Open Access

Nucleic Acids Research

, volume 48 , issue 12 , pages 6699-6714

Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

Anastasiya A Zharikova ^{1, 2, 3, 4}

Natalia M Rubanova ¹

Arkadiy K Golov ^{1, 5}

Nadezhda V. Petrova ¹

Maria D. Logacheva ⁶

Omar L. Kantidze ¹

Mikhail D Magnitov ^{1, 7}

С. В. Разин ^{1, 8}

Alexey Gavrilov ^{1, 7}

Aleksandra A Galitsyna ^{1, 2, 3, 6}

Artem V. Luzhin ^{1, 7}

Sergey V. Ulianov ^{1, 8}

Andrey E. Mironov ^{2, 3, 9}

Hide authors affiliations Show authors affiliations: 9 affiliations

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

Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia |

Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia |

⁴

National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Moscow, Russia |

⁵

Mental Health Research Center, Moscow, Russia |

⁶

Skolkovo Institute of Science and Technology, Skolkovo, Russia |

⁷

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

⁸

Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia |

⁹

Faculty of Computer Science, Higher School of Economics, Moscow, Russia |

Publication type: Journal Article

Publication date: 2020-06-01

Oxford University Press

Nucleic Acids Research

scimago Q1

wos Q1

SJR: 7.776

CiteScore: 31.7

Impact factor: 13.1

ISSN: 03051048, 13624962

DOI: 10.1093/nar/gkaa457

Copy DOI

PubMed ID: 32479626

Genetics

Abstract

Abstract Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA–DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA–DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

Found

1 citation

Shidlovskii Yulii

🥼 🤝

DSc in Biological/biomedical sciences, professor

85 publications, 1 017 citations

h-index: 17

Institute of Gene Biology of the Russian Academy of Sciences

Sechenov First Moscow State Medical University

1 citation

Dashinimaev Erdem

🥼 🤝

PhD in Biological/biomedical sciences, associate professor

56 publications, 547 citations, 3 reviews

h-index: 13

Moscow Institute of Physics and Technology

Peoples' Friendship University of Russia

Pirogov Russian National Research Medical University

Buryat State University named after D. Banzarov

Research interests

Cellular reprogramming

Genome Editing

Transgenic and knockout animals

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Zharikova A. A. et al. Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics // Nucleic Acids Research. 2020. Vol. 48. No. 12. pp. 6699-6714.

GOST all authors (up to 50) Copy

Zharikova A. A., Rubanova N. M., Golov A. K., Petrova N. V., Logacheva M. D., Kantidze O. L., Magnitov M. D., Разин С. В., Gavrilov A., Galitsyna A. A., Luzhin A. V., Ulianov S. V., Mironov A. E. Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics // Nucleic Acids Research. 2020. Vol. 48. No. 12. pp. 6699-6714.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1093/nar/gkaa457

UR - https://doi.org/10.1093/nar/gkaa457

TI - Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

T2 - Nucleic Acids Research

AU - Zharikova, Anastasiya A

AU - Rubanova, Natalia M

AU - Golov, Arkadiy K

AU - Petrova, Nadezhda V.

AU - Logacheva, Maria D.

AU - Kantidze, Omar L.

AU - Magnitov, Mikhail D

AU - Разин, С. В.

AU - Gavrilov, Alexey

AU - Galitsyna, Aleksandra A

AU - Luzhin, Artem V.

AU - Ulianov, Sergey V.

AU - Mironov, Andrey E.

PY - 2020

DA - 2020/06/01

PB - Oxford University Press

SP - 6699-6714

IS - 12

VL - 48

PMID - 32479626

SN - 0305-1048

SN - 1362-4962

ER -

BibTex |

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BibTex (up to 50 authors) Copy

@article{2020_Zharikova,

author = {Anastasiya A Zharikova and Natalia M Rubanova and Arkadiy K Golov and Nadezhda V. Petrova and Maria D. Logacheva and Omar L. Kantidze and Mikhail D Magnitov and С. В. Разин and Alexey Gavrilov and Aleksandra A Galitsyna and Artem V. Luzhin and Sergey V. Ulianov and Andrey E. Mironov},

title = {Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics},

journal = {Nucleic Acids Research},

year = {2020},

volume = {48},

publisher = {Oxford University Press},

month = {jun},

url = {https://doi.org/10.1093/nar/gkaa457},

number = {12},

pages = {6699--6714},

doi = {10.1093/nar/gkaa457}

}

MLA

Cite this

MLA Copy

Zharikova, Anastasiya A., et al. “Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics.” Nucleic Acids Research, vol. 48, no. 12, Jun. 2020, pp. 6699-6714. https://doi.org/10.1093/nar/gkaa457.

Publisher

Oxford University Press

Journal

Nucleic Acids Research

scimago Q1

wos Q1

SJR

7.776

CiteScore

31.7

Impact factor

13.1

ISSN

03051048 (Print)

13624962 (Electronic)