Abnormal large-scale chromosome structure is a hallmark of cancer and many other human diseases, but the mechanisms linking chromosome structure to function remain unresolved. The temporal order of replication is developmentally regulated at the level of large (400-800kb) """"""""replication domains"""""""" that correspond to stable units of chromosome structure. Our long-term goal is to understand the role of largescale chromosome architecture in cell fate transitions. The objective of this application is to determine the causal interdependency of changes in replication timing and its correlated chromosome properties during human embryonic stem cell (hESC) differentiation. Our central hypothesis is that differentiation signals directiy modify replication timing to alter chromatin composition, which will in turn influence 3D folding in the next cell cycle, contributing to the robustness of transcription networks. Our rationale is that knowledge of causal relationships is an essential first step of mechanistic studies linking large-scale chromosome structure to cell fate transitions.
Aimi will determine the order in which changes in replication timing, histone modifications, 3P chromatin interactions and transcription occur in response to differentiation and their dependence upon completion of prior events. Preliminary data describe newly developed hESC differentiation and cell cycle synchronization methods that can achieve this goal.
Aim2 will test the hypothesis that human Rifl protein, which we recentiy identified as essential to maintain replication timing, is redistributed during differentiation to regulate replication timing. Gene disruption, genome wide ChlP, and single cell methods will localize Rifl and determine its role in regulating replication and transcription.
These Aims are significant because identifying causal relationships and molecular players involved will remove a major obstacle in the field, paving the way to investigate mechanisms linking large-scale chromosome structure to cell fate commitment and, ultimately, human disease. The work is innovative in developing a system to study cell cycle regulated events in response to differentiation and in pioneering investigations into the newly identified role of Rifl in replication timing during early human development.

Public Health Relevance

The proposed research is relevant to public health because it will provide fundamental insight into the biological significance of long-standing cytological correlations between chromosome structure and the pathogenesis of human disease. It will also provide insight into early human development and the role of higher-order chromosome structure in gene regulation, central to the design of strategies for gene therapy.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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University of Georgia
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Chen, Li; Qin, Zhaohui S (2017) Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale. BMC Res Notes 10:530
Sasaki, Takayo; Rivera-Mulia, Juan Carlos; Vera, Daniel et al. (2017) Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia. Exp Hematol 51:71-82.e3
Rivera-Mulia, Juan Carlos; Desprat, Romain; Trevilla-Garcia, Claudia et al. (2017) DNA replication timing alterations identify common markers between distinct progeroid diseases. Proc Natl Acad Sci U S A 114:E10972-E10980
Li, Ben; Li, Yunxiao; Qin, Zhaohui S (2017) Improving Hierarchical Models Using Historical Data with Applications in High-Throughput Genomics Data Analysis. Stat Biosci 9:73-90
Cliff, Timothy S; Wu, Tianming; Boward, Benjamin R et al. (2017) MYC Controls Human Pluripotent Stem Cell Fate Decisions through Regulation of Metabolic Flux. Cell Stem Cell 21:502-516.e9
Sasaki, Takayo; Gilbert, David M (2017) Unearthing worm replication origins. Nat Struct Mol Biol 24:195-196
Sima, Jiao; Bartlett, Daniel A; Gordon, Molly R et al. (2017) Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors. Nucleic Acids Res :
Ter Huurne, Menno; Chappell, James; Dalton, Stephen et al. (2017) Distinct Cell-Cycle Control in Two Different States of Mouse Pluripotency. Cell Stem Cell 21:449-455.e4
Wilson, Korey A; Elefanty, Andrew G; Stanley, Edouard G et al. (2016) Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification. Cell Cycle 15:2464-75
Singh, Amar M; Trost, Robert; Boward, Benjamin et al. (2016) Utilizing FUCCI reporters to understand pluripotent stem cell biology. Methods 101:4-10

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