UTR Alleles Research Articles

Single-nucleotide polymorphisms in 3'-untranslated region inducible costimulator gene and the important roles of miRNA in alopecia areata.

BackgroundAlopecia areata (AA) spares the stem cell compartment and attacks only the base of the hair follicle, which is surrounded by infiltrating lymphocytes. AA is associated with polymorphisms in immune‐related genes and with decreased function of CD4+CD25+ T regulatory (Treg) cells. Treg function is modulated by the costimulatory molecules, like inducible costimulator (ICOS) that are crucial in orienting T cell differentiation and function so that they strongly impact on the immunologic decision between tolerance or autoimmunity development.ObjectiveThe aim of our study was to investigate the possible association of AA with single‐nucleotide polymorphisms (SNP) present in the ICOS 3′‐untranslated region (3′UTR) region and to elucidate how SNPs modulate ICOS gene expression by affecting miRNA binding sites.MethodsThis is a case‐control study performed in 184 patients with AA and 200 controls. ICOS gene and miRNA expression were analyzed by real‐time polymerase chain reaction.ResultsThe genotype carrying the rs4404254(C) [p = 0.012, OR (95% CI): 0.5 (0.3–0.8)] and rs4675379(C) [p = 0.015, OR (95% CI): 0.3 (0.1–0.8)] 3′ UTR alleles was more frequently observed in AA patients than in controls and correlated with a reduced ICOS expression. miR‐1276 significantly suppressed ICOS expression by binding to the 3′UTR of ICOS mRNA. Also, we observed that, miR‐101 and miR‐27b are upregulated, while miR‐103 and miR‐2355‐3p are downregulated in peripheral blood mononuclear cells of AA patients compared to controls;ConclusionOur data show that rs4404254 and rs4675379 SNPs of ICOS gene are associated with AA and also reveal that the presence of rs4404254 polymorphism correlates with ICOS post‐transcriptional repression by microRNA binding.

In vivo CRISPR screening for phenotypic targets of the mir-35-42 family in C. elegans.

Identifying miRNA target genes is difficult, and delineating which targets are the most biologically important is even more difficult. We devised a novel strategy to test the phenotypic impact of individual microRNA-target interactions by disrupting each predicted miRNA-binding site by CRISPR-Cas9 genome editing in C. elegans We developed a multiplexed negative selection screening approach in which edited loci are deep sequenced, and candidate sites are prioritized based on apparent selection pressure against mutations that disrupt miRNA binding. Importantly, our screen was conducted in vivo on mutant animals, allowing us to interrogate organism-level phenotypes. We used this approach to screen for phenotypic targets of the essential mir-35-42 family. By generating 1130 novel 3'UTR alleles across all predicted targets, we identified egl-1 as a phenotypic target whose derepression partially phenocopies the mir-35-42 mutant phenotype by inducing embryonic lethality and low fecundity. These phenotypes can be rescued by compensatory CRISPR mutations that retarget mir-35 to the mutant egl-1 3'UTR. This study demonstrates that the application of in vivo whole organismal CRISPR screening has great potential to accelerate the discovery of phenotypic negative regulatory elements in the noncoding genome.

Complexity of the 5′ Untranslated Region of EIF4A3, a Critical Factor for Craniofacial and Neural Development

Repeats in coding and non-coding regions have increasingly been associated with many human genetic disorders, such as Richieri-Costa-Pereira syndrome (RCPS). RCPS, mostly characterized by midline cleft mandible, Robin sequence and limb defects, is an autosomal-recessive acrofacial dysostosis mainly reported in Brazilian patients. This disorder is caused by decreased levels of EIF4A3, mostly due to an increased number of repeats at the EIF4A3 5′UTR. EIF4A3 5′UTR alleles are CG-rich and vary in size and organization of three types of motifs. An exclusive allelic pattern was identified among affected individuals, in which the CGCA-motif is the most prevalent, herein referred as “disease-associated CGCA-20nt motif.” The origin of the pathogenic alleles containing the disease-associated motif, as well as the functional effects of the 5′UTR motifs on EIF4A3 expression, to date, are entirely unknown. Here, we characterized 43 different EIF4A3 5′UTR alleles in a cohort of 380 unaffected individuals. We identified eight heterozygous unaffected individuals harboring the disease-associated CGCA-20nt motif and our haplotype analyses indicate that there are more than one haplotype associated with RCPS. The combined analysis of number, motif organization and haplotypic diversity, as well as the observation of two apparently distinct haplotypes associated with the disease-associated CGCA-20nt motif, suggest that the RCPS alleles might have arisen from independent unequal crossing-over events between ancient alleles at least twice. Moreover, we have shown that the number and sequence of motifs in the 5′UTR region is associated with EIF4A3 repression, which is not mediated by CpG methylation. In conclusion, this study has shown that the large number of repeats in EIF4A3 does not represent a dynamic mutation and RCPS can arise in any population harboring alleles with the CGCA-20nt motif. We also provided further evidence that EIF4A3 5′UTR is a regulatory region and the size and sequence type of the repeats at 5′UTR may contribute to clinical variability in RCPS.

Missing genetic variations in GNE myopathy: rearrangement hotspots encompassing 5'UTR and founder allele.

GNE myopathy is an autosomal recessive distal myopathy caused by loss-of-function mutations in the GNE gene, which encodes UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE), a key enzyme in sialic-acid biosynthesis. By comprehensive screening of manifesting patients using a fine-mapped targeted next-generation sequencing (NGS), we identified copy number variations (CNVs) in 13 patients from 11 unrelated families. The nine unique CNVs largely vary in size from 0.3 to 72 kb. Over half of the cases carry different deletions spanning merely exon 2, which contains the 5' untranslated region (5'UTR) of the muscle major transcript hGNE1. Of most unique CNVs, either the telomeric or the centromeric breakpoint locates within intron 2, indicating rearrangement hotspots. Haplotype analysis suggested the existence of a founder allele with exon 2 deletion. The breakpoints for all CNVs were determined by long-range PCR and sequencing. All of the breakpoints of gross deletion/duplications reside within directly oriented pairs of Alu repeats. The results of this study firstly widen the spectra of mutations to CNVs encompassing 5'UTR, underscoring the pivotal role of the hGNE1 transcript. Alu-mediated non-recurrent CNVs may have been overlooked in a wide variety of recessive phenotypes, especially in those associated with genomic Alu-rich genes such as GNE.

IL‐12B and IL‐10 gene polymorphisms in the development of Hashimoto's thyroiditis

Functional genetic polymorphisms that altered gene expression of cytokines are candidate genetic factors that could modulate the development and progression of Hashimoto's thyroiditis (HT). IL-12B gene encoded the IL-12p40 subunit, which is included in the pro-inflammatory heterodimeric cytokines IL-12p70 and IL-23. IL-10 is an important Treg cytokine suppressing inflammatory cytokine production and autoimmunity. This study was designed to compare -1082A/GIL-10 and +1188A/C3'UTRIL-12B genotype distribution in 130 patients with HT to a group of 157 healthy controls in attempts to determine an association with HT development. Genotyping for the 3'UTRA/C IL-12B polymorphism was performed using RFLP-PCR and genotyping for -1082A/G IL-10 by ARMS-PCR assay. Patients with HT were divided into euthyroid and hypothyroid stages. There were no significant differences in the genotype and allele frequencies of the IL-12B polymorphism between patients with HT and controls. We observed higher euthyroid HT risk for individuals with CC genotype, unlike to develop hypothyroidism with OR=1.68. Regarding the polymorphism rs1800896, it was shown the significantly higher frequency of homozygous genotype GG in cases vs controls (OR=2.19; P=0.024). Moreover, the combination of genotype AA of 3'UTRIL-12B with GG of -1082IL-10 was associated with a threefold increasing risk (OR=3.188; P=0.022) of developing HT compared to individuals with the presence of 3'UTR allele C (AC+CC) simultaneously with AA genotype of -1082IL-10. Our data raise the possibility that the combined effect of polymorphisms from proinflammatory and anti-inflammatory cytokines may be more decisive to HT development.

Multiple microRNA regulation of lipoprotein lipase gene abolished by 3′UTR polymorphisms in a triglyceride-lowering haplotype harboring p.Ser474Ter

BackgroundLipoprotein lipase (LPL) is a key enzyme in triglyceride (TG) metabolism. LPL gene single nucleotide polymorphisms (SNPs) are associated with TG concentrations however the functionality of many of these SNPs remains poorly understood. MicroRNAs (miR) exert post-transcriptional down-regulation and their target sequence on the 3′UTR may be altered by SNPs. We therefore investigated whether LPL 3′UTR SNPs could modulate plasma TG concentration through the alteration of miR binding-sites. Methods and resultsWe performed genetic association studies of LPL 3′UTR SNPs with TG concentrations in 271 type 2 diabetic patients and in general population samples (2997 individuals). A specific LPL haplotype (Hap4) was associated with lower plasma TG concentration (TG-0.18, IC95% [−0.30, −0.07] mmol/L or logTG-0.13, IC95% [−0.18, −0.08], p = 4.77·10−8) in the meta-analysis. Hap4 comprises seven 3′UTR SNP minor alleles and p.Ser474Ter (rs328) a well-documented nonsense mutation associated with low TG concentration although by an unknown mechanism so far. Bio-informatic studies identified several putative miRNA binding-sites on the wild-type Hap1 haplotype, lost on Hap4. Functional validation performed in HEK-293T cells using luciferase expression constructs with various LPL 3′UTR allele combinations demonstrated a binding of miR-29, miR-1277 and miR-410 on Hap1, lost on Hap4. This loss of specific miR binding-site in presence of Hap4 was independent of the allelic variation of p.Ser474Ter (rs328). ConclusionsWe report the regulation of LPL by the miR-29, miR-1277 and miR-410 that is lost in presence of Hap4, a specific LPL TG-lowering haplotype. Consequently p.Ser474Ter association with TG concentration could be at least partially explained by its strong linkage disequilibrium with these functional 3′UTR SNPs.

Discovery of a new fragrance allele and development of functional markers for identifying diverse fragrant genotypes in rice

Discovery of new fragrance alleles provides important genetic resources for breeding fragrant rice. In this study, a hybrid complementation test demonstrated the association of a new fragrance allele without mutation in the coding region with flavor formation in a fragrant rice variety Nankai 138. The new allele (badh2-p-5′UTR) has a 3-bp deletion in the 5′ untranslated region and an 8-bp insertion in the promoter (−1,314 site upstream from the initiation codon). Surprisingly, we found that there is also an 8-bp insertion in the promoter of the badh2-E7 allele. We developed a new sequence tagged site functional marker to identify the badh2-p-5′UTR and badh2-E7 alleles according to the 8-bp insertion in their promoters. A cleaved amplified polymorphic sequence (AluI) functional marker targeting a common base substitution in the intron 2 of three badh2 alleles, viz. badh2-p-5′UTR, badh2-E7 and badh2-E2, was developed to identify diverse genotypes for fragrance in rice. Based on the results of sequence alignments among the three badh2 alleles, we suggest that the badh2-E7 and badh2-p-5′UTR alleles may have the same genetic origin. In addition, the genetic distance between the badh2-E7 and badh2-p-5′UTR alleles may be closer than that between the badh2-E2 and the badh2-p-5′UTR alleles, or between the badh2-E2 and the badh2-E7 alleles.

The genetic architecture of 3′untranslated region of the MICA gene: Polymorphisms and haplotypes

In this study, the 3'untranslated region (3'UTR) of MHC class I chain-related gene A (MICA) were investigated in 104 healthy, unrelated Han individuals recruited from northern China, using PCR-sequencing method. Nine polymorphic sites were detected, which were in very strong linkage disequilibrium with each other .Seven different MICA 3'UTR alleles were identified, among which UTR1 predominated (0.6971),followed by UTR2 (0.2356). Twenty-one extended haplotypes incorporating the 3'UTR and MICA exons 2-5 were observed in this population. Phylogenetic analysis revealed the existence of two MICA lineages, each with multiple subsets. The 2 lineages were primarily linked to UTR1 and UTR2 in the 3'UTR, respectively. Ewens-Watterson homozygosity statistics at MICA coding and 3'UTR regions were consistent with neutral expectations. Our data provided for the first time the data of genetic variation in the 3'UTR of MICA gene in human populations. The findings are valuable for future studies of the mechanisms underlying MICA post-transcriptional regulation, and will inform studies of evolution of the MHC gene complex.

AB0050 Association of il12b gene polymorphisms with ankylosing spondylitis

BackgroundIL12B encodes the IL-12p40 subunit of both the IL-12 and IL-23 cytokines, which play critical and unique roles in bridging the innate and adaptive immune systems. Whereas IL-12 induces development...

Characterization of 3′untranslated region (3′UTR) of the MICB gene

In this study, the 3'untranslated region (3'UTR) of MHC class I chain-related gene B (MICB) were investigated in 104 healthy, unrelated Han individuals recruited from northern China, using PCR-sequencing method. Seven polymorphic sites were detected including a 2-bp deletion/insertion, a 6-bp deletion/insertion and 5 SNPs. Seven different 3'UTR alleles were identified with frequencies ranging from 0.0048 to 0.7981. MICB(∗)005:02, the most frequent allele in this population, exhibited significant linkage disequilibrium (LD) with UTR1; MICB(∗)004:01, which was also relatively common in this population, showed strong LD with both UTR2 and UTR3 alleles. Analysis for targets of miRNAs revealed that miRNA hsa-miR-4768-5p, whose seed region binds to positions 82-88 of MICB 3'UTR, encompasses the +11800 A/G polymorphism. Ewens-Watterson homozygosity statistics at MICB coding and 3'UTR regions were consistent with neutral expectations. Phylogenetic analysis demonstrated the existence of two main MICB lineages. Our results provided for the first time the data of genetic variation in the 3'UTR of MICB gene in human populations. The findings are valuable for future studies of the mechanisms underlying MICB post-transcriptional regulation, the potential role of regulatory region of MICB gene in disease susceptibility in related ethnic groups, and will inform studies of evolution of the MHC gene complex.

Meta-analysis of genetic variability in the ?-amyloid production, aggregation and degradation metabolic pathways and the risk of Alzheimer?s disease

Variants in genes encoding enzymes involved in production, aggregation or degradation of beta-amyloid are potential risk factors for sporadic Alzheimer's disease (AD). Meta-analyses on AD association with BACE1 exon 5, BACE1 intron 5, FE65 intron 13, CYP46 intron 2, alpha(1)-antichymotrypsine Ala17Thr, bleomycin hydrolase I443V, lectin-like oxidized low-density lipoprotein receptor (OLR1) 3'-UTR (+1071) and (+1073), and very-low-density lipoprotein receptor (VLDLR) 5'-UTR (CGG-repeat) polymorphisms. In BACE1 exon 5, genotype CC+CT acts as a protective factor in Apolipoprotein E (ApoE) epsilon 4 carriers [odds ratio (OR) = 0.57; 95% confidence interval (CI): 0.38-0.88], and as a risk factor in ApoE epsilon 4 non-carriers (OR = 1.33; 95% CI: 1.00-1.78). OLR1 3'-UTR (+1073) allele C is associated with increased risk (OR = 1.23; 95% CI: 1.01-1.50). VLDLR 5'-UTR genotype 2 is associated with increased risk (OR = 1.70; 95% CI: 1.09-2.63) in the Asian population and is protective (OR = 0.48; 95% CI: 0.26-0.86) in the non-Asian population. Other studied polymorphisms are not associated with AD. The overall impact on AD risk of the genes for which meta-analyses are now available is rather limited. Additional meta-analyses of other different genes encoding for A beta production, aggregation and degradation mediators might help in determining the risk profile for AD.

Polymorphism in the 3′ UTR of the IL12B gene is associated with Chagas’ disease cardiomyopathy

The aim of this study was to investigate the possible influence of a 3′ untranslated region (3′ UTR) polymorphism of the IL12B gene in susceptibility to Trypanosoma cruzi infection or in the development to cardiomyopathy in Chagas’ disease (CD). We determined the IL12B 3′ UTR genotypes in a sample of 200 seronegative individuals and 260 serologically positive patients (130 with Chagasic cardiomyopathy and 130 asymptomatic). All individuals are from a Colombian region where T. cruzi infection is endemic. Genotyping was performed by the PCR-restriction fragment length polymorphism (RFLP) method. The overall distribution of the IL12B 3′ UTR alleles and genotypes in seronegative compared with seropositive individuals was not statistically significant. Interestingly, we found that the IL12B 3′ UTR CC genotype was significantly increased among cardiomyopathic patients when compared to asymptomatic individuals (16% versus 5%; P = 0.005; P c = 0.015; OR = 3.39; 95% CI 1.3–9.15). In addition, we observed that the IL12B 3′ UTR C allele was present at significantly higher frequency in cardiomyopathic (33% versus 22%; P = 0.008; P c = 0.016; OR = 1.69; 95% CI 1.12–2.55) as compared to asymptomatic. Our results suggest that IL12B 3′ UTR gene polymorphisms may influence the susceptibility to develop Chagasic cardiomyopathy.

Association of variants in the IL12B gene with leprosy and tuberculosis

There is a great range in outcomes after mycobacterial infections, and this is probably due to individual variation in immune responses. One of the key cytokine regulators of the immune response is interleukin (IL-) 12. The IL12B gene encodes the p40 chain of both IL-12 and IL-23 and it has two major variant sites at which different alleles are associated with increased levels of gene expression and with susceptibility to a range of immune-related diseases. We hypothesized that IL12B variants associated with increased expression would be as associated with susceptibility to persistent mycobacterial infection. We tested this hypothesis by genotyping Indian subjects, having either leprosy or tuberculosis (TB), as well as ethnically matched controls. Subjects with leprosy were less likely to have the 3'UTR genotype associated with lower IL12B expression (P= 0.001). Subjects with TB were not only more likely to have the high-expressing IL12B promoter genotype (P= 0.01) but also more likely to have this in the same haplotype with the high expressing 3'UTR allele (P= 0.0009). These results suggest these infectious diseases may be improved by modulating IL-l2p40 production.

Associations between IL12B polymorphisms and tuberculosis in the Hong Kong Chinese population.

Interleukin (IL)-12 plays a vital role in regulating cell-mediated immunity against tuberculosis (TB). To test whether IL12B genetic polymorphisms might contribute to human TB susceptibility, we examined the genotype frequencies of 5 IL12B polymorphisms (at promoter, intron 2, intron 4, exon 5, and 3' untranslated region [UTR]) in 516 patients with TB and 514 healthy control subjects from the Hong Kong Chinese population. Individuals homozygous for the IL12B intron 2-repeat marker (ATT)8 had a 2.1-fold increased risk of developing TB (P < .001) (odds ratio, 2.14 [95% confidence interval, 1.45-3.19]). Estimation of the frequencies of multiple-locus haplotypes composed of IL12B promoter, intron 2, intron 4, and 3' UTR alleles revealed potential risk haplotypes (designated "A" and "K") and protective haplotypes (designated "B") for TB. Furthermore, combining the genotype data of the 4 informative IL12B loci revealed a strong association between a specific genotype pattern, termed "diplotype I" (heterozygous A and K haplotypes), and TB. In contrast, diplotype II (homozygous BB haplotypes) appeared protective against TB. These findings support the association between IL12B intron 2 polymorphism and TB and between specific IL12B haplotypes and TB.

A 3′-UTR variant of the inducible porcine hsp70.2 gene affects mRNA stability

Large individual differences were observed in the abundance of transcripts from the hsp70.2 gene in primary fibroblast cultures sampled from 15 different pigs. While previously described functional promoter variants of this gene can partly account for the high variability of heat-induced increased abundance of transcripts, they are unrelated to the observed highly variable absolute amounts of hsp70.2 transcripts. Comparative sequence analysis revealed an alteration of the 3′-untranslated region (3′-UTR) sequences in these samples. The variant 3′-UTR allele proved to increase the half life of the hsp70.2 mRNA in reporter gene assays. It is suggested that the cellular stress response is significantly affected by the action and interaction of both promoter and 3′-UTR variants of the hsp70.2 gene.

Linkage disequilibrium of a type 1 diabetes susceptibility locus with a regulatory IL12B allele.

Type 1 diabetes (T1D; or insulin-dependent diabetes mellitus, IDDM) is an autoimmune disease with both genetic and environmental components. In addition to the human leukocyte antigen (HLA) complex, the single major genetic contributor of susceptibility, an unknown number of other unidentified genes are required to mediate disease. Although many loci conferring susceptibility to T1D have been mapped, their identification has proven problematic due to the complex nature of this disease. Our strategy for finding T1D susceptibility genes has been to test for human homologues of loci implicated in diabetes-prone NOD (non-obese diabetic) mice, together with application of biologically relevant stratification methods. We report here a new susceptibility locus, IDDM18, located near the interleukin-12 (IL-12)p40 gene, IL12B. Significant bias in transmission of IL12B alleles was observed in affected sibpairs and was confirmed in an independent cohort of simplex families. A single base change in the 3' UTR showed strong linkage disequilibrium with the T1D susceptibility locus. The IL12B 3' UTR alleles showed different levels of expression in cell lines. Variation in IL-12p40 production may influence T-cell responses crucial for either mediating or protecting against this and other autoimmune diseases.

No evidence for mutations of the leptin or leptin receptor genes in women with polycystic ovary syndrome.

Polycystic ovarian syndrome (PCOS) is often associated with obesity and insulin resistance, both of which are features that are linked to the leptin and leptin receptor (LEPR) genes. Analysis of the leptin gene by sequencing samples from 38 well-characterized patients with PCOS revealed no mutations of the coding exons. In single-stranded conformational polymorphism (SSCP) analysis and subsequent sequencing of the LEPR gene revealed previously identified amino acid variants in exons 2, 4 and 12 as well as the pentanucleotide insertion in the 3'-untranslated region (3'-UTR). The allele frequencies of these polymorphisms did not differ from those in the general population, as assessed in 122 female controls. Compared with non-carriers, serum insulin concentrations tended to be lower in the carriers of the variant LEPR exon 12 allele as well as in the carriers of the variant LEPR 3'-UTR allele, a marker previously suggested to be associated with serum insulin concentrations. In conclusion, PCOS is not commonly a consequence of mutations of the leptin or LEPR genes. However, our data support the hypothesis that variations in the LEPR gene locus have an effect on insulin regulation.

Different positioning elements select poly(A) sites at the 3'-end of GCN4 mRNA in the yeast Saccharomyces cerevisiae.

Cleavage and polyadenylation of eukaryotic mRNA requires efficiency and positioning elements in the 3'-untranslated region (3'-UTR) of the mRNA. Specific point mutations were introduced into the yeast GCN4 3'-UTR to detect sequence motifs which are involved in the positioning of the poly(A) site. 3'-End proces-sing activities of different GCN4 3'-UTR alleles were measured in an in vivo test system. Point mutations in an AAGAA motif defocussed selection of the poly(A) sites of the GCN4 3'-UTR to various additional poly(A) sites instead of the single site of the wild-type GCN4 3'-UTR. A strain with an intact wild-type GCN4 3'-UTR but impaired in RNA15 encoding an RNA-binding processing factor showed a similar defocussed pattern of poly(A) site selection. Remarkably, two additional sequence motifs upstream of the AAGAA motif which resemble yeast efficiency motifs independently affected poly(A) site positioning but not efficiency of 3'-end processing. Mutations in one motif resulted in an additional upstream poly(A) site. Alterations of the other motif shifted the poly(A) sites exclusively to two downstream poly(A) sites. These data suggest several contact points between the precursor mRNA and the polyadenylation machinery in yeast.