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Incorrect use of the term synteny
Author: Eberhard Passarge,Bernhard Horsthemke ,Rosann A. Farber
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"correspondence nature genetics ? volume 23 ? december 1999 387 T he term ?synteny? (or syntenic) refers to gene loci on the same chromo- some regardless of whether or not they are genetically linked by classic linkage analy- sis 1 . This term was introduced in 1971 by John H. Renwick, of the London School of Hygiene and Tropical Medicine, at the 4 th Internal Congress of Human Genetics in Paris with one of us (E.P.) in attendance. The need for such a term was suggested to J.H. Renwick by E.A. Murphy, of Johns Hopkins University 2 . It arose as a conse- quence of the new methods in gene map- ping using somatic cell hybrid cells. Human genes located on the same chro- mosome with a genetic distance that could not be determined by the frequency of recombination lacked a term of reference. ?Synteny? means ?same thread? (or rib- bon), a state of being together in location, as synchrony would be together in time. Although several textbooks 3?10 and other reference works 11?15 give a correct defini- tion, the term synteny nowadays is often used to refer to gene loci in different organisms located on a chromosomal region of common evolutionary ancestry. This new usage of the term synteny does not correspond to its original definition and correct language derivation. A survey of 11 articles in Nature Genetics since 1992 using the term syntenic or synteny in either the title or the abstract revealed usage incorrect in 8 and ambiguous in 3. We believe molecular biologists ought to respect the original definition of syn- teny and its etymological derivation, espe- cially as this term is still needed to refer to genes located on the same chromosome. We recognize the need to refer to gene loci of common ancestry. Correct terms exist: ?paralogous? for genes that arose from a common ancestor gene within one species and ?orthologous? for the same gene in dif- ferent species. Eberhard Passarge 1 , Bernhard Horsthemke 1 & Rosann A. Farber 2 1 Institut f�r Humangenetik, Universit�tsklinikum Essen, Essen, Germany. 2 Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. Correspondence should be addressed to E.P. (e-mail: eberhard.passarge@uni-essen.de). 1. Renwick, J.H. Annu. Rev. Genet. 5, 81?120 (1972). 2. Renwick, J.H. in Human Genetics. Proceedings of the Fourth International Congress of Human Genetics, 6-11 September 1971 (eds de Grouchy, J., Ebling, F.J.G. & Henderson, I.W.) 443?444 (Excerpta Medica, Amsterdam, 1972). 3. Levitan, M. Textbook of Human Genetics (Oxford University Press, Oxford, 1988). 4. Sutton, M.E. An Introduction to Human Genetics (Harcourt Brace Jovanovich, San Diego, 1988). 5. Thompson, M.W., McInnes, R.R. & Willard, H.F. Genetics in Medicine (W.B. Saunders, Philadelphia, 1991). 6. Rothwell, N.V. Understanding Genetics. A Molecular Approach (Wiley-Liss, New York, 1993). 7. Connor, J.M. & Ferguson-Smith, M.A. Essential Medical Genetics (Blackwell Scientific, Oxford, 1993). 8. Mueller, R.F. & Young, I.D. Emery?s Elements of Medical Genetics (Churchill Livingstone, Edinburgh, 1995). 9. Jorde, L.B., Carey, J.C. & White, R.L. Medical Genetics (Mosby, St. Louis, 1995). 10. Gelehrter, T.D., Collins, F.S. & Ginsburg, D. Principles of Medical Genetics (Williams & Wilkins, Baltimore, 1998). 11. Murphy, E.A. & Chase, G.E. Principles of Genetic Counseling (Year Book Medical, Chicago, 1975). 12. Rieger, R., Michaelis, A. & Green, M.M. Glossary of Genetics and Cytogenetics (Springer Verlag Heidelberg, New York, 1976). 13. Ott, J. Analysis of Human Genetic Linkage (Johns Hopkins University Press, Baltimore, 1991). 14. Strachan, T. & Read, A.P. Molecular Human Genetics (BIOS Scientific, London, 1996). 15. Snustad, D.P., Simmons, M.J. & Jenkins, J.B. Principles of Genetics 749 (John Wiley & Sons, New York, 1997). Incorrect use of the term synteny H ow many human genes are expressed ubiquitously, in all human tissues, and how many are expressed in tissue-spe- cific patterns? To answer these fundamen- tal questions in molecular biology, we have analysed 3.5-million transcripts from 19 normal and diseased tissue types. We found that as many as 43,500 genes can be expressed in a single cell type. Only a small fraction of transcripts were exclusively expressed in any individual tissue, whereas nearly 1,000 genes were expressed in all cell types examined. We found 40 genes to be expressed at elevated levels in all cancer tissues but not in normal cells. Serial analysis of gene expression (SAGE) studies 1,2 of 84 libraries derived from 19 different sources identified 134,135 transcripts from approximately 84,000 different genes (Table 1; data and analysis available at http://genetics.nature. com/supplementary_info/). Expression levels for these genes ranged from 0.3 to 9,417 transcript copies per cell. The tran- script tags matched approximately 4,300 known genes and 41,000 genes with unknown functions, whereas the remaining transcript tags (46%) had no matches to existing databases (Table 2, see http://genet- ics.nature.com/supplementary_info/). The subset of expression data from col- orectal cancer cell lines provided the first relatively complete analysis of the tran- scripts expressed in a single mammalian cell type. We analysed 643,283 transcripts from colorectal cancer cell lines. As human cells contain approximately 300,000 mRNA molecules, this number was suffi- cient to provide approximately twofold coverage of the transcriptome, revealing over 83% of transcripts expected to be pre- Analysis of human transcriptomes Table 1 ? Tissues and transcript tags Libraries b Total transcripts c Unique genes d Normal tissues a colon epithelium 5?9 2 98,089 12,941 keratinocytes e 2 83,835 12,598 breast epithelium e 2 107,632 13,429 lung epithelium 10 2 111,848 11,636 melanocytes e 2 110,631 14,824 prostate e 2 98,010 9,786 monocytes e 3 66,673 9,504 kidney epithelium e 2 103,836 15,094 chondrocytes e 4 88,875 11,628 cardiomyocytes e 4 77,374 9,449 brain 9 3 202,448 23,580 Diseased tissues a colon cancer 5?9,11,e 22 1,004,509 56,153 pancreatic cancer 5?8 4 126,414 17,050 breast cancer e 5 226,630 18,685 lung cancer 10 5 221,302 22,783 melanoma e 10 269,332 25,600 polycystic kidney disease e 2 112,839 16,280 haemangiopericytoma e 5 199,985 31,351 brain cancer 9 3 186,567 23,108 Total 84 3,496,829 84,103 a Source of the RNA analysed. b The number of SAGE libraries analysed. c The total number of transcripts analysed from each tissue. d The number of unique genes observed in each tissue. e Unpublished data. See Methods (http://genetics.nature.com/supplementary_info/) for the derivation of a number of unique genes. � 1999 Nature America Inc. ? http://genetics.nature.com � 1999 Nature America Inc. ? http://genetics.nature.com "
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