Open Access

Nucleic Acids Research

, том 48 , издание 12 , страницы 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}

Скрыть аффилиации авторов Показать аффилиации авторов: 9 аффилиаций

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 |

Тип публикации: Journal Article

Дата публикации: 2020-06-01

Oxford University Press

Nucleic Acids Research

scimago Q1

wos Q1

БС1

SJR: 7.776

CiteScore: 31.7

Impact factor: 13.1

ISSN: 03051048, 13624962

DOI: 10.1093/nar/gkaa457

Скопировать DOI

PubMed ID: 32479626

Genetics

Краткое описание

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.

Найдено

1 цитирование

Шидловский Юлий

🥼 🤝

д.б.н., проф.

85 публикаций, 1 025 цитирований

Индекс Хирша: 17

Институт биологии гена РАН

Первый Московский государственный медицинский университет имени И. М. Сеченова

Области научных интересов

Биохимия

Медицинская генетика

Молекулярная биология

Молекулярная генетика

1 цитирование

Дашинимаев Эрдэм

🥼 🤝

к.б.н., доц.

56 публикаций, 558 цитирований, 3 рецензии

Индекс Хирша: 13

Московский физико-технический институт

Российский Университет Дружбы Народов

Российский национальный исследовательский медицинский университет имени Н. И. Пирогова

Бурятский государственный университет имени Доржи Банзарова

Области научных интересов

Клеточное репрограммирование

Редактирование генома

Трансгенные и нокаутные животные

Топ-30

Журналы

	1 2 3
Frontiers in Genetics	Frontiers in Genetics, 3, 5.77% Frontiers in Genetics 3 публикации, 5.77%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 3, 5.77% International Journal of Molecular Sciences 3 публикации, 5.77%
Non-coding RNA	Non-coding RNA, 3, 5.77% Non-coding RNA 3 публикации, 5.77%
F1000Research	F1000Research, 2, 3.85% F1000Research 2 публикации, 3.85%
Computational and Structural Biotechnology Journal	Computational and Structural Biotechnology Journal, 2, 3.85% Computational and Structural Biotechnology Journal 2 публикации, 3.85%
Briefings in Bioinformatics	Briefings in Bioinformatics, 2, 3.85% Briefings in Bioinformatics 2 публикации, 3.85%
NAR Genomics and Bioinformatics	NAR Genomics and Bioinformatics, 2, 3.85% NAR Genomics and Bioinformatics 2 публикации, 3.85%
Nature Communications	Nature Communications, 2, 3.85% Nature Communications 2 публикации, 3.85%
Methods in Molecular Biology	Methods in Molecular Biology, 2, 3.85% Methods in Molecular Biology 2 публикации, 3.85%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 1, 1.92% Proceedings of the National Academy of Sciences of the United States of America 1 публикация, 1.92%
Polymers	Polymers, 1, 1.92% Polymers 1 публикация, 1.92%
Genes	Genes, 1, 1.92% Genes 1 публикация, 1.92%
BMC Biology	BMC Biology, 1, 1.92% BMC Biology 1 публикация, 1.92%
Cellular and Molecular Life Sciences	Cellular and Molecular Life Sciences, 1, 1.92% Cellular and Molecular Life Sciences 1 публикация, 1.92%
BMC Bioinformatics	BMC Bioinformatics, 1, 1.92% BMC Bioinformatics 1 публикация, 1.92%
Communications Biology	Communications Biology, 1, 1.92% Communications Biology 1 публикация, 1.92%
Molecular Biology	Molecular Biology, 1, 1.92% Molecular Biology 1 публикация, 1.92%
Database : the journal of biological databases and curation	Database : the journal of biological databases and curation, 1, 1.92% Database : the journal of biological databases and curation 1 публикация, 1.92%
Trends in Biochemical Sciences	Trends in Biochemical Sciences, 1, 1.92% Trends in Biochemical Sciences 1 публикация, 1.92%
PLoS Computational Biology	PLoS Computational Biology, 1, 1.92% PLoS Computational Biology 1 публикация, 1.92%
PLoS ONE	PLoS ONE, 1, 1.92% PLoS ONE 1 публикация, 1.92%
Nucleic Acids Research	Nucleic Acids Research, 1, 1.92% Nucleic Acids Research 1 публикация, 1.92%
Computational and Structural Biotechnology Reports	Computational and Structural Biotechnology Reports, 1, 1.92% Computational and Structural Biotechnology Reports 1 публикация, 1.92%
Nature Genetics	Nature Genetics, 1, 1.92% Nature Genetics 1 публикация, 1.92%
Biochimica et Biophysica Acta - General Subjects	Biochimica et Biophysica Acta - General Subjects, 1, 1.92% Biochimica et Biophysica Acta - General Subjects 1 публикация, 1.92%
Trends in Genetics	Trends in Genetics, 1, 1.92% Trends in Genetics 1 публикация, 1.92%
	1 2 3

Издатели

	2 4 6 8 10 12
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 12, 23.08% Cold Spring Harbor Laboratory 12 публикаций, 23.08%
Springer Nature	Springer Nature, 9, 17.31% Springer Nature 9 публикаций, 17.31%
MDPI	MDPI, 8, 15.38% MDPI 8 публикаций, 15.38%
Elsevier	Elsevier, 6, 11.54% Elsevier 6 публикаций, 11.54%
Oxford University Press	Oxford University Press, 6, 11.54% Oxford University Press 6 публикаций, 11.54%
Frontiers Media S.A.	Frontiers Media S.A., 3, 5.77% Frontiers Media S.A. 3 публикации, 5.77%
F1000 Research	F1000 Research, 2, 3.85% F1000 Research 2 публикации, 3.85%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 2, 3.85% Public Library of Science (PLoS) 2 публикации, 3.85%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 1, 1.92% Proceedings of the National Academy of Sciences (PNAS) 1 публикация, 1.92%
Pleiades Publishing	Pleiades Publishing, 1, 1.92% Pleiades Publishing 1 публикация, 1.92%
	2 4 6 8 10 12

Мы не учитываем публикации, у которых нет DOI.
Статистика публикаций обновляется еженедельно.

Вы ученый?

Создайте профиль, чтобы получать персональные рекомендации коллег, конференций и новых статей.

Войти с ORCID

PDF

Метрики

Цитировать

ГОСТ |

Цитировать

ГОСТ Скопировать

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.

ГОСТ со всеми авторами (до 50) Скопировать

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 |

Цитировать

RIS Скопировать

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 |

Цитировать

BibTex (до 50 авторов) Скопировать

@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

Цитировать

MLA Скопировать

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.

Издатель

Oxford University Press

Журнал

Nucleic Acids Research

scimago Q1

wos Q1

БС1

SJR

7.776

CiteScore

31.7

Impact factor

13.1

ISSN

03051048 (Print)

13624962 (Electronic)