De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries

Namjin Cho; Byungjin Hwang; Jung Ki Yoon; Sangun Park; Joongoo Lee; Han Na Seo; Jeewon Lee; Sunghoon Huh; Jinsoo Chung; Duhee Bang

doi:10.1038/ncomms9351

De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries

Namjin Cho, Byungjin Hwang, Jung Ki Yoon, Sangun Park, Joongoo Lee, Han Na Seo, Jeewon Lee, Sunghoon Huh, Jinsoo Chung, Duhee Bang

Department of Chemistry

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

9 Citations (Scopus)

Abstract

Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.

Original language	English
Article number	8351
Journal	Nature communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms9351
Publication status	Published - 2015 Sept 21

Bibliographical note

Funding Information:
This work was supported by the Intelligent Synthetic Biology Center of Global Frontier Project (NRF-2012M3A6A8053632) and by the Pioneer Research Center Program (NRF-2012-0009557) through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning. This research was also supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI13C2163). We thank Tom Muir’s group for their kind donation of the Intein vector, and member of Bang Lab for their critical comments during this work. We also thank J. Jung for critical comments on the manuscript and E. Kwon for helping gene assembly experiment.

Publisher Copyright:
© 2015 Macmillan Publishers Limited. All rights reserved.

All Science Journal Classification (ASJC) codes

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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10.1038/ncomms9351

Cite this

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abstract = "Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.",

author = "Namjin Cho and Byungjin Hwang and Yoon, {Jung Ki} and Sangun Park and Joongoo Lee and Seo, {Han Na} and Jeewon Lee and Sunghoon Huh and Jinsoo Chung and Duhee Bang",

note = "Funding Information: This work was supported by the Intelligent Synthetic Biology Center of Global Frontier Project (NRF-2012M3A6A8053632) and by the Pioneer Research Center Program (NRF-2012-0009557) through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning. This research was also supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI13C2163). We thank Tom Muir{\textquoteright}s group for their kind donation of the Intein vector, and member of Bang Lab for their critical comments during this work. We also thank J. Jung for critical comments on the manuscript and E. Kwon for helping gene assembly experiment. Publisher Copyright: {\textcopyright} 2015 Macmillan Publishers Limited. All rights reserved.",

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AU - Huh, Sunghoon

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De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries

Abstract

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