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Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)

Zhang, Yandong and Sohn, Changho and Lee, Seoyeon and Ahn, Heejeong and Seo, Jinyoung and Cao, Junyue and Cai, Long (2020) Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET). Communications Biology, 3 . Art. No. 420. ISSN 2399-3642. https://resolver.caltech.edu/CaltechAUTHORS:20200803-104852533

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Abstract

While technologies for measuring transcriptomes in single cells have matured, methods for measuring proteins and their post-translational modification (PTM) states in single cells are still being actively developed. Unlike nucleic acids, proteins cannot be amplified, making detection of minute quantities from single cells difficult. Here, we develop a strategy to detect targeted protein and its PTM isoforms in single cells. We barcode the proteins from single cells by tagging them with oligonucleotides, pool barcoded cells together, run bulk gel electrophoresis to separate protein and its PTM isoform and quantify their abundances by sequencing the oligonucleotides associated with each protein species. We used this strategy, iDentification and qUantification sEparaTion (DUET), to measure histone protein H2B and its monoubiquitination isoform, H2Bub, in single yeast cells. Our results revealed the heterogeneities of H2B ubiquitination levels in single cells from different cell-cycle stages, which is obscured in ensemble measurements.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s42003-020-01132-8DOIArticle
https://doi.org/10.1038/s42003-020-01195-7DOIAuthor Correction
ORCID:
AuthorORCID
Sohn, Changho0000-0002-7585-1841
Seo, Jinyoung0000-0002-3260-4963
Cao, Junyue0000-0003-4097-489X
Cai, Long0000-0002-7154-5361
Additional Information:© The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Received 08 January 2020; Accepted 09 July 2020; Published 03 August 2020. We thank R. Ismagilov for helpful suggestions and discussions. We thank I. Antoschechkin from the Millard and Muriel Jacobs Genetics and Genomics Laboratory for assistance with the sequencing. We thank I. Strazhnik for help preparing the figures. This work was supported by funding from Paul G. Allen Frontiers Foundation Distinguished Investigator and Discovery Center. Data availability: Next-generation sequencing data for H2B and H2Bub from wild-type and double-knockout strains are available at the NCBI’s GEO (Accession Number: GSE153605). The single-cell protein copy number counts used in our analysis are available in Supplementary Data 3. All other relevant data are available from the corresponding author upon request. Code availability: All software and codes used in this work will be made available upon request to the authors. Author Contributions: These authors contributed equally: Yandong Zhang, Changho Sohn. L.C. conceptualized the project. Y.Z., C.S., and S.L. performed the laboratory experiments. H.A., J.S., and J.C. helped prepare the reagents and materials. Y.Z. did the analysis and visualized the data. Y.Z. and L.C. wrote the draft. The authors declare no competing interests.
Errata:In the original published version of the article, co-author Seoyeon Lee’s name was incorrectly spelled as Seoyoen Lee. The error has been corrected in the HTML and PDF versions of the article.
Group:Millard and Muriel Jacobs Genetics and Genomics Laboratory
Funders:
Funding AgencyGrant Number
Paul G. Allen Family FoundationUNSPECIFIED
Record Number:CaltechAUTHORS:20200803-104852533
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200803-104852533
Official Citation:Zhang, Y., Sohn, C., Lee, S. et al. Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET). Commun Biol 3, 420 (2020). https://doi.org/10.1038/s42003-020-01132-8
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:104701
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:03 Aug 2020 18:03
Last Modified:18 Aug 2020 21:54

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