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
Publication type: Journal Article
Publication date: 2020-06-01
Journal:
Nucleic Acids Research
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 14.9
ISSN: 03051048, 13624962
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.
Top-30
Journals
|
1
2
3
|
|
|
Frontiers in Genetics
3 publications, 7.89%
|
|
|
F1000Research
2 publications, 5.26%
|
|
|
International Journal of Molecular Sciences
2 publications, 5.26%
|
|
|
Non-coding RNA
2 publications, 5.26%
|
|
|
Computational and Structural Biotechnology Journal
2 publications, 5.26%
|
|
|
Briefings in Bioinformatics
2 publications, 5.26%
|
|
|
Proceedings of the National Academy of Sciences of the United States of America
1 publication, 2.63%
|
|
|
Polymers
1 publication, 2.63%
|
|
|
Genes
1 publication, 2.63%
|
|
|
BMC Biology
1 publication, 2.63%
|
|
|
Cellular and Molecular Life Sciences
1 publication, 2.63%
|
|
|
BMC Bioinformatics
1 publication, 2.63%
|
|
|
Communications Biology
1 publication, 2.63%
|
|
|
Molecular Biology
1 publication, 2.63%
|
|
|
Database : the journal of biological databases and curation
1 publication, 2.63%
|
|
|
Trends in Biochemical Sciences
1 publication, 2.63%
|
|
|
PLoS Computational Biology
1 publication, 2.63%
|
|
|
PLoS ONE
1 publication, 2.63%
|
|
|
NAR Genomics and Bioinformatics
1 publication, 2.63%
|
|
|
1
2
3
|
Publishers
|
2
4
6
8
10
|
|
|
Cold Spring Harbor Laboratory
10 publications, 26.32%
|
|
|
Multidisciplinary Digital Publishing Institute (MDPI)
6 publications, 15.79%
|
|
|
Springer Nature
4 publications, 10.53%
|
|
|
Oxford University Press
4 publications, 10.53%
|
|
|
Frontiers Media S.A.
3 publications, 7.89%
|
|
|
Elsevier
3 publications, 7.89%
|
|
|
F1000 Research
2 publications, 5.26%
|
|
|
Public Library of Science (PLoS)
2 publications, 5.26%
|
|
|
Proceedings of the National Academy of Sciences (PNAS)
1 publication, 2.63%
|
|
|
Pleiades Publishing
1 publication, 2.63%
|
|
|
2
4
6
8
10
|
- We do not take into account publications without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
Are you a researcher?
Create a profile to get free access to personal recommendations for colleagues and new articles.
Metrics
Cite this
GOST |
RIS |
BibTex |
MLA
Cite this
GOST
Copy
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.
Cite this
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 -
Cite this
BibTex
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}
}
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.