Open Access

Nature Communications, volume 12, issue 1, publication number 41

Order and stochasticity in the folding of individual Drosophila genomes

Ulianov Sergey V ^{1, 2}

Zakharova Vlada V. ^{1, 2, 3}

Galitsyna Aleksandra A ⁴

Kos Pavel I ⁵

Polovnikov Kirill E ^{4, 6}

Flyamer Ilya M ⁷

Mikhaleva Elena A ⁸

Khrameeva Ekaterina E. ⁴

Germini Diego ³

Logacheva Mariya D ⁴

Gavrilov Alexey A ^{2, 9}

Gorsky Alexander S. ^{10, 11}

Nechaev Sergey K ^{12, 13}

Gelfand Mikhail S. ^{4, 10}

Vassetzky Yegor S. ^{3, 14}

Chertovich Alexander V ^{5, 15}

Shevelyov Yuri Y ⁸

Разин С. В. ^{1, 2}

Hide authors affiliations Show authors affiliations: 15 affiliations

Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia |

Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia |

UMR9018, CNRS, Université Paris-Sud Paris-Saclay, Institut Gustave Roussy, Villejuif, France |

⁴

Skolkovo Institute of Science and technology, Moscow, Russia |

⁵

Faculty of Physics, M.V. Lomonosov Moscow State University, Moscow, Russia |

⁶

Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, USA |

⁷

MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK |

⁸

Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, Moscow, Russia

Institute of Molecular Genetics of NRC «Kurchatov Institute»

National Research Centre "Kurchatov Institute"

⁹

Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia |

¹⁰

Institute for Information Transmission Problems (The Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia |

¹¹

Moscow Institute for Physics and Technology, Dolgoprudnyi, Russia |

¹²

P.N. Lebedev Physical Institute, Russian Academy of Sciences, Moscow, Russia |

¹³

Interdisciplinary Scientific Center Poncelet (CNRS UMI 2615), Moscow, Russia |

¹⁴

Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia |

¹⁵

Semenov Federal Research Center for Chemical Physics, Moscow, Russia |

Publication type: Journal Article

Publication date: 2021-01-04

Springer Nature

Journal: Nature Communications

Quartile SCImago

Quartile WOS

Impact factor: 16.6

ISSN: 20411723

DOI: 10.1038/s41467-020-20292-z

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PubMed ID: 33397980

General Chemistry

General Biochemistry, Genetics and Molecular Biology

General Physics and Astronomy

Abstract

Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome. Genomes are partitioned into topologically associating domains (TADs). Here the authors present single-nucleus Hi-C maps in Drosophila at 10 kb resolution, demonstrating the presence of chromatin compartments in individual nuclei, and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which resembles population TAD profiles.

By date By citations

Citations by journals

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Frontiers in Genetics	Frontiers in Genetics, 4, 8.89% Frontiers in Genetics 4 publications, 8.89%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 3, 6.67% International Journal of Molecular Sciences 3 publications, 6.67%
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Frontiers in Molecular Biosciences	Frontiers in Molecular Biosciences, 1, 2.22% Frontiers in Molecular Biosciences 1 publication, 2.22%
Nature Protocols	Nature Protocols, 1, 2.22% Nature Protocols 1 publication, 2.22%
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Current Opinion in Genetics and Development	Current Opinion in Genetics and Development, 1, 2.22% Current Opinion in Genetics and Development 1 publication, 2.22%
Trends in Biochemical Sciences	Trends in Biochemical Sciences, 1, 2.22% Trends in Biochemical Sciences 1 publication, 2.22%
Heliyon	Heliyon, 1, 2.22% Heliyon 1 publication, 2.22%
Molecular Therapy	Molecular Therapy, 1, 2.22% Molecular Therapy 1 publication, 2.22%
PLoS Computational Biology	PLoS Computational Biology, 1, 2.22% PLoS Computational Biology 1 publication, 2.22%
Biochemistry (Moscow)	Biochemistry (Moscow), 1, 2.22% Biochemistry (Moscow) 1 publication, 2.22%
Briefings in Bioinformatics	Briefings in Bioinformatics, 1, 2.22% Briefings in Bioinformatics 1 publication, 2.22%
Nucleic Acids Research	Nucleic Acids Research, 1, 2.22% Nucleic Acids Research 1 publication, 2.22%
Science	Science, 1, 2.22% Science 1 publication, 2.22%
Bioinformatics	Bioinformatics, 1, 2.22% Bioinformatics 1 publication, 2.22%
Current Opinion in Cell Biology	Current Opinion in Cell Biology, 1, 2.22% Current Opinion in Cell Biology 1 publication, 2.22%
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Citations by publishers

	1 2 3 4 5 6
Frontiers Media S.A.	Frontiers Media S.A., 6, 13.33% Frontiers Media S.A. 6 publications, 13.33%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 6, 13.33% Multidisciplinary Digital Publishing Institute (MDPI) 6 publications, 13.33%
Elsevier	Elsevier, 6, 13.33% Elsevier 6 publications, 13.33%
Springer Nature	Springer Nature, 5, 11.11% Springer Nature 5 publications, 11.11%
Oxford University Press	Oxford University Press, 3, 6.67% Oxford University Press 3 publications, 6.67%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 1, 2.22% Public Library of Science (PLoS) 1 publication, 2.22%
Pleiades Publishing	Pleiades Publishing, 1, 2.22% Pleiades Publishing 1 publication, 2.22%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 1, 2.22% American Association for the Advancement of Science (AAAS) 1 publication, 2.22%
IEEE	IEEE, 1, 2.22% IEEE 1 publication, 2.22%
	1 2 3 4 5 6

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Ulianov S. V. et al. Order and stochasticity in the folding of individual Drosophila genomes // Nature Communications. 2021. Vol. 12. No. 1. 41

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Ulianov S. V., Zakharova V. V., Galitsyna A. A., Kos P. I., Polovnikov K. E., Flyamer I. M., Mikhaleva E. A., Khrameeva E., Germini D., Logacheva M. D., Gavrilov A. A., Gorsky A. S., Nechaev S. K., Gelfand M. S., Vassetzky Y. S., Chertovich A. V., Shevelyov Y. Y., Разин С. В. Order and stochasticity in the folding of individual Drosophila genomes // Nature Communications. 2021. Vol. 12. No. 1. 41

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RIS Copy

TY - JOUR

DO - 10.1038/s41467-020-20292-z

UR - https://doi.org/10.1038%2Fs41467-020-20292-z

TI - Order and stochasticity in the folding of individual Drosophila genomes

T2 - Nature Communications

AU - Ulianov, Sergey V

AU - Zakharova, Vlada V.

AU - Galitsyna, Aleksandra A

AU - Kos, Pavel I

AU - Polovnikov, Kirill E

AU - Flyamer, Ilya M

AU - Mikhaleva, Elena A

AU - Khrameeva, Ekaterina E.

AU - Germini, Diego

AU - Logacheva, Mariya D

AU - Gavrilov, Alexey A

AU - Gorsky, Alexander S.

AU - Nechaev, Sergey K

AU - Gelfand, Mikhail S.

AU - Vassetzky, Yegor S.

AU - Chertovich, Alexander V

AU - Shevelyov, Yuri Y

AU - Разин, С. В.

PY - 2021

DA - 2021/01/04 00:00:00

PB - Springer Nature

IS - 1

VL - 12

PMID - 33397980

SN - 2041-1723

ER -

BibTex

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@article{2021_Ulianov,

author = {Sergey V Ulianov and Vlada V. Zakharova and Aleksandra A Galitsyna and Pavel I Kos and Kirill E Polovnikov and Ilya M Flyamer and Elena A Mikhaleva and Ekaterina E. Khrameeva and Diego Germini and Mariya D Logacheva and Alexey A Gavrilov and Alexander S. Gorsky and Sergey K Nechaev and Mikhail S. Gelfand and Yegor S. Vassetzky and Alexander V Chertovich and Yuri Y Shevelyov and С. В. Разин},

title = {Order and stochasticity in the folding of individual Drosophila genomes},

journal = {Nature Communications},

year = {2021},

volume = {12},

publisher = {Springer Nature},

month = {jan},

url = {https://doi.org/10.1038%2Fs41467-020-20292-z},

number = {1},

doi = {10.1038/s41467-020-20292-z}

}

Found error?

Publisher

Springer Nature

Journal

Nature Communications

Quartile SCImago

Quartile WOS

Impact factor

16.6

ISSN

20411723 (Print)

Labs

Laboratory of Microstructured Polymer Materials

Profiles

Chertovich, Alexander V