CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells

Widia Soochit; Frank Sleutels; Gregoire Stik; Marek Bartkuhn; Sreya Basu; Silvia C. Hernandez; Sarra Merzouk; Enrique Vidal; Ruben Boers; Joachim Boers; Michael van der Reijden; Bart Geverts; Wiggert A. van Cappellen; Mirjam van den Hout; Zeliha Ozgur; Wilfred F.J. van IJcken; Joost Gribnau; Rainer Renkawitz; Thomas Graf; Adriaan Houtsmuller; Frank Grosveld; Ralph Stadhouders; Niels Galjart

doi:10.1038/s41556-021-00722-w

CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells

Widia Soochit, Frank Sleutels, Gregoire Stik, Marek Bartkuhn, Sreya Basu, Silvia C. Hernandez, Sarra Merzouk, Enrique Vidal, Ruben Boers, Joachim Boers, Michael van der Reijden, Bart Geverts, Wiggert A. van Cappellen, Mirjam van den Hout, Zeliha Ozgur, Wilfred F.J. van IJcken, Joost Gribnau, Rainer Renkawitz, Thomas Graf, Adriaan HoutsmullerFrank Grosveld^*, Ralph Stadhouders^*, Niels Galjart^*

^*Corresponding author for this work

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

34 Citations (Scopus)

Abstract

The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8–ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.

Original language	English
Pages (from-to)	881-893
Number of pages	13
Journal	Nature Cell Biology
Volume	23
Issue number	8
DOIs	https://doi.org/10.1038/s41556-021-00722-w
Publication status	Published - 29 Jul 2021

Bibliographical note

Funding Information:
We would like to thank I. Zampeta for performing the Dnmt3a western blots, and R. van der Linden, R. Janssens and M. de Bruijn for performing flow cytometry. This work was supported by grants from the Netherlands Organisation for Scientific Research (ALW 822.02.018) and the Dutch Cancer Society (KWF EMCR 2008-4109). G.S. was supported by a Marie Skłodowska-Curie fellowship (H2020-MSCA-IF-2016, miRStem) and by the ‘Fundación Científica de la Asociación Española Contra el Cáncer’. R.S. is supported by the Netherlands Organization for Scientific Research (VENI 91617114) and an Erasmus MC Fellowship.

Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature Limited.

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10.1038/s41556-021-00722-w

http://repositori.upf.edu/bitstream/10230/48420/1/Soochit_ncb_ctcf.pdf

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Soochit, W., Sleutels, F., Stik, G., Bartkuhn, M., Basu, S., Hernandez, S. C., Merzouk, S., Vidal, E., Boers, R., Boers, J., van der Reijden, M., Geverts, B., van Cappellen, W. A., van den Hout, M., Ozgur, Z., van IJcken, W. F. J., Gribnau, J., Renkawitz, R., Graf, T., ... Galjart, N. (2021). CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells. Nature Cell Biology, 23(8), 881-893. https://doi.org/10.1038/s41556-021-00722-w

@article{ee16f2aeb378435e9868eae040ec70f2,

title = "CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells",

abstract = "The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8–ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.",

author = "Widia Soochit and Frank Sleutels and Gregoire Stik and Marek Bartkuhn and Sreya Basu and Hernandez, {Silvia C.} and Sarra Merzouk and Enrique Vidal and Ruben Boers and Joachim Boers and {van der Reijden}, Michael and Bart Geverts and {van Cappellen}, {Wiggert A.} and {van den Hout}, Mirjam and Zeliha Ozgur and {van IJcken}, {Wilfred F.J.} and Joost Gribnau and Rainer Renkawitz and Thomas Graf and Adriaan Houtsmuller and Frank Grosveld and Ralph Stadhouders and Niels Galjart",

note = "Funding Information: We would like to thank I. Zampeta for performing the Dnmt3a western blots, and R. van der Linden, R. Janssens and M. de Bruijn for performing flow cytometry. This work was supported by grants from the Netherlands Organisation for Scientific Research (ALW 822.02.018) and the Dutch Cancer Society (KWF EMCR 2008-4109). G.S. was supported by a Marie Sk{\l}odowska-Curie fellowship (H2020-MSCA-IF-2016, miRStem) and by the {\textquoteleft}Fundaci{\'o}n Cient{\'i}fica de la Asociaci{\'o}n Espa{\~n}ola Contra el C{\'a}ncer{\textquoteright}. R.S. is supported by the Netherlands Organization for Scientific Research (VENI 91617114) and an Erasmus MC Fellowship. Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature Limited.",

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month = jul,

day = "29",

doi = "10.1038/s41556-021-00722-w",

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Soochit, W, Sleutels, F, Stik, G, Bartkuhn, M, Basu, S, Hernandez, SC, Merzouk, S, Vidal, E, Boers, R , Boers, J , van der Reijden, M, Geverts, B, van Cappellen, WA , van den Hout, M , Ozgur, Z, van IJcken, WFJ, Gribnau, J, Renkawitz, R, Graf, T, Houtsmuller, A , Grosveld, F , Stadhouders, R & Galjart, N 2021, 'CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells', Nature Cell Biology, vol. 23, no. 8, pp. 881-893. https://doi.org/10.1038/s41556-021-00722-w

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AU - Soochit, Widia

AU - Sleutels, Frank

AU - Stik, Gregoire

AU - Bartkuhn, Marek

AU - Basu, Sreya

AU - Hernandez, Silvia C.

AU - Merzouk, Sarra

AU - Vidal, Enrique

AU - Boers, Ruben

AU - Boers, Joachim

AU - van der Reijden, Michael

AU - Geverts, Bart

AU - van Cappellen, Wiggert A.

AU - van den Hout, Mirjam

AU - Ozgur, Zeliha

AU - van IJcken, Wilfred F.J.

AU - Gribnau, Joost

AU - Renkawitz, Rainer

AU - Graf, Thomas

AU - Houtsmuller, Adriaan

AU - Grosveld, Frank

AU - Stadhouders, Ralph

AU - Galjart, Niels

N1 - Funding Information: We would like to thank I. Zampeta for performing the Dnmt3a western blots, and R. van der Linden, R. Janssens and M. de Bruijn for performing flow cytometry. This work was supported by grants from the Netherlands Organisation for Scientific Research (ALW 822.02.018) and the Dutch Cancer Society (KWF EMCR 2008-4109). G.S. was supported by a Marie Skłodowska-Curie fellowship (H2020-MSCA-IF-2016, miRStem) and by the ‘Fundación Científica de la Asociación Española Contra el Cáncer’. R.S. is supported by the Netherlands Organization for Scientific Research (VENI 91617114) and an Erasmus MC Fellowship. Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature Limited.

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N2 - The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8–ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.

AB - The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8–ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.

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JO - Nature Cell Biology

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CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells

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