A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

Shayne D. Wierbowski; Tommy V. Vo; Pascal Falter-Braun; Timothy O. Jobe; Lars H. Kruse; Xiaomu Wei; Jin Liang; Michael J. Meyer; Nurten Akturk; Christen A. Rivera-Erick; Nicolas A. Cordero; Mauricio I. Paramo; Elnur E. Shayhidin; Marta Bertolotti; Nathaniel D. Tippens; Kazi Akther; Rita Sharma; Yuichi Katayose; Kourosh Salehi-Ashtiani; Tong Hao; Pamela C. Ronald; Joseph R. Ecker; Peter A. Schweitzer; Shoshi Kikuchi; Hiroshi Mizuno; David E. Hill; Marc Vidal; Gaurav D. Moghe; Susan R. McCouch; Haiyuan Yu

doi:10.1073/pnas.1918068117

A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

Shayne D. Wierbowski, Tommy V. Vo, Pascal Falter-Braun, Timothy O. Jobe, Lars H. Kruse, Xiaomu Wei, Jin Liang, Michael J. Meyer, Nurten Akturk, Christen A. Rivera-Erick, Nicolas A. Cordero, Mauricio I. Paramo, Elnur E. Shayhidin, Marta Bertolotti, Nathaniel D. Tippens, Kazi Akther, Rita Sharma, Yuichi Katayose, Kourosh Salehi-Ashtiani, Tong HaoPamela C. Ronald, Joseph R. Ecker, Peter A. Schweitzer, Shoshi Kikuchi, Hiroshi Mizuno, David E. Hill, Marc Vidal, Gaurav D. Moghe, Susan R. McCouch, Haiyuan Yu

Research output: Contribution to journal › Article › peer-review

Abstract

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.

Original language	English (US)
Article number	11836
Number of pages	7
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	117
Issue number	21
DOIs	https://doi.org/10.1073/pnas.1918068117
State	Published - May 26 2020

Keywords

Networks
Next-generation sequencing
ORFeome
Protein-protein interaction
Rice
Protein Interaction Mapping/methods
Open Reading Frames/genetics
Oryza/genetics
Databases, Genetic
DNA, Plant/genetics
Computational Biology/methods
Genome, Plant/genetics
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
Protein Interaction Maps/genetics

ASJC Scopus subject areas

General

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10.1073/pnas.1918068117

Cite this

Wierbowski, S. D., Vo, T. V., Falter-Braun, P., Jobe, T. O., Kruse, L. H., Wei, X., Liang, J., Meyer, M. J., Akturk, N., Rivera-Erick, C. A., Cordero, N. A., Paramo, M. I., Shayhidin, E. E., Bertolotti, M., Tippens, N. D., Akther, K., Sharma, R., Katayose, Y., Salehi-Ashtiani, K., ... Yu, H. (2020). A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proceedings of the National Academy of Sciences of the United States of America, 117(21), Article 11836. https://doi.org/10.1073/pnas.1918068117

A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. / Wierbowski, Shayne D.; Vo, Tommy V.; Falter-Braun, Pascal et al.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 117, No. 21, 11836, 26.05.2020.

Research output: Contribution to journal › Article › peer-review

Wierbowski, SD, Vo, TV, Falter-Braun, P, Jobe, TO, Kruse, LH, Wei, X, Liang, J, Meyer, MJ, Akturk, N, Rivera-Erick, CA, Cordero, NA, Paramo, MI, Shayhidin, EE, Bertolotti, M, Tippens, ND, Akther, K, Sharma, R, Katayose, Y, Salehi-Ashtiani, K, Hao, T, Ronald, PC, Ecker, JR, Schweitzer, PA, Kikuchi, S, Mizuno, H, Hill, DE, Vidal, M, Moghe, GD, McCouch, SR & Yu, H 2020, 'A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice', Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21, 11836. https://doi.org/10.1073/pnas.1918068117

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abstract = "Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.",

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AU - Wierbowski, Shayne D.

AU - Vo, Tommy V.

AU - Falter-Braun, Pascal

AU - Jobe, Timothy O.

AU - Kruse, Lars H.

AU - Wei, Xiaomu

AU - Liang, Jin

AU - Meyer, Michael J.

AU - Akturk, Nurten

AU - Rivera-Erick, Christen A.

AU - Cordero, Nicolas A.

AU - Paramo, Mauricio I.

AU - Shayhidin, Elnur E.

AU - Bertolotti, Marta

AU - Tippens, Nathaniel D.

AU - Akther, Kazi

AU - Sharma, Rita

AU - Katayose, Yuichi

AU - Salehi-Ashtiani, Kourosh

AU - Hao, Tong

AU - Ronald, Pamela C.

AU - Ecker, Joseph R.

AU - Schweitzer, Peter A.

AU - Kikuchi, Shoshi

AU - Mizuno, Hiroshi

AU - Hill, David E.

AU - Vidal, Marc

AU - Moghe, Gaurav D.

AU - McCouch, Susan R.

AU - Yu, Haiyuan

PY - 2020/5/26

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N2 - Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.

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KW - ORFeome

KW - Protein-protein interaction

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KW - Protein Interaction Mapping/methods

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KW - DNA, Plant/genetics

KW - Computational Biology/methods

KW - Genome, Plant/genetics

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ER -

A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

Abstract

Keywords

ASJC Scopus subject areas

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