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

Author:

Gavrilov Alexey A12,Zharikova Anastasiya A1345,Galitsyna Aleksandra A1346,Luzhin Artem V12,Rubanova Natalia M1,Golov Arkadiy K17,Petrova Nadezhda V1,Logacheva Maria D6,Kantidze Omar L1ORCID,Ulianov Sergey V18,Magnitov Mikhail D12,Mironov Andrey A349,Razin Sergey V18ORCID

Affiliation:

1. Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia

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

3. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia

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

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

6. Skolkovo Institute of Science and Technology, Skolkovo, Russia

7. Mental Health Research Center, Moscow, Russia

8. Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia

9. Faculty of Computer Science, Higher School of Economics, Moscow, Russia

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.

Funder

Russian Science Foundation

Skoltech Center of Life Sciences Systems Biology

Publisher

Oxford University Press (OUP)

Subject

Genetics

Cited by 36 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3