Open Access
Proceedings of the National Academy of Sciences of the United States of America, volume 119, issue 1, pages e2116222119
RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins
Gavrilov Alexey
1
,
Sultanov Rinat I
2
,
Magnitov Mikhail D
1
,
Galitsyna Aleksandra A.
1
,
Dashinimaev Erdem B.
3
,
Lieberman Aiden Erez
4, 5
,
Разин С. В.
1, 6
4
The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
|
Publication type: Journal Article
Publication date: 2021-12-30
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 11.1
ISSN: 00278424, 10916490
Multidisciplinary
Abstract
Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However, neither of these techniques examines proteins involved in RNA–chromatin interactions. Here, we introduce RedChIP, a technique combining RNA–DNA proximity ligation and chromatin immunoprecipitation for identifying RNA–chromatin interactions mediated by a particular protein. Using antibodies against architectural protein CTCF and the EZH2 subunit of the Polycomb repressive complex 2, we identify a spectrum of cis- and trans-acting ncRNAs enriched at Polycomb- and CTCF-binding sites in human cells, which may be involved in Polycomb-mediated gene repression and CTCF-dependent chromatin looping. By providing a protein-centric view of RNA–DNA interactions, RedChIP represents an important tool for studies of nuclear ncRNAs.
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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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Gavrilov A. et al. RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins // Proceedings of the National Academy of Sciences of the United States of America. 2021. Vol. 119. No. 1. p. e2116222119.
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Gavrilov A., Sultanov R. I., Magnitov M. D., Galitsyna A. A., Dashinimaev E. B., Lieberman Aiden E., Разин С. В. RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins // Proceedings of the National Academy of Sciences of the United States of America. 2021. Vol. 119. No. 1. p. e2116222119.
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TY - JOUR
DO - 10.1073/pnas.2116222119
UR - https://doi.org/10.1073%2Fpnas.2116222119
TI - RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins
T2 - Proceedings of the National Academy of Sciences of the United States of America
AU - Gavrilov, Alexey
AU - Galitsyna, Aleksandra A.
AU - Lieberman Aiden, Erez
AU - Разин, С. В.
AU - Magnitov, Mikhail D
AU - Dashinimaev, Erdem B.
AU - Sultanov, Rinat I
PY - 2021
DA - 2021/12/30 00:00:00
PB - Proceedings of the National Academy of Sciences (PNAS)
SP - e2116222119
IS - 1
VL - 119
SN - 0027-8424
SN - 1091-6490
ER -
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@article{2021_Gavrilov,
author = {Alexey Gavrilov and Aleksandra A. Galitsyna and Erez Lieberman Aiden and С. В. Разин and Mikhail D Magnitov and Erdem B. Dashinimaev and Rinat I Sultanov},
title = {RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2021},
volume = {119},
publisher = {Proceedings of the National Academy of Sciences (PNAS)},
month = {dec},
url = {https://doi.org/10.1073%2Fpnas.2116222119},
number = {1},
pages = {e2116222119},
doi = {10.1073/pnas.2116222119}
}
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MLA
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Gavrilov, Alexey, et al. “RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 1, Dec. 2021, p. e2116222119. https://doi.org/10.1073%2Fpnas.2116222119.
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