TY - JOUR
T1 - An apex2 proximity ligation method for mapping interactions with the nuclear lamina
AU - Tran, Joseph R.
AU - Paulson, Danielle I.
AU - Moresco, James J.
AU - Adam, Stephen A.
AU - Yates, John R.
AU - Goldman, Robert D.
AU - Zheng, Yixian
N1 - Funding Information:
This study was funded by the National Institutes of Health, National Institute of General Medical Sciences (GM106023 to R.D. Goldman and Y. Zheng, GM110151 to Y. Zheng, and 8 P41 GM103533 to J.R. Yates III). The authors declare no competing financial interests.
Publisher Copyright:
© 2020 Tran et al.
PY - 2021/1/4
Y1 - 2021/1/4
N2 - 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 39 UTR bias, a finding consistent with an observed bias toward longer 39 UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 39 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.
AB - 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 39 UTR bias, a finding consistent with an observed bias toward longer 39 UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 39 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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U2 - 10.1083/jcb.202002129
DO - 10.1083/jcb.202002129
M3 - Article
C2 - 33306092
AN - SCOPUS:85098471804
VL - 220
JO - Journal of Cell Biology
JF - Journal of Cell Biology
SN - 0021-9525
IS - 1
M1 - e202002129
ER -