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Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
- Juan Carlos Rivera-Mulia,
- Sebo Kim,
- Haitham Gabr,
- Abhijit Chakraborty,
- Ferhat Ay,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
...as the replication timing (RT) program and is regulated during development, coordinated with 3D organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit -wide RT profiles from 15 human cell...
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Research: Allele-specific control of replication timing and genome organization during development
- Juan Carlos Rivera-Mulia,
- Andrew Dimond,
- Daniel Vera,
- Claudia Trevilla-Garcia,
- Takayo Sasaki,
- Jared Zimmerman,
- Catherine Dupont,
- Joost Gribnau,
- Peter Fraser,
- and David M. Gilbert
Genome Res. June 2018 28: 800-811; Published in Advance May 7, 2018, doi:10.1101/gr.232561.117
...Allele-specific control of replication timing and organization during development Juan Carlos Rivera-Mulia1, Andrew Dimond2, Daniel Vera3, Claudia Trevilla-Garcia1, Takayo Sasaki1, Jared Zimmerman1, Catherine Dupont4, Joost Gribnau4, Peter Fraser1,2,3 and David M. Gilbert1,3 1Department...
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Research: Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells
- Juan Carlos Rivera-Mulia,
- Quinton Buckley,
- Takayo Sasaki,
- Jared Zimmerman,
- Ruth A. Didier,
- Kristopher Nazor,
- Jeanne F. Loring,
- Zheng Lian,
- Sherman Weissman,
- Allan J. Robins,
- Thomas C. Schulz,
- Laura Menendez,
- Michael J. Kulik,
- Stephen Dalton,
- Haitham Gabr,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. August 2015 25: 1091-1103; Published in Advance June 8, 2015, doi:10.1101/gr.187989.114
...order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400–800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competence and changes in subnuclear position. We generated -wide...
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Research: Synchronized replication of genes encoding the same protein complex in fast-proliferating cells
- Ying Chen,
- Ke Li,
- Xiao Chu,
- Lucas B. Carey,
- and Wenfeng Qian
Genome Res. December 2019 29: 1929-1938; Published in Advance October 29, 2019, doi:10.1101/gr.254342.119
..., Battaglia D, Chang BH, Shirley JW, Buckley Q, Pope BD, Devidas M, Druker BJ, Gilbert DM. 2012. Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia. Genome Res 22: 1833–1844. doi:10.1101/gr.138511.112 ↵Schübeler D, Scalzo D, Kooperberg C, van Steensel B...
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Research: Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila
- Robin L. Armstrong,
- Taylor J.R. Penke,
- Brian D. Strahl,
- A. Gregory Matera,
- Daniel J. McKay,
- David M. MacAlpine,
- and Robert J. Duronio
Genome Res. November 2018 28: 1688-1700; Published in Advance October 2, 2018, doi:10.1101/gr.239913.118
...replication initiation events that results in characteristically early and late replicating regions of the (Rhind and Gilbert 2013). Such “replication timing” (RT) programs appear at early stages of animal development and ensure integrity during cell proliferation (Shermoen et al. 2010; Mantiero et al. 2011...
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Method: Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
- Maxwell W. Libbrecht,
- Ferhat Ay,
- Michael M. Hoffman,
- David M. Gilbert,
- Jeffrey A. Bilmes,
- and William Stafford Noble
Genome Res. April 2015 25: 544-557; Published in Advance February 12, 2015, doi:10.1101/gr.184341.114
.... Developmentally consistent domain boundaries are marked by identifiable sequence elements Previous research has shown that domain boundaries tend to be consistent between cell types even when the state of the domain changes. For example, when a region’s replication time is perturbed by leukemia, the boundaries...

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