Parallel selection on TRPV6 in human populations

PLoS ONE

Volumn 3, Issue 2, 2008, Pages

  Hughes, David A ^a   Tang, Kun ^a   Strotmann, Rainer ^b   Schöneberg, Torsten ^b   Prenen, Jean ^c   Nilius, Bernd ^c   Stoneking, Mark ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; VANILLOID RECEPTOR 6; CALCIUM CHANNEL; TRPV6 PROTEIN, HUMAN; VANILLOID RECEPTOR;

AFRICAN AMERICAN; AGE DISTRIBUTION; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; ASIAN; CALCIUM SIGNALING; CELL STRAIN HEK293; CONTROLLED STUDY; ELECTROPHYSIOLOGY; ETHNIC DIFFERENCE; EUROPEAN AMERICAN; EXPRESSION VECTOR; GENE LOCUS; GENETIC SELECTION; GENETIC TRANSFECTION; GENETIC VARIABILITY; HAPLOTYPE; HOMOZYGOSITY; HUMAN; HUMAN CELL; MOLECULAR CLONING; PATCH CLAMP; POPULATION GENETICS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE; CAUCASIAN; GENETICS; PHYSIOLOGY; RACE;

AMINO ACID SUBSTITUTION; CALCIUM CHANNELS; CONTINENTAL POPULATION GROUPS; ELECTROPHYSIOLOGY; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETICS, POPULATION; HUMANS; PATCH-CLAMP TECHNIQUES; SELECTION (GENETICS); TRPV CATION CHANNELS; VARIATION (GENETICS);

EID: 45949104374     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001686     Document Type: Article

References (72)

1. Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, et al. (2004) Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes. PLoS Biol 2: E286.
2. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12: 1805-1814.
3. Bostamante CD, Fledel-Alon A, Williamson S, Nielsen R, Todd Hubisz M, et al. (2005) Natural selection on protein-coding genes in the human genome. Nature 437: 1153.
4. Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, et al. (2005) Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 15: 1558-1565.
5. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, et al. (2003) Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios. Science 302: 1960-1963.
6. Kayser M, Brauer S, Stoneking M (2003) A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol Biol Evol 20: 893-900.
7. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: c170.
8. Stajich JE, Hahn MW (2005) Disentangling the effects of demography and selection in human history. Mol Biol Evol 22: 63-73.
9. Storz JF, Payseur BA, Nachman MW (2004) Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol Biol Evol 21: 1800-1811.
10. Voigbt BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4: c72.
11. Walsh EC, Sabeti P, Hutcheson HB, Fry B, Schaffner SF, et al. (2006) Searching for signals of evolutionary selection in 168 genes related to immune function. Hum Genet 119: 92-102.
12. 2+ channel 1 and 2. J Physiol (Lond) 537: 747-761.
13. Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, et al. (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74: 1111-1120.
14. Thomson G (1977) The effect of a selected locus on linked neutral loci. Genetics 85: 753-788.
15. Akey JM, Swanson WJ, Madeoy J, Eberle M, Shriver MD (2006) TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations. Hum Mol Genet 15: 2106-2113.
16. Yang Z, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19: 908-917.
17. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, et al. (2002) A human genome diversity cell line panel. Science 296: 261-262.
18. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
19. Tang K, Thornton KR, Stoneking M (2007) A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome. PLoS Biol 5: e171.
20. Fry AE, Trafford CJ, Kimber MA, Chan M, Rockett KA, et al. (2006) Haplotype homozygosity and derived alleles in the human genome. Am J Hum Genet 78.
21. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, et al. (2006) Positive natural selection in the human lineage. Science 312: 1614-1620.
22. Wang Y, Zhao LP, Dudoit S (2006) A Fine-Scale Linkage-Disequilibrium Measure Based on Length of Haplotype Sharing. Am J Hum Genet 78: 615-628.
23. The International HapMap C (2005) A haplotype map of the human genome. Nature 437: 1299.
24. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, et al. (2001) Linkage disequilibrium in the human genome. Nature 411: 199.
25. The International HapMap Consortium (2003) The International HapMap Project. Nature 426: 789.
26. Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, et al. (1998) Genetic traces of ancient demography. PNAS 95: 1961-1967.
27. Jorde LB, Bamshad M, Rogers AR (1998) Using mitochondrial and nuclear DNA markers to reconstruct human evolution. Bioessays 20: 126-136.
28. Marth GT, Czabarka E, Murvai J, Sherry ST (2004) The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166: 351-372.
29. Ray N, Currat M, Berthier P, Excoffier L (2005) Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations. Genome Res 15: 1161-1167.
30. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, et al. (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15: 1576-1583.
31. Zhivotovsky LA, Bennett L, Bowcock AM, Feldman MW (2000) Human Population Expansion and Microsatellite Variation. Mol Biol Evol 17: 757-767.
32. Zhivotovsky LA, Rosenberg NA, Feldman MW (2003) Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet 72: 1171-1186.
33. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
34. Przeworski M, Coop G, Wall JD (2005) The signature of positive selection on standing genetic variation. Evolution Int J Org Evolution 59: 2312-2323.
35. Teshima KM, Coop G, Przeworski M (2006) How reliable are empirical genomic scans for selective sweeps? Genome Res 16: 702-712.
36. 2+-dependent gating and strong inward rectification of the cation channel TRPV6. J Gen Physiol 121: 245-260.
37. 2+ channel. J Biol Chem 275: 3963-3969.
38. 2+ channel ECaC. J Physiol Lond 527: 239-248.
39. 2+. Cell Calcium 29: 417-428.
40. Voets T, Janssens A, Droogmans G, Nilius B (2003) A single pore residue determines calcium selectivity, inward rectification and pore size of TRPV6 (CaT1/ECaC2). Biophys J (Annual Meeting Abstracts) 2724-Pos.
41. 2+ channel. J Biol Chem 276: 1020-1025.
42. 2+ channels ECaC1 and ECaC2 (TRPV5 and TRPV6). Role of the intracellular loop located between transmembrane segments 2 and 3. J Biol Chem 277: 30852-30858.
43. Nilius B, Weidema F, Prenen J, Hoenderop JG, Vennekens R, et al. (2003) The carboxyl terminus of the epithelial Ca(2+) channel ECaC1 is involved in Ca(2+)-dependent inactivation. Pflugers Arch.445: 584-588.
44. Hoenderop JG, Nilius B, Bindels RJ (2005) Calcium absorption across epithelia. Physiol Rev 85: 373-422.
45. Vennekens R, Prenen J, Hoenderop JG, Bindels RJ, Droogmans G, et al. (2001) Pore properties and ionic block of the rabbit epithelial calcium channel expressed in HEK 293 cells. J Physiol 530: 183-191.
46. Erler I, Hirnet D, Wissenbach U, Flockerzi V, Niemeyer BA (2004) Ca2+-selective transient receptor potential V channel architecture and function require a specific ankyrin repeat. J Biol Chem 279: 34456-34463.
47. Niemeyer BA, Bergs C, Wissenbach U, Flockerzi V, Trost C (2001) Competitive regulation of CaT-like-mediated Ca2+ entry by protein kinase C and calmodulin. Proc Natl Acad Sci U S A 98: 3600-3605.
48. Nijenhuis T, Hoenderop JG, Nilius B, Bindels RJ (2003) (Patho)physiological implications of the novel epithebal Ca2+ channels TRPV5 and TRPV6. Pflugers Arch 446: 401-409.
49. Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G Jr, Dickson M, et al. 2005) Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles. Science 307: 1928-1933.
50. Hermisson J, Pennings PS (2005) Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335-2352.
51. Orr HA, Betancourt AJ (2001) Haldane's sieve and adaptation from the standing genetic variation. Genetics 157: 875-884.
52. Pennings PS, Hermisson J (2006) Soft Sweeps III: The Signature of Positive Selection from Recurrent Mutation. PLoS Genel 2: e186.
53. Prugnolle F, Manica A, Balloux F (2005) Geography predicts neutral genetic diversity of human populations. Curr Biol 15: R159-160.
54. Goebel T, Waters MR, Dikova M (2003) The Archaeology of Ushki Lake, Kamchatka, and the Pleistocene Peopling of the Americas. Science 301: 501-505.
55. Haynes G (2002) The Early Settlement of North America: The Clovis Era. Cambridge: Cambridge Univ. Press.
56. Hope GS, Haberle SG (2005) The history of the human landscapes of New Guinea. In: Pawley A, Attenborough R, Golson J, Hide R, eds. Papuan Pasts: Cultural, linguistic and biological histories of Papuan-speaking peoples. Canberra: Pacific Linguistics, Research School of Pacific and Asian Studies, Australian National University. pp 541-554.
57. Schwarz EC, Wissenbach U, Niemeyer BA, Strauss B, Philipp SE, et al. (2006) TRPV6 potentiates calcium-dependent cell proliferation. Cell Calcium 39: 163-173.
58. Lehen'kyi V, Flourakis M, Skryma R, Prevarskaya N (2007) TRPV6 channel controls prostate cancer cell proliferation via Ca(2+)/NFAT-dependent pathways. Oncogene 26: 7380-7385.
59. Prevarskaya N, Zhang L, Barritt G (2007) TRP channels in cancer. Biochim Biophys Acta 1772: 937-946.
60. Lehen'kyi V, Beck B, Polakowska, R, Charveron M, Bordat P, et al. (2007) TRPV6 Is a Ca2+ Entry Channel Essential for Ca2+-induced Differentiation of Human Keratinocytes. J Biol Chem 282: 22582-22591.
61. van de Graaf SF, Boullart I, Hoenderop JG, Bindels RJ (2004) Regulation of the epithelial Ca2+ channels TRPV5 and TRPV6 by lalpha,25-dihydroxy Vitamin D3 and dietary Ca2+. J Steroid Biochem Mol Biol 89-90: 303-308.
62. Bessou-Touya S, Picardo M, Maresca V, Surleve-Bazeille JE, Pain C, et al. (1998) Chimeric human epidermal reconstructs to study the role of melanocytes and keratinocytes in pigmentation and photoprotection. J Invest Dermatol 111: 1103-1108.
63. Minwalla L, Zhao Y, Le Poole IC, Wickett RR, Boissy RE (2001) Keratinocytes play a role in regulating distribution patterns of recipient melanosomes in vitro. J Invest Dermatol 117: 341-347.
64. Diamond J, Bellwood P (2003) Farmers and Their Languages: The First Expansions. Science 300: 597-603.
65. Oota H, Pakendorf B, Weiss G, von Haeseler A, Pookajorn S, et al. (2005) Recent origin and cultural reversion of a hunter-gathertr group. PLoS Biel 3: e71.
66. Stephens M, Scheet P (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet 76: 449-462.
67. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
68. Ptak SE, Voelpel K, Przeworski M (2004) Insights into recombination from patterns of linkage disequilibrium in humans. Genetics 167: 387-397.
69. Stoneking M, Jorde LB, Bhatia K, Wilson AC (1990) Geographic variation in human mitochondrial DNA from Papua New Guinea. Genetics 124: 717-733.
70. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, et al. (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.
71. Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucl Acids Res 33: D501-504.
72. Muller D, JGJ H, Vennekens R, Eggert P, Harangi F, et al. (2002) Epithehal Ca channel 1 (ECaC1) in autosomal dominant hypercalciuria. Nephrol Dial Transplant 17: (9): 1614-1620.