Evolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3

Physiological Genomics

Volumn 45, Issue 15, 2013, Pages 667-683

  Geahlen, Jessica H ^a   Lapid, Carlo ^b   Thorell, Kaisa ^c   Nikolskiy, Igor ^b   Huh, Won Jae ^a   Oates, Edward L ^a   Lennerz, Jochen K M ^a   Tian, Xiaolin ^a   Weis, Victoria G ^a   Khurana, Shradha S ^a   Lundin, Samuel B ^c   Templeton, Alan R ^b   Mills, Jason C ^a  

^a Division of Gastroenterology   (United States)

^b WASHINGTON UNIVERSITY   (United States)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

1000 genomes data; BRICHOS domain; Population genetics; Selective sweeps

Indexed keywords

CELL PROTEIN; GASTROKINE 3; TRYPTOPHAN; UNCLASSIFIED DRUG;

ALLELE; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DIRECTIONAL SELECTION; EXON; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; GENETIC SCREENING; HAPLOTYPE; HUMAN; HUMAN CELL; HUMAN TISSUE; METAPLASIA; MOLECULAR EVOLUTION; MOUSE; MUCOUS CELL; NONHUMAN; POPULATION GENETICS; PRIORITY JOURNAL; RACE; SELECTIVE SWEEP; SINGLE NUCLEOTIDE POLYMORPHISM; STOMACH; STOMACH ANTRUM; STOP CODON;

EID: 84881020432     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00169.2012     Document Type: Article

References (57)

1. Amin SB, Shah PK, Yan A, Adamia S, Minvielle S, Avet-Loiseau H, Munshi NC, Li C. The dChip survival analysis module for microarray data. BMC Bioinformatics 12: 72, 2011.
2. Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G. LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9: 323, 2008.
3. Beaumont MA, Nichols RA. Evaluating loci for use in the genetic analysis of population structure. Proc R Soc Lond B 263: 1619-1626, 1996.
4. Bredemeyer AJ, Geahlen JH, Weis VG, Huh WJ, Zinselmeyer BH, Srivatsan S, Miller MJ, Shaw AS, Mills JC. The gastric epithelial progenitor cell niche and differentiation of the zymogenic (chief) cell lineage. Dev Biol 325: 211-224, 2009.
5. Brunak S, Engelbrecht J, Knudsen S. Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol 220: 49-65, 1991.
6. Castro LF, Lopes-Marques M, Goncalves O, Wilson JM. The evolution of pepsinogen C genes in vertebrates: duplication, loss and functional diversification. PLoS One 7: e32852, 2012.
7. Chu G, Qi S, Yang G, Dou K, Du J, Lu Z. Gastrointestinal tract specific gene GDDR inhibits the progression of gastric cancer in a TFF1 dependent manner. Mol Cell Biochem 359: 369-374, 2012.
8. Desai MM, Plotkin JB. The polymorphism frequency spectrum of finitely many sites under selection. Genetics 180: 2175-2191, 2008.
9. Du JJ, Dou KF, Peng SY, Wang WZ, Wang ZH, Xiao HS, Guan WX, Liu YB, Gao ZQ. [Down-regulated full-length novel gene GDDR and its effect on gastric cancer]. Zhonghua Yi Xue Za Zhi 83: 1166-1168, 2003.
10. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797, 2004.
11. Gargiulo AM, Ceccarelli P, Dall'aglio C, Pedini V. Ultrastructural study on the stomach of Tilapia spp (Teleostei). Anat Histol Embryol 26: 331-336, 1997.
12. Hanby AM, Poulsom R, Playford RJ, Wright NA. The mucous neck cell in the human gastric corpus: a distinctive, functional cell lineage. J Pathol 187: 331-337, 1999.
13. Hebsgaard SM, Korning PG, Tolstrup N, Engelbrecht J, Rouze P, Brunak S. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucl Acids Res 24: 3439-3452, 1996.
14. Hu J, Ge H, Newman M, Liu K. OSA: a fast and accurate alignment tool for RNA-Seq. Bioinformatics 28: 1933-1934, 2012.
15. Huh WJ, Khurana SS, Geahlen JH, Kohli K, Waller RA, Mills JC. Tamoxifen induces rapid, reversible atrophy, and metaplasia in mouse stomach. Gastroenterology 142: 21-24, 2012.
16. Kalyana-Sundaram S, Kumar-Sinha C, Shankar S, Robinson DR, Wu YM, Cao X, Asangani IA, Kothari V, Prensner JR, Lonigro RJ, Iyer MK, Barrette T, Shanmugam A, Dhanasekaran SM, Palanisamy N, Chinnaiyan AM. Expressed pseudogenes in the transcriptional landscape of human cancers. Cell 149: 1622-1634, 2012.
17. Karam SM, Leblond CP. Identifying and counting epithelial cell types in the "corpus" of the mouse stomach. Anat Rec 232: 231-246, 1992.
18. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D493-D496, 2004.
19. Kouznetsova I, Laubinger W, Kalbacher H, Kalinski T, Meyer F, Roessner A, Hoffmann W. Biosynthesis of gastrokine-2 in the human gastric mucosa: restricted spatial expression along the antral gland axis and differential interaction with TFF1, TFF2 and mucins. Cell Physiol Biochem 20: 899-908, 2007.
20. Lewontin RC, Krakauer J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195, 1973.
21. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98: 31-36, 2001.
22. Mao W, Chen J, Peng TL, Yin XF, Chen LZ, Chen MH. Downregu-lation of gastrokine-1 in gastric cancer tissues and restoration of its expression induced gastric cancer cells to apoptosis. J Exp Clin Cancer Res 31: 49, 2012.
23. Martin TE, Powell CT, Wang Z, Bhattacharyya S, Walsh-Reitz MM, Agarwal K, Toback FG. A novel mitogenic protein that is highly expressed in cells of the gastric antrum mucosa. Am J Physiol Gastrointest Liver Physiol 285: G332-G343, 2003.
24. McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654, 1991.
25. Menheniott TR, Peterson AJ, O'Connor L, Lee KS, Kalantzis A, Kondova I, Bontrop RE, Bell KM, Giraud AS. A novel gastrokine, Gkn3, marks gastric atrophy and shows evidence of adaptive gene loss in humans. Gastroenterology 138: 1823-1835, 2010.
26. Moss SF, Lee JW, Sabo E, Rubin AK, Rommel J, Westley BR, May FE, Gao J, Meitner PA, Tavares R, Resnick MB. Decreased expression of gastrokine 1 and the trefoil factor interacting protein TFIZ1/GKN2 in gastric cancer: influence of tumor histology and relationship to prognosis. Clin Cancer Res 14: 4161-4167, 2008.
27. Narum SR, Hess JE. Comparison of F(ST) outlier tests for SNP loci under selection. Mol Ecol Resour 11, Suppl 1: 184-194, 2011.
28. Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res 11: 863-874, 2001.
29. Ogawa M, Nomura S, Varro A, Wang TC, Goldenring JR. Altered metaplastic response of waved-2 EGF receptor mutant mice to acute oxyntic atrophy. Am J Physiol Gastrointest Liver Physiol 290: G793-G804, 2006.
30. Oien KA, McGregor F, Butler S, Ferrier RK, Downie I, Bryce S, Burns S, Keith WN. Gastrokine 1 is abundantly and specifically expressed in superficial gastric epithelium, down-regulated in gastric carcinoma, and shows high evolutionary conservation. J Pathol 203: 789-797, 2004.
31. Ordoñez GR, Hillier LW, Warren WC, Grützner F, López-Otín C, Puente XS. Loss of genes implicated in gastric function during platypus evolution. Genome Biol 9: R81, 2008.
32. Otto WR, Patel K, McKinnell I, Evans MD, Lee CY, Frith D, Hanrahan S, Blight K, Blin N, Kayademir T, Poulsom R, Jeffery R, Hunt T, Wright NA, McGregor F, Oien KA. Identification of blottin: a novel gastric trefoil factor family-2 binding protein. Proteomics 6: 4235-4245, 2006.
33. Otto WR, Thim L. Trefoil factor family-interacting proteins. Cell Mol Life Sci 62: 2939-2946, 2005.
34. Paradis E. Pegas: an R package for population genetics with an integrat-ed-modular approach. Bioinformatics 26: 419-420, 2010.
35. Pink RC, Wicks K, Caley DP, Punch EK, Jacobs L, Carter DR. Pseudogenes: pseudo-functional or key regulators in health and disease? RNA 17: 792-798, 2011.
36. Ramsey VG, Doherty JM, Chen CC, Stappenbeck TS, Konieczny SF, Mills JC. The maturation of mucus-secreting gastric epithelial progenitors into digestive-enzyme secreting zymogenic cells requires Mist1. Development 134: 211-222, 2007.
37. Rippa E, La Monica G, Allocca R, Romano MF, De Palma M, Arcari P. Overexpression of gastrokine 1 in gastric cancer cells induces Fas-mediated apoptosis. J Cell Physiol 226: 2571-2578, 2011.
38. Roca X, Sachidanandam R, Krainer AR. Intrinsic differences between authentic and cryptic 5= splice sites. Nucl Acids Res 31: 6321-6333, 2003.
39. Rousset F, Raymond M. Testing heterozygote excess and deficiency. Genetics 140: 1413-1419, 1995.
40. Sanchez-Pulido L, Devos D, Valencia A. BRICHOS: a conserved domain in proteins associated with dementia, respiratory distress and cancer. Trends Biochem Sci 27: 329-332, 2002.
41. Stevens EC, Hume ID. Comparative Physiology of the Vertebrate Digestive System. Cambrige, UK: Cambridge University Press, 1995.
42. Stirling W. On the ferments or enzymes of the digestive tract in fishes. J Anat Physiol 18: 426-435, 1884.
43. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739, 2011.
44. Tang K, Thornton KR, Stoneking M. A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 5: e171, 2007.
45. Templeton AR. Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates. Genetics 144: 1263-1270, 1996.
46. Templeton AR, Clark AG, Weiss KM, Nickerson DA, Boerwinkle E, Sing CF. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am J Hum Genet 66: 69-83, 2000.
47. The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature: 1061-1073, 2010.
48. Tishkoff SA, Kidd KK. Implications of biogeography of human populations for 'race' and medicine. Nat Genet 36: S21-S27, 2004.
49. Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Res 13: 2559-2567, 2003.
50. Vigna S. Evolution of the cholecystokinin and gastrin peptides and receptors. Am Zool 40: 287-295, 2000.
51. Vorechovsky I. Aberrant 3= splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res 34: 4630-4641, 2006.
52. Westley BR, Griffin SM, May FE. Interaction between TFF1, a gastric tumor suppressor trefoil protein, and TFIZ1, a brichos domain-containing protein with homology to SP-C. Biochemistry 44: 7967-7975, 2005.
53. Wilcox R. Kolmogorov-Smirnov test. Encyclopedia of Biostatistics 2005.
54. Willander H, Hermansson E, Johansson J, Presto J. BRICHOS domain associated with lung fibrosis, dementia and cancer-a chaperone that prevents amyloid fibril formation? FEBS J 278: 3893-3904, 2011.
55. Wright S. Coefficients of inbreeding and relationship. Am Nat 56: 330-338, 1922.
56. Yoon JH, Kang YH, Choi YJ, Park IS, Nam SW, Lee JY, Lee YS, Park WS. Gastrokine 1 functions as a tumor suppressor by inhibition of epithelial-mesenchymal transition in gastric cancers. J Cancer Res Clin Oncol 137: 1697-1704, 2011.
57. Yoshikawa Y, Mukai H, Hino F, Asada K, Kato I. Isolation of two novel genes, down-regulated in gastric cancer. Jpn J Cancer Res 91: 459-463, 2000.