Functional Interaction Between SNPs and Microsatellite in the Transcriptional Regulation of Insulin-Like Growth Factor 1

Abstract

A CA-repeat microsatellite in insulin-like growth factor 1 (IGF1) promoter was associated with interindividual variation of circulating IGF1 level. Previously, we reported that such association was due to variation of haplotype unit in a linkage disequilibrium block composed of microsatellite and single-nucleotide polymorphisms (SNPs), suggesting the presence of an interaction between them. In this study, reporter assays were performed to investigate the regulatory effect and interaction of genetic variants on gene expression. We used an in vitro system to compare the transcriptional activities of haplotypes (rs35767:T>C, the CA-repeat microsatellite, rs5742612:T>C, and rs2288377:T>A) in evolutionarily conserved region of IGF1 promoter. In haplotype C-T-T, a longer microsatellite had a lower transcriptional activity (17.6 ± 2.4-fold for 17 repeats and 8.3 ± 1.1-fold for 21 repeats), whereas in haplotype T-C-A, such trend could not be observed, as the microsatellite with 21 repeats had the highest transcriptional activity (17.5 ± 2.3-fold). Because the microsatellite and SNPs affected the transcriptional activity of each other, there may be an interaction between them in the regulation of IGF1 expression. For the first time, we demonstrated that a noncoding microsatellite polymorphism could act as a functional unit and interact with SNPs in the regulation of transcription in human genome.

The mechanism of transactivation regulation due to polymorphic short tandem repeats (STRs) using IGF1 promoter as a model

“…Our early results were consistent with genetic epidemiological findings and supported a biological basis for the association between the blood concentration of IGF1 and the alleles of the STR in IGF1 promoter2829. Near the transcription starting site, the promoter of IGF1 contains three tagging SNPs and one STR (a CA dinucleotide repeat) within a common haploblock28.…”

“…1. For reporter constructs of the common promoter haplotypes (Supplementary Table T1)29, 1.5-kb long fragments of the IGF1 promoter region, ranging from −1491 to −5 relative to the translation start site, were synthesized by PCR using genomic DNA from normal subjects. The fragment was amplified by a forward primer containing a BglII restriction site (underlined) (5′-AGC AGATCT GCCCCAGGATAACACAAAGA-3′) and a reverse primer containing a HindIII restriction site (underlined) (5′-AGC AAGCTT GCTTCTGAAGTACAAAGTCT-3′).…”

Type 2 diabetes-related variants influence the risk of developing multiple myeloma: results from the IMMEnSE consortium

“…Interestingly, several authors have also reported that IGF1 and its analogues are associated with an increased death in patients with progressive MM (Standal et al 2002, Chou et al 2012, Wu et al 2014, whereas the administration of metformin results in the reduction of deaths in patients with progressive disease (Wu et al 2014). In fact, Chen et al (2013) recently demonstrated that the IGF1 rs35767 SNP together with two neighbour SNPs constitutes a haplotype that efficiently regulates transcriptional activity (Chen et al 2013). Similarly, several studies have consistently reported that carriers of the IGF1 rs35767T allele showed significantly higher levels of circulating IGF1 than those harbouring the WT allele (Mannino et al 2013, Sesti et al 2014 and that the presence of this variant is associated with an increased risk of developing several types of cancer (Ollberding et al 2012, Qian et al 2014.…”

Repeat polymorphism analysis for examining genetic variability and the implications for specific traits in dog breeds

“…In human, an impact of microsatellite length on transcriptional activity was investigated in the background of haplotypes (rs35767:T > C, the CArepeat microsatellite, rs5742612:T > C, and rs2288377:T > A). As a form of T-(CA-repeat microsatellite)-C-A The (CA) 17 repeat microsatellite with a C-T-T haplotype in the promoter region of the insulin-like growth factor 1 (IGF1) gene showed relatively low transcriptional activity, whereas the (CA) 21 repeat microsatellite with a T-C-A SNP, exhibited high transcriptional activity, suggesting that microsatellite length variation could control gene expression with a neighboring SNP event (Chen et al, 2013). While this study is limited to human genome, it demonstrates that analyses of microsatellite with SNP allow us to understand the genetic variability in dogs.…”

“…Firstly, microsatellites related to behavior-related genes had a variable repeat size (or number) and affected behavioral characteristics in dog breeds (Takeuchi et al, 2009a(Takeuchi et al, , 2009bKonno et al, 2011), and could also interact with SNPs in the regulation of transcription (Chen et al, 2013). Secondly, VNTRs of the dopaminergic neurotransmitter genes such as DRD4, TH, DBH, and DAT were reviewed in dogs (Hejjas et al, 2007(Hejjas et al, , 2009, and a repeat polymorphism of the TH gene was related to behavioral tests (Kubinyi et al, 2012).…”