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

In a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck an... Full description

Journal Title: Physiological genomics August 1, 2013, Vol.45(15), pp.667-683
Main Author: Geahlen, Jessica H
Other Authors: Lapid, Carlo , Thorell, Kaisa , Nikolskiy, Igor , Huh, Won Jae , Oates, Edward L , Lennerz, Jochen K M , Tian, Xiaolin , Weis, Victoria G , Khurana, Shradha S , Lundin, Samuel B , Templeton, Alan R , Mills, Jason C
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1531-2267 ; DOI: 10.1152/physiolgenomics.00169.2012
Link: http://search.proquest.com/docview/1417532107/?pq-origsite=primo
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title: Evolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3.
format: Article
creator:
  • Geahlen, Jessica H
  • Lapid, Carlo
  • Thorell, Kaisa
  • Nikolskiy, Igor
  • Huh, Won Jae
  • Oates, Edward L
  • Lennerz, Jochen K M
  • Tian, Xiaolin
  • Weis, Victoria G
  • Khurana, Shradha S
  • Lundin, Samuel B
  • Templeton, Alan R
  • Mills, Jason C
subjects:
  • Animals–Genetics
  • Carrier Proteins–Metabolism
  • Computational Biology–Genetics
  • Continental Population Groups–Genetics
  • DNA Primers–Metabolism
  • Evolution, Molecular–Genetics
  • Fluorescent Antibody Technique–Genetics
  • Gastric Mucosa–Genetics
  • Genetic Loci–Genetics
  • Genetics, Population–Metabolism
  • Genotype–Genetics
  • Haplotypes–Genetics
  • Humans–Genetics
  • Likelihood Functions–Genetics
  • Macaca Mulatta–Genetics
  • Membrane Proteins–Genetics
  • Mice–Genetics
  • Mice, Inbred C57bl–Genetics
  • Microarray Analysis–Genetics
  • Microscopy, Confocal
ispartof: Physiological genomics, August 1, 2013, Vol.45(15), pp.667-683
description: In a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck and antrum base and is prominently expressed in metaplastic lesions. GKN3 was proposed originally to be expressed in some human populations and a pseudogene in others. To investigate that hypothesis, we studied human GKN3 evolution in the context of its paralogous genomic neighbors, GKN1 and GKN2. Haplotype analysis revealed that GKN3 mimics GKN2 in patterns of exonic SNP allocation, whereas GKN1 appeared to be more stringently selected. GKN3 showed signatures of both directional selection and population based selective sweeps in humans. One such selective sweep includes SNP rs10187256, originally identified as an ancestral tryptophan to premature STOP codon mutation. The derived (nonancestral) allele went to fixation in Asia. We show that another SNP, rs75578132, identified 5 bp downstream of rs10187256, exhibits a second selective sweep in almost all Europeans, some Latinos, and some Africans, possibly resulting from a reintroduction of European genes during African colonization. Finally, we identify a mutation that would destroy the splice donor site in the putative exon3-intron3 boundary, which occurs in all human genomes examined to date. Our results highlight a stomach-specific human genetic locus, which has undergone various selective sweeps across European, Asian, and African populations and thus reflects geographic and ethnic patterns in genome evolution.
language: eng
source:
identifier: E-ISSN: 1531-2267 ; DOI: 10.1152/physiolgenomics.00169.2012
fulltext: fulltext
issn:
  • 15312267
  • 1531-2267
url: Link


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titleEvolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3.
creatorGeahlen, Jessica H ; Lapid, Carlo ; Thorell, Kaisa ; Nikolskiy, Igor ; Huh, Won Jae ; Oates, Edward L ; Lennerz, Jochen K M ; Tian, Xiaolin ; Weis, Victoria G ; Khurana, Shradha S ; Lundin, Samuel B ; Templeton, Alan R ; Mills, Jason C
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ispartofPhysiological genomics, August 1, 2013, Vol.45(15), pp.667-683
identifierE-ISSN: 1531-2267 ; DOI: 10.1152/physiolgenomics.00169.2012
subjectAnimals–Genetics ; Carrier Proteins–Metabolism ; Computational Biology–Genetics ; Continental Population Groups–Genetics ; DNA Primers–Metabolism ; Evolution, Molecular–Genetics ; Fluorescent Antibody Technique–Genetics ; Gastric Mucosa–Genetics ; Genetic Loci–Genetics ; Genetics, Population–Metabolism ; Genotype–Genetics ; Haplotypes–Genetics ; Humans–Genetics ; Likelihood Functions–Genetics ; Macaca Mulatta–Genetics ; Membrane Proteins–Genetics ; Mice–Genetics ; Mice, Inbred C57bl–Genetics ; Microarray Analysis–Genetics ; Microscopy, Confocal
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descriptionIn a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck and antrum base and is prominently expressed in metaplastic lesions. GKN3 was proposed originally to be expressed in some human populations and a pseudogene in others. To investigate that hypothesis, we studied human GKN3 evolution in the context of its paralogous genomic neighbors, GKN1 and GKN2. Haplotype analysis revealed that GKN3 mimics GKN2 in patterns of exonic SNP allocation, whereas GKN1 appeared to be more stringently selected. GKN3 showed signatures of both directional selection and population based selective sweeps in humans. One such selective sweep includes SNP rs10187256, originally identified as an ancestral tryptophan to premature STOP codon mutation. The derived (nonancestral) allele went to fixation in Asia. We show that another SNP, rs75578132, identified 5 bp downstream of rs10187256, exhibits a second selective sweep in almost all Europeans, some Latinos, and some Africans, possibly resulting from a reintroduction of European genes during African colonization. Finally, we identify a mutation that would destroy the splice donor site in the putative exon3-intron3 boundary, which occurs in all human genomes examined to date. Our results highlight a stomach-specific human genetic locus, which has undergone various selective sweeps across European, Asian, and African populations and thus reflects geographic and ethnic patterns in genome evolution.
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titleEvolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3.
authorGeahlen, Jessica H ; Lapid, Carlo ; Thorell, Kaisa ; Nikolskiy, Igor ; Huh, Won Jae ; Oates, Edward L ; Lennerz, Jochen K M ; Tian, Xiaolin ; Weis, Victoria G ; Khurana, Shradha S ; Lundin, Samuel B ; Templeton, Alan R ; Mills, Jason C
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