Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Jiao Sima; Abhijit Chakraborty; Vishnu Dileep; Marco Michalski; Kyle N. Klein; Nicolas P. Holcomb; Jesse L. Turner; Michelle T. Paulsen; Juan Carlos Rivera-Mulia; Claudia Trevilla-Garcia; Daniel A. Bartlett; Peiyao A. Zhao; Brian K. Washburn; Elphège P. Nora; Katerina Kraft; Stefan Mundlos; Benoit G. Bruneau; Mats Ljungman; Peter Fraser; Ferhat Ay; David M. Gilbert

doi:10.1016/j.cell.2018.11.036

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Jiao Sima, Abhijit Chakraborty, Vishnu Dileep, Marco Michalski, Kyle N. Klein, Nicolas P. Holcomb, Jesse L. Turner, Michelle T. Paulsen, Juan Carlos Rivera-Mulia, Claudia Trevilla-Garcia, Daniel A. Bartlett, Peiyao A. Zhao, Brian K. Washburn, Elphège P. Nora, Katerina Kraft, Stefan Mundlos, Benoit G. Bruneau, Mats Ljungman, Peter Fraser, Ferhat AyDavid M. Gilbert

Research output: Contribution to journal › Article › peer-review

109 Scopus citations

Abstract

cis-regulatory elements control the three-dimensional compartmentalization, architecture of the genome, and replication timing in a CTCF-independent manner.

Original language	English (US)
Pages (from-to)	816-830.e18
Journal	Cell
Volume	176
Issue number	4
DOIs	https://doi.org/10.1016/j.cell.2018.11.036
State	Published - Feb 7 2019
Externally published	Yes

Bibliographical note

Funding Information:
We thank G. Church lab for advice on CRISPRology, S. Schoenfelder for cHi-C, S. Wingett for HiCUP, S. Andrews for cHi-C probe design, F. Krueger for SNPsplit, D. Vera for bioinformatics, R. Didier for FACS, C. Pye and K. Poduch for molecular cloning, C. Huffstetler for figure graphics, R. Tjian for Klf4 enhancer deletion, R. Young and N. Behnam for YY1 samples, B. Chadwick for px458, M. Mechali for SNS origin data, and A. Belmont for helpful discussions. F.A. and A.C. were partially funded by Institute Leadership Funds from La Jolla Institute for Allergy and Immunology and NIH ( R35GM128938 to F.A.). This work was supported by NIH ( R01GM083337 and U54DK107965 to D.M.G.).

Publisher Copyright:
© 2018 Elsevier Inc.

Keywords

CTCF
Dppa
ERCEs
chromatin interactions
genome architecture
replication timing
sub-nuclear compartment
super-enhancer
topologically associating domain

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Sima, J., Chakraborty, A., Dileep, V., Michalski, M., Klein, K. N., Holcomb, N. P., Turner, J. L., Paulsen, M. T., Rivera-Mulia, J. C., Trevilla-Garcia, C., Bartlett, D. A., Zhao, P. A., Washburn, B. K., Nora, E. P., Kraft, K., Mundlos, S., Bruneau, B. G., Ljungman, M., Fraser, P., ... Gilbert, D. M. (2019). Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell, 176(4), 816-830.e18. https://doi.org/10.1016/j.cell.2018.11.036

Sima, J, Chakraborty, A, Dileep, V, Michalski, M, Klein, KN, Holcomb, NP, Turner, JL, Paulsen, MT, Rivera-Mulia, JC, Trevilla-Garcia, C, Bartlett, DA, Zhao, PA, Washburn, BK, Nora, EP, Kraft, K, Mundlos, S, Bruneau, BG, Ljungman, M, Fraser, P, Ay, F & Gilbert, DM 2019, 'Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication', Cell, vol. 176, no. 4, pp. 816-830.e18. https://doi.org/10.1016/j.cell.2018.11.036

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AU - Turner, Jesse L.

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AU - Rivera-Mulia, Juan Carlos

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AU - Bartlett, Daniel A.

AU - Zhao, Peiyao A.

AU - Washburn, Brian K.

AU - Nora, Elphège P.

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AU - Bruneau, Benoit G.

AU - Ljungman, Mats

AU - Fraser, Peter

AU - Ay, Ferhat

AU - Gilbert, David M.

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Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Abstract

Bibliographical note

Keywords

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