The Xenopus ORFeome: A resource that enables functional genomics

Developmental Biology

Volumn 408, Issue 2, 2015, Pages 345-357

  Grant, Ian M ^a   Balcha, Dawit ^b   Hao, Tong ^b   Shen, Yun ^b   Trivedi, Prasad ^e   Patrushev, Ilya ^a   Fortriede, Joshua D ^c   Karpinka, John B ^d   Liu, Limin ^e   Zorn, Aaron M ^c   Stukenberg, P Todd ^e   Hill, David E ^b   Gilchrist, Michael J ^a  

^a THE FRANCIS CRICK INSTITUTE   (United Kingdom)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^d UNIVERSITY OF CALGARY   (Canada)

^e UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Gateway; Gene annotation; Open reading frame; ORFeome; Recombinational cloning; Xenopus

Indexed keywords

ARTICLE; CLONE; DATA BASE; DISEASE MODEL; EXPRESSION VECTOR; FUNCTIONAL GENOMICS; NONHUMAN; OPEN READING FRAME; PREDICTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; XENOPUS; XENOPUS LAEVIS; XENOPUS TROPICALIS; ANIMAL; BIOLOGICAL MODEL; DISEASES; GENETIC DATABASE; GENETICS; GENOMICS; HUMAN; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; VALIDATION STUDY;

COMPLEMENTARY DNA; XENOPUS PROTEIN;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; DATABASES, GENETIC; DISEASE; DNA, COMPLEMENTARY; GENOMICS; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; XENOPUS; XENOPUS LAEVIS; XENOPUS PROTEINS;

EID: 84955273160     PISSN: 00121606     EISSN: 1095564X     Source Type: Journal    
DOI: 10.1016/j.ydbio.2015.09.004     Document Type: Article

References (46)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. Bell M.R., Belarde J.A., Johnson H.F., Aizenman C.D. A neuroprotective role for polyamines in a Xenopus tadpole model of epilepsy. Nat. Neurosci. 2011, 14:505-512.
3. Bischof J., Björklund M., Furger E., Schertel C., Taipale J., Basler K. A versatile platform for creating a comprehensive UAS-ORFeome library in Drosophila. Development 2013, 140:2434-2442.
4. Bowes J.B., Snyder K.A., Segerdell E., Gibb R., Jarabek C., Noumen E., Pollet N., Vize P.D. Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res. 2008, 36:D761-D767.
5. Brandner C.J., Maier R.H., Henderson D.S., Hintner H., Bauer J.W., Onder K. The ORFeome of Staphylococcus aureus v1.1. BMC Genom. 2008, 9:321.
6. Brasch M.A., Hartley J.L., Vidal M. ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res. 2004, 14:2001-2009.
7. Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. BLAST+: architecture and applications. BMC Bioinform. 2009, 10:421.
8. Cheeseman I.M., Desai A. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci. Signal. 2005, 2005:pl1.
9. Cheeseman I.M., Hori T., Fukagawa T., Desai A. KNL1 and the CENP-H/I/K complex coordinately direct kinetochore assembly in vertebrates. Mol. Biol. Cell. 2008, 19:587-594. http://dx.doi.org/10.1091/mbc.E07-10-1051.
10. Chernet B.T., Levin M. Transmembrane voltage potential is an essential cellular parameter for the detection and control of tumor development in a Xenopus model. Dis. Model. Mech. 2013, 6:595-607.
11. Dricot A., Rual J.-F., Lamesch P., Bertin N., Dupuy D., Hao T., Lambert C., Hallez R., Delroisse J.-M., Vandenhaute J., Lopez-Goñi I., Moriyon I., Garcia-Lobo J.M., Sangari F.J., Macmillan A.P., Cutler S.J., Whatmore A.M., Bozak S., Sequerra R., Doucette-Stamm L., Vidal M., Hill D.E., Letesson J.-J., De Bolle X. Generation of the Brucella melitensis ORFeome version 1.1. Genome Res. 2004, 14:2201-2206.
12. Fakhro K.A., Choi M., Ware S.M., Belmont J.W., Towbin J.A., Lifton R.P., Khokha M.K., Brueckner M. Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning. Proc. Natl. Acad. Sci. USA 2011, 108:2915-2920.
13. Gelperin D.M., White M.A., Wilkinson M.L., Kon Y., Kung L.A., Wise K.J., Lopez-Hoyo N., Jiang L., Piccirillo S., Yu H., Gerstein M., Dumont M.E., Phizicky E.M., Snyder M., Grayhack E.J. Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev. 2005, 19:2816-2826.
14. Gerhard D.S., Wagner L., Feingold E.A., Shenmen C.M., Grouse L.H., Schuler G., Klein S.L., Old S., Rasooly R., Good P., Guyer M., Peck A.M., Derge J.G., Lipman D., Collins F.S., Jang W., Sherry S., Feolo M., Misquitta L., Lee E., Rotmistrovsky K., Greenhut S.F., Schaefer C.F., Buetow K., Bonner T.I., Haussler D., Kent J., Kiekhaus M., Furey T., Brent M., Prange C., Schreiber K., Shapiro N., Bhat N.K., Hopkins R.F., Hsie F., Driscoll T., Soares M.B., Casavant T.L., Scheetz T.E., Brown-stein M.J., Usdin T.B., Toshiyuki S., Carninci P., Piao Y., Dudekula D.B., Ko M.S., Kawakami K., Suzuki Y., Sugano S., Gruber C.E., Smith M.R., Simmons B., Moore T., Waterman R., Johnson S.L., Ruan Y., Wei C.L., Mathavan S., Gunaratne P.H., Wu J., Garcia A.M., Hulyk S.W., Fuh E., Yuan Y., Sneed A., Kowis C., Hodgson A., Muzny D.M., McPherson J., Gibbs R.A., Fahey J., Helton E., Ketteman M., Madan A., Rodrigues S., Sanchez A., Whiting M., Madari A., Young A.C., Wetherby K.D., Granite S.J., Kwong P.N., Brinkley C.P., Pearson R.L., Bouffard G.G., Blakesly R.W., Green E.D., Dickson M.C., Rodriguez A.C., Grimwood J., Schmutz J., Myers R.M., Butterfield Y.S., Griffith M., Griffith O.L., Krzywinski M.I., Liao N., Morin R., Palmquist D., Petrescu A.S., Skalska U., Smailus D.E., Stott J.M., Schnerch A., Schein J.E., Jones S.J., Holt R.A., Baross A., Marra M.A., Clifton S., Makowski K.A., Bosak S., Malek J. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004, 14:2121-2127.
15. Gilchrist M.J. From expression cloning to gene modeling: the development of Xenopus gene sequence resources. Genesis 2012, 50:143-154.
16. Gilchrist M.J., Zorn A.M., Voigt J., Smith J.C., Papalopulu N., Amaya E. Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev. Biol. 2004, 271:498-516.
17. Gilchrist M.J., Sobral D., Khoueiry P., Daian F., Laporte B., Patrushev I., Matsumoto J., Dewar K., Hastings K.E., Satou Y., Lemaire P., Rothbacher U. A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: application to the ascidian Ciona intestinalis. Dev. Biol. 2015, 404:149-163.
18. Glinka A., Wu W., Delius H., Monaghan a P., Blumenstock C., Niehrs C. Dickkopf-1 is a member of a new family of secreted proteins and functions in head induction. Nature 1998, 391:357-362.
19. Harland R.M., Grainger R.M. Xenopus research: metamorphosed by genetics and genomics. Trends Genet. 2011, 27:507-515.
20. Hartley J.L., Temple G.F., Brasch M.A. DNA cloning using in vitro site-specific recombination. Genome Res. 2000, 10:1788-1795.
21. Hellsten U., Harland R.M., Gilchrist M.J., Hendrix D., Jurka J., Kapitonov V., Ovcharenko I., Putnam N.H., Shu S., Taher L., Blitz I.L., Blumberg B., Dichmann D.S., Dubchak I., Amaya E., Detter J.C., Fletcher R., Gerhard D.S., Goodstein D., Graves T., Grigoriev I.V., Grimwood J., Kawashima T., Lindquist E., Lucas S.M., Mead P.E., Mitros T., Ogino H., Ohta Y., Poliakov A.V., Pollet N., Robert J., Salamov A., Sater A.K., Schmutz J., Terry A., Vize P.D., Warren W.C., Wells D., Wills A., Wilson R.K., Zimmerman L.B., Zorn A.M., Grainger R.M., Grammer T., Khokha M.K., Richardson P.M., Rokhsar D.S. The genome of the Western clawed frog Xenopus tropicalis. Science 2010, 328:633-636.
22. Karpinka J.B., Fortriede J.D., Burns K.A., James-Zorn C., Ponferrada V.G., Lee J., Karimi K., Zorn A.M., Vize P.D. Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res. 2014, 1-8.
23. Klein S.L., Strausberg R.L., Wagner L., Pontius J., Clifton S.W., Richardson P.M. Genetic and genomic tools for Xenopus research: the NIH Xenopus initiative. Dev. Dyn. 2002, 225:384-391.
24. Lage K., Hansen N.T., Karlberg E.O., Eklund A.C., Roque F.S., Donahoe P.K., Szallasi Z., Jensen T.S., Brunak S. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc. Natl Acad. Sci. USA 2008, 105:20870-20875.
25. Lamesch P., Li N., Milstein S., Fan C., Hao T., Szabo G., Hu Z., Venkatesan K., Bethel G., Martin P., Rogers J., Lawlor S., McLaren S., Dricot A., Borick H., Cusick M.E., Vandenhaute J., Dunham I., Hill D.E., Vidal M. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 2007, 89:307-315.
26. Maier C.J., Maier R.H., Virok D.P., Maass M., Hintner H., Bauer J.W., Onder K. Construction of a highly flexible and comprehensive gene collection representing the ORFeome of the human pathogen Chlamydia pneumoniae. BMC Genom. 2012, 13:632.
27. Matsuda Y., Uno Y., Kondo M., Gilchrist M.J., Zorn A.M., Rokhsar D.S., Schmid M., Taira M. A new nomenclature of Xenopus laevis chromosomes based on the phylogenetic relationship to Silurana/Xenopus tropicalis. Cytogenet Genome Res. 2015, 145:187-191.
28. McGarry T.J., Kirschner M.W. Geminin, an inhibitor of DNA replication, is degraded during mitosis. Cell 1998, 93:1043-1053.
29. Mii Y., Taira M. Secreted frizzled-related proteins enhance the diffusion of Wnt ligands and expand their signalling range. Development 2009, 136:4083-4088.
30. Morin R.D., Chang E., Petrescu A., Liao N., Griffith M., Chow W., Kirkpatrick R., Butterfield Y.S., Young A.C., Stott J., Barber S., Babakaiff R., Dickson M.C., Matsuo C., Wong D., Yang G.S., Smailus D.E., Wetherby K.D., Kwong P.N., Grimwood J., Brinkley C.P., Brown-John M., Reddix-Dugue N.D., Mayo M., Schmutz J., Beland J., Park M., Gibson S., Olson T., Bouffard G.G., Tsai M., Featherstone R., Chand S., Siddiqui A.S., Jang W., Lee E., Klein S.L., Blakesley R.W., Zeeberg B.R., Narasimhan S., Weinstein J.N., Pennacchio C.P., Myers R.M., Green E.D., Wagner L., Gerhard D.S., Marra M.A., Jones S.J., Holt R.A. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res. 2006, 16:796-803.
31. Raines R.T., McCormick M., Oosbree T.R.V., Mierendorf R.C. The S·tag fusion system for protein purification. Methods Enzymol. 2000, 326:362-376.
32. Rajagopala S.V., Yamamoto N., Zweifel A.E., Nakamichi T., Huang H.-K., Mendez-Rios J.D., Franca-Koh J., Boorgula M.P., Fujita K., Suzuki K.-I., Hu J.C., Wanner B.L., Mori H., Uetz P. The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology. BMC Genom. 2010, 11:470.
33. Rankin S., Ayad N.G., Kirschner M.W. Sororin, a substrate of the anaphase-promoting complex, is required for sister chromatid cohesion in vertebrates. Mol. Cell 2005, 18:185-200.
34. Reboul J., Vaglio P., Tzellas N., Thierry-Mieg N., Moore T., Jackson C., Shin-I T., Kohara Y., Thierry-Mieg D., Thierry-Mieg J., Lee H., Hitti J., Doucette-Stamm L., Hartley J.L., Temple G.F., Brasch M.A., Vandenhaute J., Lamesch P.E., Hill D.E., Vidal M. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat. Genet. 2001, 27:332-336.
35. Reboul J., Vaglio P., Rual J.-F., Lamesch P., Martinez M., Armstrong C.M., Li S., Jacotot L., Bertin N., Janky R.S., Moore T., Hudson J.R., Hartley J.L., Brasch M.A., Vandenhaute J., Boulton S., Endress G.A., Jenna S., Chevet E., Papasotiropoulos V., Tolias P.P., Ptacek J., Snyder M.P., Huang R., Chance M.R., Lee H., Doucette-Stamm L., Hill D.E., Vidal M. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 2003, 34:35-41.
36. Rual J.-F., Hirozane-Kishikawa T., Hao T., Bertin N., Li S., Dricot A., Li N., Rosenberg J., Lamesch P., Vidalain P.-O., Clingingsmith T.R., Hartley J.L., Esposito D., Cheo D., Moore T., Simmons B., Sequerra R., Bosak S.A., Doucette-Stamm L., Le Peuch C., Vandenhaute J., Cusick M.E., Albala J.S., Hill D.E., Vidal M. Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res. 2004, 14:2128-2135.
37. Rupp R.A., Snider L., Weintraub H. Xenopus embryos regulate the nuclear localization of XMyoD. Genes Dev. 1994, 8:1311-1323.
38. Smith W.C., Harland R.M. Expression cloning of noggin, a new dorsalizing factor localized to the Spemann organizer in Xenopus embryos. Cell 1992, 70:829-840.
39. Soto X., Li J., Lea R., Dubaissi E., Papalopulu N., Amaya E. Inositol kinase and its product accelerate wound healing by modulating calcium levels, Rho GTPases, and F-actin assembly. Proc. Natl. Acad. Sci. USA 2013, 110:11029-11034.
40. Stapleton M., Liao G., Brokstein P., Hong L., Carninci P., Shiraki T., Hayashizaki Y., Champe M., Pacleb J., Wan K., Yu C., Carlson J., George R., Celniker S., Rubin G.M. The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res. 2002, 12:1294-1300.
41. Stukenberg P.T., Lustig K.D., McGarry T.J., King R.W., Kuang J., Kirschner M.W. Systematic identification of mitotic phosphoproteins. Curr. Biol. 1997, 7:338-348.
42. Temple G.F., Gerhard D.S., Rasooly R., Feingold E.A., Good P.J., Robinson C., Mandich A., Derge J.G., Lewis J., Shoaf D., Collins F.S., Jang W., Wagner L., Shenmen C.M., Misquitta L., Schaefer C.F., Buetow K.H., Bonner T.I., Yankie L., Ward M., Phan L., Astashyn A., Brown G., Farrell C., Hart J., Landrum M., Maidak B.L., Murphy M., Murphy T., Rajput B., Riddick L., Webb D., Weber J., Wu W., Pruitt K.D., Maglott D., Siepel A., Brejova B., Diekhans M., Harte R., Baertsch R., Kent J., Haussler D., Brent M., Langton L., Comstock C.L.G., Stevens M., Wei C., van Baren M.J., Salehi-Ashtiani K., Murray R.R., Ghamsari L., Mello E., Lin C., Pennacchio C., Schreiber K., Shapiro N., Marsh A., Pardes E., Moore T., Lebeau A., Muratet M., Simmons B., Kloske D., Sieja S., Hudson J., Sethupathy P., Brownstein M., Bhat N., Lazar J., Jacob H., Gruber C.E., Smith M.R., McPherson J., Garcia A.M., Gunaratne P.H., Wu J., Muzny D., Gibbs R.A., Young A.C., Bouffard G.G., Blakesley R.W., Mullikin J., Green E.D., Dickson M.C., Rodriguez A.C., Grimwood J., Schmutz J., Myers R.M., Hirst M., Zeng T., Tse K., Moksa M., Deng M., Ma K., Mah D., Pang J., Taylor G., Chuah E., Deng A., Fichter K., Go A., Lee S., Wang J., Griffith M., Morin R., Moore R.A., Mayo M., Munro S., Wagner S., Jones S.J.M., Holt R.A., Marra M.A., Lu S., Yang S., Hartigan J., Graf M., Wagner R., Letovksy S., Pulido J.C., Robison K., Esposito D., Hartley J., Wall V.E., Hopkins R.F., Ohara O., Wiemann S. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009, 19:2324-2333.
43. Uno Y., Nishida C., Takagi C., Ueno N., Matsuda Y. Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication. Heredity 2013, 111:430-436.
44. Walhout A.J.M., Temple G.F., Brasch M.A., Hartley J.L., Lorson M.A., van den Heuvel S., Vidal M. Gateway recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 2000, 328:575-592.
45. Yang X., Boehm J.S., Yang X., Salehi-Ashtiani K., Hao T., Shen Y., Lubonja R., Thomas S.R., Alkan O., Bhimdi T., Green T.M., Johannessen C.M., Silver S.J., Nguyen C., Murray R.R., Hieronymus H., Balcha D., Fan C., Lin C., Ghamsari L., Vidal M., Hahn W.C., Hill D.E., Root D.E. A public genome-scale lentiviral expression library of human ORFs. Nat. Methods 2011, 8:659-661.
46. Zou H., McGarry T.J., Bernal T., Kirschner M.W. Identification of a vertebrate sister-chromatid separation inhibitor involved in transformation and tumorigenesis. Science 1999, 285:418-422.