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

Nature Communications

Volumn 6, Issue , 2015, Pages

  Cho, Namjin ^a   Hwang, Byungjin ^a   Yoon, Jung Ki ^b   Park, Sangun ^c   Lee, Joongoo ^d   Seo, Han Na ^a   Lee, Jeewon ^a   Huh, Sunghoon ^a   Chung, Jinsoo ^e   Bang, Duhee ^a  

^a Yonsei University   (South Korea)

^b Seoul National University   (South Korea)

^c Korea Military Academy   (South Korea)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN VARIANT; BACTERIAL PROTEIN; CODON;

EPISTASIS; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC STRUCTURE; GENETIC VARIATION; GENOMICS; MOLECULAR ANALYSIS; MUTATION; PHENOTYPE; PROTEIN; SOFTWARE;

AMINO ACID SEQUENCE; ARTICLE; CODON; CONTROLLED STUDY; DNA BARCODING; FUNCTIONAL GENOMICS; GENE LIBRARY; GENE MUTATION; GENE SEQUENCE; GENOTYPE; MUTAGENESIS; NEXT GENERATION SEQUENCING; NONHUMAN; PHENOTYPE; SIMULATION; DEVICES; EVALUATION STUDY; GENETICS; HIGH THROUGHPUT SEQUENCING; NOSTOC; PROCEDURES;

BACTERIAL PROTEINS; CODON; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NOSTOC;

EID: 84942133031     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms9351     Document Type: Article

References (36)

1. Zhou, Y., Zhang, X. & Ebright, R. H. Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase. Nucleic Acids Res. 19, 6052-6052 (1991).
2. Stemmer, W. P. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389-391 (1994).
3. Jain, P. C. & Varadarajan, R. A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. Anal. Biochem. 449, 90-98 (2014).
4. Firnberg, E. & Ostermeier, M. PFunkel: efficient, expansive, user-defined mutagenesis. PLoS ONE 7, e52031 (2012).
5. Zha, D., Eipper, A. & Reetz, M. T. Assembly of designed oligonucleotides as an efficient method for gene recombination: a new tool in directed evolution. ChemBioChem. 4, 34-39 (2003).
6. Lütke-Eversloh, T. & Stephanopoulos, G. Feedback inhibition of chorismate mutase/prephenate dehydrogenase (TyrA) of Escherichia coli: generation and characterization of tyrosine-insensitive mutants. Appl. Environ. Microbiol. 71, 7224-7228 (2005).
7. Jarosz, D. F. & Lindquist, S. Hsp90 and environmental stress transform the adaptive value of natural genetic variation. Science 330, 1820-1824 (2010).
8. Whitehead, T. A. et al. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat. Biotechnol. 30, 543-548 (2012).
9. Gold, M. G. et al. Engineering A-kinase anchoring protein (AKAP)-selective regulatory subunits of protein kinase A (PKA) through structure-based phage selection. J. Biol. Chem. 288, 17111-17121 (2013).
10. Fowler, D. M. et al. High-resolution mapping of protein sequence-function relationships. Nat. Methods 7, 741-746 (2010).
11. Fowler, D. M. & Fields, S. Deep mutational scanning: a new style of protein science. Nat. Methods 11, 801-807 (2014).
12. Starita, L. M. et al. Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis. Proc. Natl Acad. Sci. USA 110, E1263-E1272 (2013).
13. Doolan, K. M. & Colby, D. W. Conformation-dependent epitopes recognized by prion protein antibodies probed using mutational scanning and deep sequencing. J. Mol. Biol. 427, 328-340 (2015).
14. Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138 (2009).
15. Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
16. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
17. Hiatt, J. B., Patwardhan, R. P., Turner, E. H., Lee, C. & Shendure, J. Parallel, tag-directed assembly of locally derived short sequence reads. Nat. Methods 7, 119-122 (2010).
18. Kitzman, J. O., Starita, L. M., Lo, R. S., Fields, S. & Shendure, J. Massively parallel single-amino-acid mutagenesis. Nat. Methods 12, 203-206 (2015).
19. Pan, W. et al. DNA polymerase preference determines PCR priming efficiency. BMC Biotechnol. 14, 10 (2014).
20. Simpson, J. T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117-1123 (2009).
21. Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
22. Compeau, P. E. C., Pevzner, P. A. & Tesler, G. How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol. 29, 987-991 (2011).
23. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652 (2011).
24. Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
25. Lockless, S. W. & Muir, T. W. Traceless protein splicing utilizing evolved split inteins. Proc. Natl Acad. Sci. USA 106, 10999-11004 (2009).
26. Chu, J. et al. Non-invasive intravital imaging of cellular differentiation with a bright red-excitable fluorescent protein. Nat. Methods 11, 572-578 (2014).
27. DeVito, J. A. Recombineering with tolC as a selectable/counter-selectable marker: remodeling the rRNA operons of Escherichia coli. Nucleic Acids Res. 36, e4 (2008).
28. Stemmer, W. P. C., Crameri, A., Ha, K. D., Brennan, T. M. & Heyneker, H. L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164, 49-53 (1995).
29. Chain, L., Wiedmann, M., Wilson,W. I., Luo, J. & Batt, A. Ligase chain reaction (LCR) - overview and applications. Genome Res. 3, S51-S64 (1994).
30. Kosuri, S. & Church, G. M. Large-scale de novo DNA synthesis: technologies and applications. Nat. Methods 11, 499-507 (2014).
31. Kosuri, S. et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc. Natl Acad. Sci. USA 110, 14024-14029 (2013).
32. Kabat, E. A., Wu, T T., Perry, H., Gottesman, K. & Foeller, C. Sequences of Proteins of Immunological Interest. 5th edn. NIH Publication No. 91-3242 (1991).
33. Tomlinson, I. M., Walter, G., Marks, J. D., Llewelyn, M. B. & Winter, G. The repertoire of human germline VH sequences reveals about fifty groups of VH segments with different hypervariable loops. J. Mol. Biol. 227, 776-798 (1992).
34. Cox, J. P., Tomlinson, I. M. & Winter, G. A directory of human germ-line V kappa segments reveals a strong bias in their usage. Eur. J. Immunol. 24, 827-836 (1994).
35. Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345 (2009).
36. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 26, 589-595 (2010).