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
Разин С. В.
1, 2
,
Luzhin Artem V.
1, 3
,
Kantidze Omar L.
1
,
Logacheva Maria D.
4
,
Ulianov Sergey V.
1, 2
,
Magnitov Mikhail D
1, 3
,
Gavrilov Alexey
1, 3
,
Petrova Nadezhda V.
1
,
Golov Arkadiy K
1, 5
,
Zharikova Anastasiya A
1, 6, 7, 8
,
Rubanova Natalia M
1
,
Galitsyna Aleksandra A
1, 4, 6, 8
,
Mironov Andrey E.
6, 8, 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.
Citations by journals
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1
2
3
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Frontiers in Genetics
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Frontiers in Genetics
3 publications, 9.68%
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F1000Research
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F1000Research
2 publications, 6.45%
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International Journal of Molecular Sciences
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International Journal of Molecular Sciences
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Non-coding RNA
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Computational and Structural Biotechnology Journal
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2 publications, 6.45%
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Briefings in Bioinformatics
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2 publications, 6.45%
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Proceedings of the National Academy of Sciences of the United States of America
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Proceedings of the National Academy of Sciences of the United States of America
1 publication, 3.23%
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Polymers
|
Polymers
1 publication, 3.23%
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Genes
|
Genes
1 publication, 3.23%
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BMC Biology
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BMC Biology
1 publication, 3.23%
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Cellular and Molecular Life Sciences
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Cellular and Molecular Life Sciences
1 publication, 3.23%
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BMC Bioinformatics
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BMC Bioinformatics
1 publication, 3.23%
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Communications Biology
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Communications Biology
1 publication, 3.23%
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Molecular Biology
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Molecular Biology
1 publication, 3.23%
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Database : the journal of biological databases and curation
|
Database : the journal of biological databases and curation
1 publication, 3.23%
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1
2
3
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Citations by publishers
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1
2
3
4
5
6
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
6 publications, 19.35%
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Springer Nature
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Springer Nature
4 publications, 12.9%
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Frontiers Media S.A.
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Frontiers Media S.A.
3 publications, 9.68%
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Oxford University Press
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Oxford University Press
3 publications, 9.68%
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F1000 Research
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F1000 Research
2 publications, 6.45%
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Elsevier
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Elsevier
2 publications, 6.45%
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Proceedings of the National Academy of Sciences (PNAS)
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Proceedings of the National Academy of Sciences (PNAS)
1 publication, 3.23%
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Pleiades Publishing
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Pleiades Publishing
1 publication, 3.23%
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Cold Spring Harbor Laboratory
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Cold Spring Harbor Laboratory
1 publication, 3.23%
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1
2
3
4
5
6
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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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.
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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.
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TY - JOUR
DO - 10.1093/nar/gkaa457
UR - https://doi.org/10.1093%2Fnar%2Fgkaa457
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 00:00:00
PB - Oxford University Press
SP - 6699-6714
IS - 12
VL - 48
PMID - 32479626
SN - 0305-1048
SN - 1362-4962
ER -
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@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%2Fnar%2Fgkaa457},
number = {12},
pages = {6699--6714},
doi = {10.1093/nar/gkaa457}
}
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MLA
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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%2Fnar%2Fgkaa457.