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Transposase-assisted tagmentation: an economical and scalable strategy for single-worm whole-genome sequencing
Open accessPublished version of a preprint
Abstract
AlphaMissense identifies 23 million human missense variants as likely pathogenic, but only 0.1% have been clinically classified. To experimentally validate these predictions, chemical mutagenesis presents a rapid, cost-effective method to produce billions of mutations in model organisms. However, the prohibitive costs and limitations in the throughput of whole-genome sequencing (WGS) technologies, crucial for variant identification, constrain its widespread application. Here, we introduce a Tn5 transposase-assisted tagmentation technique for conducting WGS in Caenorhabditis elegans, Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii. This method, demands merely 20 min of hands-on time for a single-worm or single-cell clones and incurs a cost below 10 US dollars. It effectively pinpoints causal mutations in mutants defective in cilia or neurotransmitter secretion and in mutants synthetically sterile with a variant analogous to the B-Raf Proto-oncogene, Serine/Threonine Kinase (BRAF) V600E mutation. Integrated with chemical mutagenesis, our approach can generate and identify missense variants economically and efficiently, facilitating experimental investigations of missense variants in diverse species.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 45
- Adli, 2018, The CRISPR tool kit for genome editing and beyond, Nat Commun, 9, 1911, 10.1038/s41467-018-04252-2 · DOI · Paper page
- Barstead, 1991, Cloning, sequencing, and mapping of an alpha-actinin gene from the nematode Caenorhabditis elegans, Cell Motil Cytoskeleton, 20, 69, 10.1002/cm.970200108 · DOI
- Bentsen, 2020, ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation, Nat Commun, 11, 4267, 10.1038/s41467-020-18035-1 · DOI
- Bock, 2022, High-content CRISPR screening, Nat Rev Methods Primers, 2, 9, 10.1038/s43586-022-00098-7 · DOI
- Brenner, 1974, The genetics of Caenorhabditis elegans, Genetics, 77, 71, 10.1093/genetics/77.1.71 · DOI
- Burghoorn, 2007, Mutation of the MAP kinase DYF-5 affects docking and undocking of kinesin-2 motors and reduces their speed in the cilia of Caenorhabditis elegans, Proc Natl Acad Sci U S A, 104, 7157, 10.1073/pnas.0606974104 · DOI
- Cheng, 2023, Accurate proteome-wide missense variant effect prediction with AlphaMissense, Science, 381, eadg7492, 10.1126/science.adg7492 · DOI · Paper page
- Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143 · DOI · Paper page
- Cupples, 1990, A set of lacZ mutations in Escherichia coli that allow rapid detection of specific frameshift mutations, Genetics, 125, 275, 10.1093/genetics/125.2.275 · DOI
- Cupples, 1989, A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions, Proc Natl Acad Sci U S A, 86, 5345, 10.1073/pnas.86.14.5345 · DOI
- Davies, 2000, Three-dimensional structure of the Tn5 synaptic complex transposition intermediate, Science, 289, 77, 10.1126/science.289.5476.77 · DOI
- Davies, 2002, Mutations of the BRAF gene in human cancer, Nature, 417, 949, 10.1038/nature00766 · DOI · Paper page
- Di, 2020, RNA sequencing by direct tagmentation of RNA/DNA hybrids, Proc Natl Acad Sci U S A, 117, 2886, 10.1073/pnas.1919800117 · DOI
- Gopalan, 2021, Simultaneous profiling of multiple chromatin proteins in the same cells, Mol Cell, 81, 4736, 10.1016/j.molcel.2021.09.019 · DOI
- Greene, 2003, Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis, Genetics, 164, 731, 10.1093/genetics/164.2.731 · DOI
- Hedgecock, 1985, Axonal guidance mutants of Caenorhabditis elegans identified by filling sensory neurons with fluorescein dyes, Dev Biol, 111, 158, 10.1016/0012-1606(85)90443-9 · DOI
- Hennig, 2018, Large-Scale low-cost NGS library preparation using a robust Tn5 purification and tagmentation protocol, G3 (Bethesda), 8, 79, 10.1534/g3.117.300257 · DOI
- Jorgensen, 2002, The art and design of genetic screens: caenorhabditis elegans, Nat Rev Genet, 3, 356, 10.1038/nrg794 · DOI
- Kim, 2018, OrthoList 2: a new comparative genomic analysis of human and Caenorhabditis elegans genes, Genetics, 210, 445, 10.1534/genetics.118.301307 · DOI
- Lavoie, 2018, MEK drives BRAF activation through allosteric control of KSR proteins, Nature, 554, 549, 10.1038/nature25478 · DOI
- Lee, 2020, Recruitment of mRNAs to P granules by condensation with intrinsically-disordered proteins, Elife, 9, e52896, 10.7554/eLife.52896 · DOI
- Li, 2006, BRAF mutations are associated with distinctive clinical, pathological and molecular features of colorectal cancer independently of microsatellite instability status, Mol Cancer, 5, 2, 10.1186/1476-4598-5-2 · DOI
- Liu, 2007, BRAF v600e maintains proliferation, transformation, and tumorigenicity of BRAF-mutant papillary thyroid cancer cells, J Clin Endocrinol Metab, 92, 2264, 10.1210/jc.2006-1613 · DOI
- Liu, 1999, High-throughput isolation of Caenorhabditis elegans deletion mutants, Genome Res, 9, 859, 10.1101/gr.9.9.859 · DOI
- Loppes, 1969, Effect of the selective medium on the manifestation of mutations induced with mono-alkylating agents in Chlamydomonas reinhardi, Mutat Res, 7, 25, 10.1016/0027-5107(69)90046-3 · DOI
- Lu, 2020, Transposase-assisted tagmentation of RNA/DNA hybrid duplexes, Elife, 9, e54919, 10.7554/eLife.54919 · DOI
- Mali, 2013, RNA-guided human genome engineering via Cas9, Science, 339, 823, 10.1126/science.1232033 · DOI · Paper page
- Mello, 1991, Efficient gene transfer in C. elegans: extrachromosomal maintenance and integration of transforming sequences, EMBO J, 10, 3959, 10.1002/j.1460-2075.1991.tb04966.x · DOI
- Omori, 2010, Negative regulation of ciliary length by ciliary male germ cell-associated kinase (Mak) is required for retinal photoreceptor survival, Proc Natl Acad Sci U S A, 107, 22671, 10.1073/pnas.1009437108 · DOI
- Ou, 2005, Functional coordination of intraflagellar transport motors, Nature, 436, 583, 10.1038/nature03818 · DOI · Paper page
- Page, 2002, The art and design of genetic screens: Arabidopsis thaliana, Nat Rev Genet, 3, 124, 10.1038/nrg730 · DOI
- Picelli, 2014, Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, Genome Res, 24, 2033, 10.1101/gr.177881.114 · DOI
- Ritterhouse, 2015, BRAF v600e mutation-specific antibody: a review, Semin Diagn Pathol, 32, 400, 10.1053/j.semdp.2015.02.010 · DOI
- Russell, 1979, Specific-locus test shows ethylnitrosourea to be the most potent mutagen in the mouse, Proc Natl Acad Sci U S A, 76, 5818, 10.1073/pnas.76.11.5818 · DOI · Paper page
- Sanchez-Torres, 2013, BRAF mutant non-small cell lung cancer and treatment with BRAF inhibitors, Transl Lung Cancer Res, 2, 244, 10.3978/j.issn.2218-6751.2013.04.01 · DOI
- Sassa, 1999, Regulation of the UNC-18-Caenorhabditis elegans syntaxin complex by UNC-13, J Neurosci, 19, 4772, 10.1523/JNEUROSCI.19-12-04772.1999 · DOI
- Sega, 1984, A review of the genetic effects of ethyl methanesulfonate, Mutat Res, 134, 113, 10.1016/0165-1110(84)90007-1 · DOI
- Shen, 2013, Phosphorylation of BRAF by AMPK impairs BRAF-KSR1 association and cell proliferation, Mol Cell, 52, 161, 10.1016/j.molcel.2013.08.044 · DOI
- Tan, 2018, Three-dimensional genome structures of single diploid human cells, Science, 361, 924, 10.1126/science.aat5641 · DOI
- Thompson, 2013, The million mutation project: a new approach to genetics in Caenorhabditis elegans, Genome Res, 23, 1749, 10.1101/gr.157651.113 · DOI
- Vaezeslami, 2007, Site-directed mutagenesis studies of Tn5 transposase residues involved in synaptic complex formation, J Bacteriol, 189, 7436, 10.1128/JB.00524-07 · DOI
- Williams, 1992, A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites, Genetics, 131, 609, 10.1093/genetics/131.3.609 · DOI
- Winston, 2008, EMS and UV mutagenesis in yeast, Curr Protoc Mol Biol, Chapter 13, Unit. 13.3B, 10.1002/0471142727.mb1303bs82 · DOI
- Wu, 2016, The landscape of accessible chromatin in mammalian preimplantation embryos, Nature, 534, 652, 10.1038/nature18606 · DOI
- Yates, 2020, Ensembl 2020, Nucleic Acids Res, 48, D682, 10.1093/nar/gkz966 · DOI
Metadata
- Authors
- Wang, Z., Ke, J., Guo, Z., Wang, Y., Lei, K., Wang, S., Chen, G., Shen, Z., Li, W., & Ou, G.
- Affiliations
- Center for Life Sciences (CN)
- Tsinghua University (CN)
- Corresponding author
- Ou, Guangshuo
- ORCID
- Venue
- G3: Genes, Genomes, Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-06-10
- Volume
- 14
- Issue
- 7
- ISSN
- 2160-1836 (ISSN-L)
- PMC
- PMC11228870
- OpenAlex
- W4399497879
- Cited by
- 5
- References
- 1
- Citations by year
- 2026: 2 · 2025: 3
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- G3 Genes Genomes Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (32270721, 31991190, 32070706, 32021002, 31970180, 31900535, 32071191, 31971160)
- National Key R & D Program of China (2017YFA0503501, 2019YFA0508401, 2017YFA0102900)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- Tn5 transposase, whole genome sequencing, low-cost sequencing, chemical mutagenesis, missense mutations, AlphaMissense, Caenorhabditis elegans, Escherichia coli, Saccharomyces cerevisiae, Chlamydomonas reinhardtii, BRAF V600E mutation, single-cell clones
- MeSH terms
- Whole Genome Sequencing, Animals, Escherichia coli, Saccharomyces cerevisiae, Chlamydomonas reinhardtii, Caenorhabditis elegans, Transposases
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