TransgeneOmics - A transgenic platform for protein localization based function exploration

Methods

Volumn 96, Issue , 2016, Pages 69-74

  Hasse, Susanne ^a   Hyman, Anthony A ^a   Sarov, Mihail ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR CELL BIOLOGY AND GENETICS   (Germany)

Author keywords

BAC transgenesis; Genome engineering; Protein localization; Protein tagging; Recombineering

Indexed keywords

DNA; COMPLEMENTARY DNA; FLUORESCENT DYE;

BACTERIAL ARTIFICIAL CHROMOSOME; CONTROLLED STUDY; GENE CONSTRUCT; GENE TECHNOLOGY; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; TRANSGENICS; ANIMAL; CAENORHABDITIS ELEGANS; CHEMISTRY; DROSOPHILA MELANOGASTER; GENETIC ENGINEERING; GENETICS; GENOMICS; METABOLISM; MOLECULAR IMAGING; PROCEDURES; STAINING; TRANSGENE;

ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA, COMPLEMENTARY; DROSOPHILA MELANOGASTER; FLUORESCENT DYES; GENETIC ENGINEERING; GENOMICS; HUMANS; MOLECULAR IMAGING; STAINING AND LABELING; TRANSGENES;

EID: 84958155400     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2015.10.005     Document Type: Review

References (94)

1. Stadler C., et al. RNA- and antibody-based profiling of the human proteome with focus on chromosome 19. J. Proteome Res. 2014, 13(4):2019-2027.
2. Fagerberg L., et al. Mapping the subcellular protein distribution in three human cell lines. J. Proteome Res. 2011, 10(8):3766-3777.
3. Ponten F., Jirstrom K., Uhlen M. The Human Protein Atlas - a tool for pathology. J. Pathol. 2008, 216(4):387-393.
4. Uhlen M., et al. A Human Protein Atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 2005, 4(12):1920-1932.
5. Uhlen M., et al. Proteomics. Tissue-based map of the human proteome. Science 2015, 347(6220):1260419.
6. Rothbauer U., et al. Targeting and tracing antigens in live cells with fluorescent nanobodies. Nat. Methods 2006, 3(11):887-889.
7. Panza P., et al. Live imaging of endogenous protein dynamics in zebrafish using chromobodies. Development 2015, 142(10):1879-1884.
8. Burgess A., Lorca T., Castro A. Quantitative live imaging of endogenous DNA replication in mammalian cells. PLoS One 2012, 7(9):e45726.
9. Schnell U., et al. Immunolabeling artifacts and the need for live-cell imaging. Nat. Methods 2012, 9(2):152-158.
10. Whelan D.R., Bell T.D. Image artifacts in single molecule localization microscopy: why optimization of sample preparation protocols matters. Sci. Rep. 2015, 5:7924.
11. Stadler C., et al. Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells. Nat. Methods 2013, 10(4):315-323.
12. Hoffman R.M. Application of GFP imaging in cancer. Lab. Invest. 2015, 95(4):432-452.
13. Hoffman R.M. Imaging metastatic cell trafficking at the cellular level in vivo with fluorescent proteins. Methods Mol. Biol. 2014, 1070:171-179.
14. Filhol O., et al. Live-cell fluorescence imaging reveals the dynamics of protein kinase CK2 individual subunits. Mol. Cell. Biol. 2003, 23(3):975-987.
15. Chalfie M., et al. Green fluorescent protein as a marker for gene expression. Science 1994, 263(5148):802-805.
16. Mishin A.S., et al. Novel uses of fluorescent proteins. Curr. Opin. Chem. Biol. 2015, 27:1-9.
17. Zhang J., et al. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 2002, 3(12):906-918.
18. Simpson J.C., et al. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Reports 2000, 1(3):287-292.
19. Kumar A., et al. Subcellular localization of the yeast proteome. Genes Dev. 2002, 16(6):707-719.
20. Bischof J., et al. Generation of a transgenic ORFeome library in Drosophila. Nat. Protoc. 2014, 9(7):1607-1620.
21. Lamesch P., et al. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 2007, 89(3):307-315.
22. Reboul J., et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 2003, 34(1):35-41.
23. Uetz P., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623-627.
24. Yamada K., et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 2003, 302(5646):842-846.
25. Temple G., et al. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009, 19(12):2324-2333.
26. Lamesch P., et al. C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res. 2004, 14(10B):2064-2069.
27. Santarius T., et al. A census of amplified and overexpressed human cancer genes. Nat. Rev. Cancer 2010, 10(1):59-64.
28. Liu Y., et al. A genomic screen for activators of the antioxidant response element. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(12):5205-5210.
29. Ross-Macdonald P., et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 1999, 402(6760):413-418.
30. Morin X., et al. A protein trap strategy to detect GFP-tagged proteins expressed from their endogenous loci in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 2001, 98(26):15050-15055.
31. Buszczak M., et al. The carnegie protein trap library: a versatile tool for Drosophila developmental studies. Genetics 2007, 175(3):1505-1531.
32. Quinones-Coello A.T., et al. Exploring strategies for protein trapping in Drosophila. Genetics 2007, 175(3):1089-1104.
33. Nagarkar-Jaiswal S., et al. A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila. Elife 2015, 4.
34. Ding S., et al. Efficient transposition of the piggyBac (PB) transposon in mammalian cells and mice. Cell 2005, 122(3):473-483.
35. Venken K.J., et al. MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes. Nat. Methods 2011, 8(9):737-743.
36. Huh W.K., et al. Global analysis of protein localization in budding yeast. Nature 2003, 425(6959):686-691.
37. Ding D.Q., et al. Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library. Genes Cells 2000, 5(3):169-190.
38. Janke D.L., et al. Interpreting a sequenced genome: toward a cosmid transgenic library of Caenorhabditis elegans. Genome Res. 1997, 7(10):974-985.
39. Le Y., Dobson M.J. Stabilization of yeast artificial chromosome clones in a rad54-3 recombination-deficient host strain. Nucleic Acids Res. 1997, 25(6):1248-1253.
40. Palmieri G., et al. Construction of a pilot human YAC library in a recombination-defective yeast strain. Gene 1997, 188(2):169-174.
41. Zhang Y., et al. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 1998, 20(2):123-128.
42. Sharan S.K., et al. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 2009, 4(2):206-223.
43. Copeland N.G., Jenkins N.A., Court D.L. Recombineering: a powerful new tool for mouse functional genomics. Nat. Rev. Genet. 2001, 2(10):769-779.
44. Testa G., et al. Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles. Nat. Biotechnol. 2003, 21(4):443-447.
45. Hofemeister H., et al. Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis. Methods 2011, 53(4):437-452.
46. Ciotta G., et al. Recombineering BAC transgenes for protein tagging. Methods 2011, 53(2):113-119.
47. Skarnes W.C., et al. A conditional knockout resource for the genome-wide study of mouse gene function. Nature 2011, 474(7351):337-342.
48. Pfander C., et al. A scalable pipeline for highly effective genetic modification of a malaria parasite. Nat. Methods 2011, 8(12):1078-1082.
49. Hubner N.C., et al. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J. Cell Biol. 2010, 189(4):739-754.
50. Hutchins J.R., et al. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 2010, 328(5978):593-599.
51. Maliga Z., et al. A genomic toolkit to investigate kinesin and myosin motor function in cells. Nat. Cell Biol. 2013, 15(3):325-334.
52. Ejsmont R.K., et al. Recombination-mediated genetic engineering of large genomic DNA transgenes. Methods Mol. Biol. 2011, 772:445-458.
53. Ejsmont R.K., et al. A toolkit for high-throughput, cross-species gene engineering in Drosophila. Nat. Methods 2009, 6(6):435-437.
54. Sarov M., et al. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell 2012, 150(4):855-866.
55. Tursun B., et al. A toolkit and robust pipeline for the generation of fosmid-based reporter genes in C. elegans. PLoS One 2009, 4(3):e4625.
56. Dolphin C.T., Hope I.A. Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones. Nucleic Acids Res. 2006, 34(9):e72.
57. Hirani N., et al. A simplified counter-selection recombineering protocol for creating fluorescent protein reporter constructs directly from C. elegans fosmid genomic clones. BMC Biotechnol. 2013, 13:1.
58. Minorikawa S., Nakayama M. Recombinase-mediated cassette exchange (RMCE) and BAC engineering via VCre/VloxP and SCre/SloxP systems. Biotechniques 2011, 50(4):235-246.
59. Sarov M., et al. A recombineering pipeline for functional genomics applied to Caenorhabditis elegans. Nat. Methods 2006, 3(10):839-844.
60. Poser I., et al. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat. Methods 2008, 5(5):409-415.
61. Sarov M., et al. A genome-wide resource for the analysis of protein localisation in Drosophila. BioRxiv 2015.
62. Morra F., et al. FBXW7 and USP7 regulate CCDC6 turnover during the cell cycle and affect cancer drugs susceptibility in NSCLC. Oncotarget 2015, 6(14):12697-12709.
63. Andersen P.R., et al. The human cap-binding complex is functionally connected to the nuclear RNA exosome. Nat. Struct. Mol. Biol. 2013, 20(12):1367-1376.
64. Hegemann B., et al. Systematic phosphorylation analysis of human mitotic protein complexes. Sci. Signal. 2011, 4(198):rs12.
65. de Vree P.J., et al. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nat. Biotechnol. 2014, 32(10):1019-1025.
66. Bischof J., et al. An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(9):3312-3317.
67. Knapp J.M., Chung P., Simpson J.H. Generating customized transgene landing sites and multi-transgene arrays in Drosophila using phiC31 integrase. Genetics 2015, 199(4):919-934.
68. Rostovskaya M., et al. Transposon-mediated BAC transgenesis in human ES cells. Nucleic Acids Res. 2012, 40(19):e150.
69. Zhao L., Ng E.T., Koopman P. A piggyBac transposon- and gateway-enhanced system for efficient BAC transgenesis. Dev. Dyn. 2014, 243(9):1086-1094.
70. Frokjaer-Jensen C., et al. Random and targeted transgene insertion in Caenorhabditis elegans using a modified Mos1 transposon. Nat. Methods 2014, 11(5):529-534.
71. Maresca M., et al. Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Res. 2013, 23(3):539-546.
72. Gibson T.J., Seiler M., Veitia R.A. The transience of transient overexpression. Nat. Methods 2013, 10(8):715-721.
73. Cheeseman I.M., Desai A. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci. STKE 2005, (266):pl1.
74. Ong S.E., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1(5):376-386.
75. Ong S.E., Mann M. Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol. Biol. 2007, 359:37-52.
76. Wong J.W., Cagney G. An overview of label-free quantitation methods in proteomics by mass spectrometry. Methods Mol. Biol. 2010, 604:273-283.
77. Lei H., et al. A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques. PLoS One 2010, 5(12):e15898.
78. Gerstein M.B., et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010, 330(6012):1775-1787.
79. Niu W., et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 2011, 21(2):245-254.
80. Zhong M., et al. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010, 6(2):e1000848.
81. Jungkamp A.C., et al. In vivo and transcriptome-wide identification of RNA binding protein target sites. Mol. Cell 2011, 44(5):828-840.
82. Ahier A., Jarriault S. Simultaneous expression of multiple proteins under a single promoter in Caenorhabditis elegans via a versatile 2A-based toolkit. Genetics 2014, 196(3):605-613.
83. Diao F., White B.H. A novel approach for directing transgene expression in Drosophila: T2A-Gal4 in-frame fusion. Genetics 2012, 190(3):1139-1144.
84. Gonzalez M., et al. Generation of stable Drosophila cell lines using multicistronic vectors. Sci. Rep. 2011, 1:75.
85. Atkins J.F., et al. A case for "StopGo": reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go). RNA 2007, 13(6):803-810.
86. Underhill M.F., et al. Transient gene expression levels from multigene expression vectors. Biotechnol. Prog. 2007, 23(2):435-443.
87. Torres V., et al. A bicistronic lentiviral vector based on the 1D/2A sequence of foot-and-mouth disease virus expresses proteins stoichiometrically. J. Biotechnol. 2010, 146(3):138-142.
88. Kittler R., et al. RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells. Proc. Natl. Acad. Sci. U.S.A. 2005, 102(7):2396-2401.
89. Ueda T., et al. Generation of functional gut-like organ from mouse induced pluripotent stem cells. Biochem. Biophys. Res. Commun. 2010, 391(1):38-42.
90. Mathur A., et al. Human induced pluripotent stem cell-based microphysiological tissue models of myocardium and liver for drug development. Stem Cell Res. Ther. 2013, 4(Suppl. 1):S14.
91. Sterneckert J.L., Reinhardt P., Scholer H.R. Investigating human disease using stem cell models. Nat. Rev. Genet. 2014, 15(9):625-639.
92. Hynds R.E., Giangreco A. Concise review: the relevance of human stem cell-derived organoid models for epithelial translational medicine. Stem Cells 2013, 31(3):417-422.
93. Fischer U., Englbrecht C., Chari A. Biogenesis of spliceosomal small nuclear ribonucleoproteins. Wiley Interdiscip. Rev. RNA 2011, 2(5):718-731.
94. Okada M., et al. The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat. Cell Biol. 2006, 8(5):446-457.