Functional Single Nucleotide Polymorphisms (SNPs) in the Genes Encoding the Human Deoxyribonuclease (DNase) Family Potentially Relevant to Autoimmunity.
OBJECTIVE
To continue our previous investigations, we have extensively investigated the function of the 61, 41, and 35 non-synonymous single nucleotide polymorphisms (SNPs) in the human genes encoding DNASE1, DNASE1L3, and DNASE2, respectively, potentially relevant to autoimmune diseases.


METHODS
The site-directed mutagenesis was employed to amino acid-substituted constructs corresponding to each SNP. The COS-7 cells were transfected with each vector and DNase activity was assayed by the single radial enzyme diffusion method. By using PolyPhen-2, changes in the DNase function of each non-synonymous SNP were predicted. Genotyping of all the non-synonymous SNPs was performed in 14 different populations including 3 ethnic groups using the polymerase chain reaction followed by the restriction fragment length polymorphism method.


RESULTS
Expression analysis demonstrated these SNPs to be classified into four categories with regard to the effect on DNase activity: SNPs not affecting the activity level, ones reducing it, ones abolishing it, and ones elevating it. In particular, 9, 5, and 4 SNPs producing a loss-of-function variant of the enzymes in DNASE1, DNASE1L3, and DNASE2, respectively, were confirmed. SNPs producing DNase loss of function can be estimated by PolyPhen-2 to be "probably damaging" with a high accuracy of prediction. Almost all of these functional SNPs producing a loss of function or substantially low activity-harboring forms exhibited a mono-allelic distribution in all of the populations.


CONCLUSIONS
A minor allele of functional SNPs, despite the remarkably low genetic heterogeneity of the SNPs, might be a genetic risk factor for autoimmune diseases.
a Department of Legal Medicine , Shimane University School of Medicine , Shimane , Japan.
Junko
J
Fujihara
b Division of Medical Genetics and Biochemistry , University of Fukui , Fukui , Japan.
Misuzu
M
Ueki
a Department of Legal Medicine , Shimane University School of Medicine , Shimane , Japan.
Kaori
K
Kimura-Kataoka
c Division of Life Sciences, Faculty of Medical Sciences , University of Fukui , Fukui , Japan.
Reiko
R
Iida
a Department of Legal Medicine , Shimane University School of Medicine , Shimane , Japan.
Haruo
H
Takeshita
b Division of Medical Genetics and Biochemistry , University of Fukui , Fukui , Japan.
Toshihiro
T
Yasuda
D019943:Amino Acid Substitution; D000818:Animals; D001327:Autoimmune Diseases / Q000235:genetics*; D019556:COS Cells; D002522:Chlorocebus aethiops; D003850:Deoxyribonuclease I / Q000235:genetics*; D004706:Endodeoxyribonucleases / Q000235:genetics*; D057075:Enzyme Assays; D020022:Genetic Predisposition to Disease; D006801:Humans; D016297:Mutagenesis, Site-Directed; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide
C485421:DNASE1L3 protein, human; D004706:Endodeoxyribonucleases; C085693:DNASE1 protein, human; D003850:Deoxyribonuclease I; C019329:deoxyribonuclease II
Autoimmunity; deoxyribonuclease (DNase) family; functional SNPs; genetic distribution; genotype; loss-of-function