Abnormal temporal control of replication is observed in many diseases but causal linkages are unknown. This gap will remain incomprehensible until the mechanisms regulating replication timing during normal development are understood. The long-term goal is to understand the relationship of replication timing to cellular epigenetic states and disease. The immediate goal is to identify cis-acting DNA/chromatin elements that regulate changes in replication timing during differentiation of mouse embryonic stem cells (ESCs). Mouse ESCs are an ideal experimental system due to the availability of chromosome engineering tools, directed cell differentiation systems, and comprehensive genome-wide maps of replication timing and transcription. These maps have identified the molecular coordinates of programmed changes in replication timing that occur in 400-800kb units termed """"""""replication domains"""""""". The central hypothesis is that discrete identifiable chromatin or DNA sequence features dictate the boundaries of replication domains and the developmentally induced changes in their replication time. The rationale for this proposal is that identifying DNA/chromatin elements regulating replication timing is the essential next step in elucidating mechanisms regulating replication timing and its relationship to disease.
Aim1 will test the hypothesis that replication domains are fundamental units of chromosome structure and function that can be transferred to an ectopic location. Large pieces of cloned genomic DNA from a developmentally regulated replication domain will be introduced into a region of constitutive replication timing. Repli- cation timing of the insert and flanking DNA will be monitored during differentiation to identify the minimal sequences constituting a unit of regulation.
Aim2 will distinguish between models in which specific boundary elements punctuate temporally distinct domains vs. models of boundaries as passively replicated chromatin between actively programmed domains. Nested deletions will be engineered in developmentally controlled replication timing transition regions and the effects of deletions on the regulation of replication timing will be determined.
Aim3 will test the hypothesis that transcription within a silent late replicating domain initiates a switch to early replication. Promoter and regulatory elements controlling transcription within a developmentally regulated replication domain will be deleted, replaced with an inducible promoter, and the effects of such manipulations on the regulation of replication timing will be analyzed. Studies described here will identify cis-acting elements regulating the developmental control of replication timing. This contribution is significant because identifying regulatory elements of replication timing control is a pre-requisite to understanding the role of replication timing in chromosome-based diseases. The work proposed here is innovative in that it proposes a novel combination of chromosome engineering and directed embryonic stem cell (ESC) differentiation to address the mechanisms eliciting developmentally programmed changes in replication timing.

Public Health Relevance

Accurate duplication of chromosomes during each cell division is essential to normal growth and development. The proposed project is important for public health because abnormalities in the temporal order in which chromosome segments are duplicated have been detected in many diseases and are expected to reflect the origins of these diseases, yet we have a poor understanding of how replication timing is regulated and why it is disrupted in disease states. Thus, the proposed experiments are relevant to the part of NIH's mission that pertains to developing fundamental knowledge that will increase our understanding of the pathogenesis of disease, suggest novel treatments, and reduce the burdens of human disability.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-GGG-E (91))
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Carter, Anthony D
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Florida State University
Schools of Arts and Sciences
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Rivera-Mulia, Juan Carlos; Gilbert, David M (2016) Replication timing and transcriptional control: beyond cause and effect-part III. Curr Opin Cell Biol 40:168-78
Rivera-Mulia, Juan Carlos; Gilbert, David M (2016) Replicating Large Genomes: Divide and Conquer. Mol Cell 62:756-65
Lu, Junjie; Li, Hu; Baccei, Anna et al. (2016) Influence of ATM-Mediated DNA Damage Response on Genomic Variation in Human Induced Pluripotent Stem Cells. Stem Cells Dev 25:740-7
Libbrecht, Maxwell W; Ay, Ferhat; Hoffman, Michael M et al. (2015) Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. Genome Res 25:544-57
Dileep, Vishnu; Rivera-Mulia, Juan Carlos; Sima, Jiao et al. (2015) Large-Scale Chromatin Structure-Function Relationships during the Cell Cycle and Development: Insights from Replication Timing. Cold Spring Harb Symp Quant Biol 80:53-63
Gilbert, David M; Fraser, Peter (2015) Three Dimensional Organization of the Nucleus: adding DNA sequences to the big picture. Genome Biol 16:181
Gordon, Molly R; Pope, Benjamin D; Sima, Jiao et al. (2015) Many paths lead chromatin to the nuclear periphery. Bioessays 37:862-6
Rivera-Mulia, Juan Carlos; Buckley, Quinton; Sasaki, Takayo et al. (2015) Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells. Genome Res 25:1091-103
Dileep, Vishnu; Ay, Ferhat; Sima, Jiao et al. (2015) Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. Genome Res 25:1104-13
Gabr, Haitham; Rivera-Mulia, Juan Carlos; Gilbert, David M et al. (2015) Computing interaction probabilities in signaling networks. EURASIP J Bioinform Syst Biol 2015:10

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