetected can affect genomic integrity, triggering genomic instability that eventually might result in cancer drug resistance. Hence, many anti-cancer drugs target various aspects of DNA replication and the effectiveness of such drugs critically depends on the nature of the lesions affected in particular cancers. Because signals from cell cycle regulatory networks ultimately converge on chromatin, we aim to understand how the location and the timing of replication events are linked to particular modifications on chromatin and how replication coordinates with other chromatin transactions such as transcription, DNA repair and chromosome condensation. To that end, we take two complementary approaches. First, we use biochemical and genetic approaches to dissect DNA sequences that facilitate replication and proteins that bind such sequences in an effort to understand how cells determine where and when replication initiates. Second, we use massively parallel sequencing and replication imaging approaches to study the dynamics of DNA replication throughout the genome and determine how replication patterns respond to alterations in gene expression, chromatin modifications and drugs that perturb replication. For the first approach, we study DNA sequences (termed replicators) that facilitate initiation of DNA replication at their endogenous chromosomal sites or when they are removed from their endogenous location and transferred to ectopic chromosomal sites. In previous studies, we have identified replicator sequences in mammalian cells and dissected the genetic determinants essential for replicator activity in one genomic locus, the human beta globin locus on chromosome 11 (Aladjem, Rodewald et al. 1998;Wang, Lin et al. 2004;Wang, Lin et al. 2006). We have observed that not all potential replicators initiate replication during each cell cycle and that epigenetic processes play a role in determining if and when a particular replicator will be used during each S-phase ((Fu, Wang et al. 2006) reviewed in (Aladjem 2007)) . Recently, we identified sites of protein-DNA interactions in replicator sequences and observed that replicator activity depends on the integrity of these protein-binding sites. This year, we identified two discrete DNA-protein complexes within a replicator, RepP, located at the human beta globin locus. One RepP-associated complex includes chromatin-remodeling proteins, affects replication timing and transcriptional activity in adjacent sequences and mediates the interaction of the replicator with a distal locus control region (Huang, Fu et al. 2011). The other RepP-associated complex (unpublished) includes a member of the DCAF protein family, interacts with the pre-replication complex and is essential for initiation of DNA replication. These findings imply that the locations of initiation events depend on interactions of cell cycle regulatory proteins with sequence modules that reside within potential replicators and that the proteins that regulate initiation function in a cooperative and combinatorial manner. Such interactions may underlie the variable use of initiation sites observed in mammalian chromosomes and determine the timing of replication. To assess how replication associates with gene expression in other loci, we determined the genome-wide distribution of replication initiation events in human cells (Martin, Ryan et al. 2011). The dataset created by the genome wide studies encompasses the locations of replication initiation sites throughout the entire non-repetitive genomes of the analyzed transformed and non-transformed cells. We found that the frequency of replication initiation events increased in genomic regions that were transcribed in moderate levels but that initiation frequency was reduced in genes with high transcription rates. In concordance, high-resolution mapping showed that replication initiation events were excluded from promoter regions and enriched immediately downstream of transcribed promoters. We also found that the frequency of initiation events was affected by chromatin condensation and methylation at CpG sequences. These findings lead us to propose a model suggesting a role for replicator sequences in coordinating replication, transcription and chromatin condensation. In addition, we utilized single fiber analyses of DNA replication to identify a new pathway involved in the cellular response to replicative stress. We showed that low non-toxic doses of replication inhibitors decelerate replication by a mechanism involving the cancer-predisposing protein BLM helicase, Mus81 nuclease and ATR kinase. In early stages of the pathway, inhibitors induce transient DNA breaks that are rapidly repaired by the non-homologous end-joining (NHEJ) pathway in a reaction involving DNA-PK and XRCC4. Rapid repair of the DNA breaks prevents cell cycle arrest despite minor changes in the rate of replication fork progression(Shimura, Martin et al. 2007;Shimura, Torres et al. 2008). In other studies, we collaborated with Dr. Pommiers group in LMP to characterize the response of cancer cells to drugs that perturb DNA replication (Seiler, Conti et al. 2007;Conti, Leo et al. 2010). The combination of genome-scale sequencing of replication initiation sites and single fiber analyses provide important insights into the organization of replication initiation events and the cellular responses to signals that might perturb DNA replication. Current studies focus on the impact of the Mus81 endonuclease pathway on the frequency of initiation and the pace of DNA replication. Aladjem, M. I. (2007). """"""""Replication in context: dynamic regulation of DNA replication patterns in metazoans."""""""" Nat Rev Genet 8(8): 588-600. Aladjem, M. I., L. W. Rodewald, et al. (1998). """"""""Genetic dissection of a mammalian replicator in the human beta-globin locus."""""""" Science 281(5379): 1005-1009. Conti, C., E. Leo, et al. (2010). """"""""Inhibition of histone deacetylase in cancer cells slows down replication forks, activates dormant origins, and induces DNA damage."""""""" Cancer Res 70(11): 4470-4480. Fu, H., L. Wang, et al. (2006). """"""""Preventing gene silencing with human replicators."""""""" Nat Biotechnol 24(5): 572-576. Huang, L., H. Fu, et al. (2011). """"""""Prevention of Transcriptional Silencing by a Replicator-Binding Complex Consisting of SWI/SNF, MeCP1, and hnRNP C1/C2."""""""" Mol Cell Biol 31(16): 3472-3484. Martin, M. M., M. Ryan, et al. (2011). """"""""Genome-wide depletion of replication initiation events in highly transcribed regions."""""""" Genome Res. Seiler, J. A., C. Conti, et al. (2007). """"""""The intra-S-phase checkpoint affects both DNA replication initiation and elongation: single-cell and -DNA fiber analyses."""""""" Mol Cell Biol 27(16): 5806-5818. Shimura, T., M. M. Martin, et al. (2007). """"""""DNA-PK is involved in repairing a transient surge of DNA breaks induced by deceleration of DNA replication."""""""" J Mol Biol 367(3): 665-680. Shimura, T., M. J. Torres, et al. (2008). """"""""Bloom's syndrome helicase and Mus81 are required to induce transient double-strand DNA breaks in response to DNA replication stress."""""""" J Mol Biol 375(4): 1152-1164. Wang, L., C. M. Lin, et al. (2004). """"""""The human beta-globin replication initiation region consists of two modular independent replicators."""""""" Mol Cell Biol 24(8): 3373-3386. Wang, L., C. M. Lin, et al. (2006). """"""""Cooperative sequence modules determine replication initiation sites at the human beta-globin locus."""""""" Hum Mol Genet 15(17): 2613-2622.

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Fu, Haiqing; Baris, Adrian; Aladjem, Mirit I (2018) Replication timing and nuclear structure. Curr Opin Cell Biol 52:43-50
Utani, Koichi; Aladjem, Mirit I (2018) Extra View: Sirt1 Acts As A Gatekeeper Of Replication Initiation To Preserve Genomic Stability. Nucleus 9:261-267
Warburton, Alix; Redmond, Catherine J; Dooley, Katharine E et al. (2018) HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression. PLoS Genet 14:e1007179
Jang, Sang-Min; Redon, Christophe E; Aladjem, Mirit I (2018) Chromatin-Bound Cullin-Ring Ligases: Regulatory Roles in DNA Replication and Potential Targeting for Cancer Therapy. Front Mol Biosci 5:19
Aladjem, Mirit I; Redon, Christophe E (2017) Order from clutter: selective interactions at mammalian replication origins. Nat Rev Genet 18:101-116
Wang, Yating; Khan, Abid; Marks, Anna B et al. (2017) Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization. Nucleic Acids Res 45:2490-2502
Marks, Anna B; Fu, Haiqing; Aladjem, Mirit I (2017) Regulation of Replication Origins. Adv Exp Med Biol 1042:43-59
Utani, Koichi; Fu, Haiqing; Jang, Sang-Min et al. (2017) Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability. Nucleic Acids Res 45:7807-7824
Marks, Anna B; Smith, Owen K; Aladjem, Mirit I (2016) Replication origins: determinants or consequences of nuclear organization? Curr Opin Genet Dev 37:67-75
Smith, Owen K; Kim, RyanGuk; Fu, Haiqing et al. (2016) Distinct epigenetic features of differentiation-regulated replication origins. Epigenetics Chromatin 9:18

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