Accurate DNA replication is essential for the maintenance of the genetic information during cell proliferation in all organisms. Defects in DNA replication factors are associated with human diseases including cancer. The complexity of eukaryotic DNA replication has previously confounded efforts to directly address biochemical mechanisms involved in this process in vitro. We have developed functional in vitro assays that allow us to overcome this limitation. We have shown previously that pre-replicative complexes (pre-RCs), which license origins in G1 phase for subsequent activation in S phase, can be reconstituted with proteins purified from budding yeast, Saccharomyces cerevisiae. Importantly, we recently found that reconstituted pre-RCs also support regulated DNA replication in vitro, exhibiting the fundamental hallmarks of cellular DNA replication. These functional assays enable us to use interdisciplinary approaches to address key problems in eukaryotic DNA replication initiation that were previously intractable, forming the basis for experiments proposed here:
Aim 1) Mcm2-7 is loaded onto origins in inactive form by the pre-RC in G1 phase. Activation of the Mcm2-7 helicase, and concomitant replisome assembly in S phase, requires the formation of a pre-initiation complex (pre-IC) around the pre-RC. The goal is to delineate the mechanism of origin activation by the pre-IC using reconstitution studies with purified budding yeast proteins. We will characterize the order of pre-IC assembly, determine the structure of pre-IC subassemblies, define the steps that induce local origin unwinding, and assign biochemical functions to pre-IC components. These studies form the basis for our long-term goal to reconstitute the entire eukaryotic DNA replication reaction in vitro.
Aim 2) Mcm2-7 complexes can passively slide along DNA prior to activation of the helicase. We will characterize this sliding ability and test its role in initiatin site determination, which has important implications for the eukaryotic origin specification mechanism. Upon activation, Mcm2-7 complexes actively translocate along DNA in a directed manner to unwind DNA at the fork. We will use biochemistry, electron microscopy, and advanced single molecule fluorescence microscopy to analyze the structural configuration of active Mcm2-7 helicase complexes and determine if Mcm2-7 hexamers of opposite orientation physically separate or remain associated during elongation. These studies will provide insight into the Mcm2-7 DNA unwinding mechanism, which underlies eukaryotic replisome organization.
Aim 3) We have found previously that two Mcm2-7 hexamers are cooperatively loaded in opposite orientation around double stranded DNA by the pre-RC. To elucidate the mechanism for Mcm2-7 loading we will define the interaction network of Cdc6 during pre-RC assembly using site-specific protein-protein cross-linking in vitro and in vivo. This approach will both identify the functional interaction partners for Cdc6 in the pre-RC and inform structural models for the pre-RC.

Public Health Relevance

Each time a cell divides it must produce an accurate copy of its genome. This process, termed DNA replication, is essential and defects in DNA replication can lead to mutations, chromosomal rearrangements and cancer. This project will generate novel assays and tools for the study of DNA replication in vitro and elucidate molecular mechanisms that control the initiation of DNA replication.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics A Study Section (MGA)
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Reddy, Michael K
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Sloan-Kettering Institute for Cancer Research
New York
United States
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Gan, Haiyun; Yu, Chuanhe; Devbhandari, Sujan et al. (2017) Checkpoint Kinase Rad53 Couples Leading- and Lagging-Strand DNA Synthesis under Replication Stress. Mol Cell 68:446-455.e3
Devbhandari, Sujan; Jiang, Jieqing; Kumar, Charanya et al. (2017) Chromatin Constrains the Initiation and Elongation of DNA Replication. Mol Cell 65:131-141
Kumar, Charanya; Remus, Dirk (2016) Eukaryotic replication origins: Strength in flexibility. Nucleus 7:292-300
Gros, Julien; Kumar, Charanya; Lynch, Gerard et al. (2015) Post-licensing Specification of Eukaryotic Replication Origins by Facilitated Mcm2-7 Sliding along DNA. Mol Cell 60:797-807