Expression quantitative trait loci analysis of 13 genes in the rat prostate.
Differential expression of mRNA among animal strains is one of the mechanisms for their diversity. cDNA microarray analysis of the prostates of BUF/Nac (BUF) and ACI/N (ACI) rats, which show different susceptibility to prostate cancers, found 195 differentially expressed genes. To identify loci that control differential expression of 13 genes with diverse expression levels, their expression levels were measured by quantitative RT-PCR in 89 backcross rats, and expression quantitative trait locus (eQTL) analysis was performed. Nine genes [Aldh1a1, Aldr1, Bmp6, Cdkn1a (p21), Cntn6, Ghr, Jund, Nupr1, and RT1-M3] were controlled by cis-acting loci. Cdkn1a, a cell cycle regulator and a candidate for a prostate cancer susceptibility gene, was mapped to its own locus and had polymorphisms, including a 119-bp insertion in the 5' upstream region in BUF rats. Four genes (Kclr, Pbsn, Psat1, and Ptn) were controlled by trans-acting loci. Pbsn, a prostate-specific gene on chromosome X, was controlled by a QTL on chromosome 8. Depending upon which gene that we selected from the genes widely used for normalization (Actb, Gapd, or Ppia), different QTL were mapped for Kclr, Psat1, and Ptn. Normalization using Actb most appropriately explained the expression levels in a congenic strain for chromosome 3. eQTL analysis with precise measurement of expression levels and appropriate normalization was shown to be effective for mapping loci that control gene expression in vivo.
Yamashita
Satoshi
S
Carcinogenesis Division, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan.
Wakazono
Kuniko
K
Nomoto
Tomoko
T
Tsujino
Yoshimi
Y
Kuramoto
Takashi
T
Ushijima
Toshikazu
T
D000818:Animals; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000096:biosynthesis / Q000235:genetics; D020869:Gene Expression Profiling; D008297:Male; D008969:Molecular Sequence Data; D009928:Organ Specificity / Q000235:genetics; D011467:Prostate / Q000378:metabolism*; D040641:Quantitative Trait Loci; D051381:Rats; D011912:Rats, Inbred ACI; D011914:Rats, Inbred BN; D011915:Rats, Inbred BUF; D011916:Rats, Inbred F344
C493958:Cdkn1a protein, rat; D050759:Cyclin-Dependent Kinase Inhibitor p21