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A Crisis in Postgenomic Nomenclature

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A Crisis in Postgenomic Nomenclature S CIENCE’ S C OMPASS 65 7. A.W. Segal et al., Nature 290, 406 (1981). 13. S. J. Klebanoff, J. Bacteriol. 95, 2131 (1968). 20. C. Spiegelhalder et al., Infect. Immun. 61, 5315 64 8. L. M. Henderson, J. B. Chappell, O. T. G. Jones, 14. J. M. Albrich, J. K. Hurst, FEBS Lett. 144, 157 (1982). (1993). Biochem. J. 246, 325 (1987). 15. J. P. Gaut et al., Proc. Natl. Acad. Sci. U.S.A. 98, 11961 21. P. R. Langford, B. M. Loynds, J. S. Kroll, Infect. Immun. 63 9. Nanda, S. Grinstein, Proc. Natl. Acad. Sci. U.S.A. 88, (2001). 64, 5035 (1997). 62 10816 (1991). 16. A. J. Kettle, C. C. Winterbourn, Biochemistry 40, 22. B. L. Beaman et al., Infect. Immun. 47, 135 (1985). 61 10. G. L. Mandell, E. W. Hook, J. Bacteriol. 100, 531 10204 (2001). 23. L. Beaman, B. L. Beaman, Infect. Immun. 58, 3122 60 (1969). 17. M. B. Hampton, A. J. Kettle, C. C. Winterbourn, Infect. (1990). 11. R. B. Johnston Jr., R.L. Baehner, Blood 35, 350 Immun. 64, 3512 (1996). 24. A. A.Voetman et al., J. Clin. Invest. 67, 1541 (1981). 59 (1970). 18. E. Kusunose et al., J. Biochem. 80, 1343 (1994). 25. G. L. Mandell, Infect. Immun. 9, 337 (1974). 58 12. C. E. Gerber et al., Blood 98, 3097 (2001). 19. B. L. Beaman et al., J. Biol. Chem. 258, 91 (1994). 26. J.Weiss et al., J. Clin. Invest. 69, 959 (1982). 57 56 PERSPECTIVES: GENOMICS 55 fine a cell’s glycosylome at time zero, 54 and seconds later the cell undergoes pro- 53 A Crisis in Postgenomic grammed cell death, its carbohydrate 52 moieties are likely to give up the ghost 51 nonuniformly, with some persisting to 50 Nomenclature the last. At what point in this process do 49 Stanley Fields and Mark Johnston we define the glycosylome? 48 To circumvent these difficulties and 47 e all know what a genome is, and century old, and “nucleosome” and “repli- others sure to emerge, we propose some 46 we think we understand the term some” originated more than a quarter cen- simple rules. First, considerable precision 45 Wproteome, but can anyone tell us tury ago (1). Even “spliceosome” and “pro- can be gained by a more circumscribed 44 the constituents of a functome? As the teasome” are approaching two decades of representation of the ’ome’s constituents, 43 availability of complete genome sequences service. This relatively modest growth in for example, phospholipidome rather than 42 has spawned analyses of entire comple- the application of the suffix ’some contrasts lipidome; inositol phospholipidome 41 ments of proteins, RNAs, metabolites, and with that for ’ome. Although “genome” was rather than phospholipidome. Of course, 40 other cellular constituents, there has arisen coined by German scientists (“genom”) in this has the potential to be abused and to 39 a need for a terminology expansive enough 1920 and first used in English in 1930 (1), lead to absurdly finer subdivisions. For 38 to encompass the global scale of the data. none of the other ’omes can lay claim to example, do we want the transcription fac- 37 A sensible suffix was appropriated for this more than a few years torome to be subdivid- 36 purpose, but now is proliferating uncon- of history. ed into the transcrip- 35 trollably: genome, proteome, transcrip- There are two un- tional activatorome 34 tome, metabolome, interactome, even phe- derappreciated and so and the transcriptional 33 nome, with many more ’omes sure to be in far unresolved predica- repressorome? Does 32 various stages of gestation. Perhaps it is not ments with the ’ome not the transcription- 31 completely coincidental that ’ome is also terminology. First, there al activatorome then 30 the anglicized form of ’oma (1), commonly is a problem with its include the zincfin- 29 used to name such unwelcome intrusions scope. Whereas the ex- gerome, which itself 28 as sarcoma, lipoma, and fibroma. This tent of the genome is Image not includes the Cys-His 27 metastatic growth of the ’ome is spreading clear (all the genetic zincfingerome and the 26 imprecision and confusion. Meanwhile, re- material of a cell), what available for Cys-Cys zincfinger- 25 search summaries in the front of major sci- constitutes a transcrip- online use. ome? To avoid this pit- 24 entific weeklies with titles like ’Ome Sweet tome is not so obvious. fall, we propose that 23 ’Ome, and ’Ome…’Ome…’Ome: The Ge- Is it just the mRNAs, the minimum number 22 nomicist’s New Mantra, and our personal or does it include the of similar cellular con- 21 favorite, The ’Ome: A Pièce de Résistance, transcripts produced stituents that consti- 20 only serve to confuse us further. Because a by RNA polymerases I tute an ’ome be clearly 19 clear and widely accepted nomenclature is and III? What about defined. Seven or eight 18 essential for the health of any discipline, a transcripts that end up seems to us a conser- 17 systematic solution to this problem is ur- in the enzymes telom- vative yet valuable cut- 16 gently needed. erase or RNaseP, or in off. Thus, there can be 15 It is often instructive to look to the past ribonucleoprotein par- no “nucleicacidome” 14 for guidance. A now familiar nomenclature ticles such as snRNPs? (there’s only DNA and 13 grew up around the related suffix ’some (for The precise constituents of an ’ome are RNA, after all), but there certainly is a 12 which ’ome is sometimes mistaken), mean- often not well specified. “nucleotideome” (A, T, G, C, U, I, plus 11 ing “body,” which has been used to name A second, and much more severe, myriad modified purines and pyrimidines); 10 various intracellular particles. “Chromo- problem is the conditional nature of no “actinome,” of course (humans have 9 some” dates back more than 100 years, “ri- some ’omes. The genome—notwith- only six actin isoforms), but definitely a 8 bosome” and “lysosome” are nearly half a standing the occasional hop of a transpo- “tubulome” (multiple α and β tubulin iso- 7 son or rearrangement of an immunoglob- types, not to mention γ, δ, ε, ζ, and η 6 S. Fields is in the Department of Genome Sciences and ulin gene—is a relatively fixed entity, tubulins). 5 Department of Medicine, Howard Hughes Medical In- and reasonable people can agree on its Second, it would be helpful if the state 4 stitute, University of Washington, Seattle, WA 98195, definition. But the proteome present in a of the cells for which an ’ome is defined 3 USA. M. Johnston is in the Department of Genetics, Washington University Medical School, St. Louis, MO cell at one moment will differ drastically were apparent in the nomenclature. If ini- 2 63110, USA. E-mail: [email protected], from that in the same cell moments after tially we use basic parameters like temper- 1 CREDIT: JOE SUTLIFF [email protected] it has been heated to 65°C. Or, if we de- ature, pH, cell cycle stage, and subcellular www.sciencemag.org SCIENCE VOL 296 26 APRIL 2002 671 S CIENCE’ S C OMPASS 65 localization, we can obtain a definition Enzyme Commission (E.C.)–style nomen- Which brings us to a final thought. As bi- 64 such as, “the 37°-7.4-G1-Golgi-N-but-not- clature should be established that allows ologists approach a definition of all of the 63 O-linked glycosylome.” This system has the incorporation of as many specifica- various machines that carry out life’s basic 62 enormous versatility and can be suitably tions as needed. In this format, the particu- processes, we should be able to define the 61 expanded to incorporate other parameters, lar glycosylome mentioned above has been ultimate ’ome, the collection of all of these 60 including cell source, developmental tim- provisionally designated the 4.7.5.3.8ome. machines: the “someome.” Others might 59 ing, and much more. Perhaps at first this We expect that these numerical names, af- prefer to call this the “omesome,” given 58 may seem a bit cumbersome. But please ter a sufficient number of citations, will that it defines the machine comprising all 57 remember that this nomenclature is no become as familiar as many E.C. numbers. the ’omes. Either one is a vast improve- 56 more intricate than the (±)-N-methyl-γ-[4- The adoption of our simplified system ment over their imprecise and prosaic syn- 55 (trifluoromethyl)phenoxy]-benzene- means that as new technologies emerge onym currently in wide use: the cell. 54 propanamine used so effectively by enabling the assay of yet more cellular Reference 53 chemists and many others. As a more constituents, the nomenclature is already 1. Oxford English Dictionary Online (Oxford Univ. Press, 52 wieldy alternative, we also propose that an in hand to deal with the discoveries. Oxford, UK, ed. 2, 2002). 51 50 RETROSPECTIVE 49 choice, not only for particle physics but al- 48 so for the future of synchrotron radiation. 47 Willibald Jentschke From 1971 to 1975, Jentschke served 46 as director general of CERN Laboratory I 45 (the original Meyrin site). He oversaw the 44 (1911–2002) exploitation of important new research in- 43 Albrecht Wagner vestments, notably the Intersecting Stor- 42 age Rings (ISR), high-intensity proton 41 illibald Jentschke, founder of Geneva. Soon after high-energy physics ex- beams, and an ambitious research program 40 Germany’s particle physics labo- periments with accelerated electrons began for neutrino physics. In 1973, this effort 39 Wratory DESY near Hamburg and at DESY, research with synchrotron radia- enabled physicists using the Gargamelle 38 former director general of CERN, passed tion, emitted by the electrons during accel- bubble chamber to discover the neutral 37 away on 11 March 2002, a few months af- eration, became the second strong research currents of the weak inter- 36 ter his 90th birthday.
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