The nuclear lamina (NL) is a meshwork found beneath the inner nuclear membrane. The study of the NL is hindered by the insolubility of the meshwork and has driven the development of proximity ligation methods to identify the NL-associated/proximal proteins, RNA, and DNA. To simplify and improve temporal labeling, we fused APEX2 to the NL protein lamin-B1 to map proteins, RNA, and DNA. The identified NL-interacting/proximal RNAs show a long 3′ UTR bias, a finding consistent with an observed bias toward longer 3′ UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 3′ UTR. Our APEX2-based proteomics identifies a C-rich motif binding regulatory protein that exhibits altered localization in lamin-null cells. Finally, we use APEX2 to map lamina-associated domains (LADs) during the cell cycle and uncover short, H3K27me3-rich variable LADs. Thus, the APEX2-based tools presented here permit identification of proteomes, transcriptomes, and genome elements associated with or proximal to the NL.
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4 January 2021
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December 11 2020
An APEX2 proximity ligation method for mapping interactions with the nuclear lamina
Joseph R. Tran,
1
Carnegie Institution for Science, Department of Embryology, Baltimore, MD
Correspondence to Joseph R. Tran: tran@carnegiescience.edu
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Danielle I. Paulson,
Danielle I. Paulson
1
Carnegie Institution for Science, Department of Embryology, Baltimore, MD
2
Horace Mann School, The Bronx, NY
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James J. Moresco,
James J. Moresco
3
The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
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Stephen A. Adam,
Stephen A. Adam
4
Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
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John R. Yates, III,
John R. Yates, III
3
The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
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Robert D. Goldman,
Robert D. Goldman
4
Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
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Yixian Zheng
1
Carnegie Institution for Science, Department of Embryology, Baltimore, MD
Yixian Zheng: zheng@carnegiescience.edu
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Joseph R. Tran
1
Carnegie Institution for Science, Department of Embryology, Baltimore, MD
Danielle I. Paulson
1
Carnegie Institution for Science, Department of Embryology, Baltimore, MD
2
Horace Mann School, The Bronx, NY
James J. Moresco
3
The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
Stephen A. Adam
4
Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
John R. Yates, III
3
The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
Robert D. Goldman
4
Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
Yixian Zheng
1
Carnegie Institution for Science, Department of Embryology, Baltimore, MD
Correspondence to Joseph R. Tran: tran@carnegiescience.edu
Yixian Zheng: zheng@carnegiescience.edu
Received:
February 24 2020
Revision Received:
October 19 2020
Accepted:
October 29 2020
Online Issn: 1540-8140
Print Issn: 0021-9525
Funding:
National Institute of General Medical Sciences
(GM106023, GM110151, 8 P41 GM103533)
National Institutes of Health
(NO AWARD)
© 2020 Tran et al.
2020
This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).
J Cell Biol (2021) 220 (1): e202002129.
Article history
Received:
February 24 2020
Revision Received:
October 19 2020
Accepted:
October 29 2020
Citation
Joseph R. Tran, Danielle I. Paulson, James J. Moresco, Stephen A. Adam, John R. Yates, Robert D. Goldman, Yixian Zheng; An APEX2 proximity ligation method for mapping interactions with the nuclear lamina. J Cell Biol 4 January 2021; 220 (1): e202002129. doi: https://doi.org/10.1083/jcb.202002129
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