DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Josef Redolfi; Yinxiu Zhan; Christian Valdes-Quezada; Mariya Kryzhanovska; Isabel Guerreiro; Vytautas Iesmantavicius; Tim Pollex; Ralph S Grand; Eskeatnaf Mulugeta; Jop Kind; Guido Tiana; Sebastien A Smallwood; Wouter de Laat; Luca Giorgetti

doi:10.1038/s41594-019-0231-0

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Josef Redolfi, Yinxiu Zhan, Christian Valdes-Quezada, Mariya Kryzhanovska, Isabel Guerreiro, Vytautas Iesmantavicius, Tim Pollex, Ralph S Grand, Eskeatnaf Mulugeta, Jop Kind, Guido Tiana, Sebastien A Smallwood, Wouter de Laat, Luca Giorgetti

Hubrecht Institute

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

56 Citations (Scopus)

Abstract

Current understanding of chromosome folding is largely reliant on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after chromatin crosslinking. To measure chromosome structure in vivo, quantitatively and without crosslinking and ligation, we implemented a modified version of DNA adenine methyltransferase identification (DamID) named DamC, which combines DNA methylation-based detection of chromosomal interactions with next-generation sequencing and biophysical modeling of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of topologically associating domains (TADs), CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining DamC with transposon-mediated genomic engineering shows that new loops can be formed between ectopic and endogenous CTCF sites, which redistributes physical interactions within TADs. DamC provides the first crosslinking- and ligation-free demonstration of the existence of key structural features of chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.

Original language	English
Pages (from-to)	471-480
Number of pages	10
Journal	Nature Structural & Molecular Biology
Volume	26
Issue number	6
DOIs	https://doi.org/10.1038/s41594-019-0231-0
Publication status	Published - Jun 2019

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Redolfi, J., Zhan, Y., Valdes-Quezada, C., Kryzhanovska, M., Guerreiro, I., Iesmantavicius, V., Pollex, T., Grand, R. S., Mulugeta, E., Kind, J., Tiana, G., Smallwood, S. A., de Laat, W., & Giorgetti, L. (2019). DamC reveals principles of chromatin folding in vivo without crosslinking and ligation. Nature Structural & Molecular Biology, 26(6), 471-480. https://doi.org/10.1038/s41594-019-0231-0

@article{86e61634b3314f87b9e60adba04ad1fe,

title = "DamC reveals principles of chromatin folding in vivo without crosslinking and ligation",

abstract = "Current understanding of chromosome folding is largely reliant on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after chromatin crosslinking. To measure chromosome structure in vivo, quantitatively and without crosslinking and ligation, we implemented a modified version of DNA adenine methyltransferase identification (DamID) named DamC, which combines DNA methylation-based detection of chromosomal interactions with next-generation sequencing and biophysical modeling of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of topologically associating domains (TADs), CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining DamC with transposon-mediated genomic engineering shows that new loops can be formed between ectopic and endogenous CTCF sites, which redistributes physical interactions within TADs. DamC provides the first crosslinking- and ligation-free demonstration of the existence of key structural features of chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.",

author = "Josef Redolfi and Yinxiu Zhan and Christian Valdes-Quezada and Mariya Kryzhanovska and Isabel Guerreiro and Vytautas Iesmantavicius and Tim Pollex and Grand, {Ralph S} and Eskeatnaf Mulugeta and Jop Kind and Guido Tiana and Smallwood, {Sebastien A} and {de Laat}, Wouter and Luca Giorgetti",

year = "2019",

month = jun,

doi = "10.1038/s41594-019-0231-0",

language = "English",

volume = "26",

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journal = "Nature Structural & Molecular Biology",

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Redolfi, J, Zhan, Y, Valdes-Quezada, C, Kryzhanovska, M, Guerreiro, I, Iesmantavicius, V, Pollex, T, Grand, RS, Mulugeta, E, Kind, J, Tiana, G, Smallwood, SA, de Laat, W & Giorgetti, L 2019, 'DamC reveals principles of chromatin folding in vivo without crosslinking and ligation', Nature Structural & Molecular Biology, vol. 26, no. 6, pp. 471-480. https://doi.org/10.1038/s41594-019-0231-0

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T1 - DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

AU - Redolfi, Josef

AU - Zhan, Yinxiu

AU - Valdes-Quezada, Christian

AU - Kryzhanovska, Mariya

AU - Guerreiro, Isabel

AU - Iesmantavicius, Vytautas

AU - Pollex, Tim

AU - Grand, Ralph S

AU - Mulugeta, Eskeatnaf

AU - Kind, Jop

AU - Tiana, Guido

AU - Smallwood, Sebastien A

AU - de Laat, Wouter

AU - Giorgetti, Luca

PY - 2019/6

Y1 - 2019/6

N2 - Current understanding of chromosome folding is largely reliant on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after chromatin crosslinking. To measure chromosome structure in vivo, quantitatively and without crosslinking and ligation, we implemented a modified version of DNA adenine methyltransferase identification (DamID) named DamC, which combines DNA methylation-based detection of chromosomal interactions with next-generation sequencing and biophysical modeling of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of topologically associating domains (TADs), CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining DamC with transposon-mediated genomic engineering shows that new loops can be formed between ectopic and endogenous CTCF sites, which redistributes physical interactions within TADs. DamC provides the first crosslinking- and ligation-free demonstration of the existence of key structural features of chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.

AB - Current understanding of chromosome folding is largely reliant on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after chromatin crosslinking. To measure chromosome structure in vivo, quantitatively and without crosslinking and ligation, we implemented a modified version of DNA adenine methyltransferase identification (DamID) named DamC, which combines DNA methylation-based detection of chromosomal interactions with next-generation sequencing and biophysical modeling of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of topologically associating domains (TADs), CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining DamC with transposon-mediated genomic engineering shows that new loops can be formed between ectopic and endogenous CTCF sites, which redistributes physical interactions within TADs. DamC provides the first crosslinking- and ligation-free demonstration of the existence of key structural features of chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.

U2 - 10.1038/s41594-019-0231-0

DO - 10.1038/s41594-019-0231-0

M3 - Article

C2 - 31133702

SN - 1545-9993

VL - 26

SP - 471

EP - 480

JO - Nature Structural & Molecular Biology

JF - Nature Structural & Molecular Biology

IS - 6

ER -

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

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