scholarly journals Risk variant in miR-544a binding site in CCDC170 is associated with osteoporosis

2019 ◽  
Author(s):  
Xinhong Liu ◽  
Yang Wang ◽  
Qin Tan ◽  
Yunqi He ◽  
Xin Zhao
Keyword(s):  
Mirna Target ◽  
Disease Risk ◽  
Potential Therapeutic Target ◽  
Osteoporosis Therapy ◽  
Risk Variant ◽  
Genomic Variations ◽  
Target Sites ◽  
Allele Specific ◽  
Specific Regulation ◽  
Osteoporosis Risk

AbstractMicroRNAs (miRNAs) play essential roles in regulating bone formation and homeostasis. Genomic variations within miRNA target sites may therefore be important sources of genetic differences in osteoporosis risk. To investigate this possibility, we searched for miRNA recognition sites within genes using the TargetScan, miRNASNP and miRbase databases. In this study, we showed that miR-544a differentially regulated the allele variants of rs6932603 in the CCDC170 3 ′ untranslated (3′-UTR). We also showed that miR-544a suppressed osteogenesis and promoted osteoclastogenesis by regulating the expressions of Runx2, Osterix, Alp, Col1a1, Osteopontin (OPN) ,Osteocalcin (OCN) and Osteoprotegerin (OPG). Our results suggest that allele-specific regulation of CCDC170 by miR-544a explains the observed disease risk, and provides a potential therapeutic target for osteoporosis therapy.

scholarly journals Three functional polymorphisms in CCDC170 were associated with osteoporosis phenotype

Biology Open ◽  
2021 ◽  
pp. bio.050930
Author(s):  
Xinhong Liu ◽  
Yu-Gang Li ◽  
Fang Tan ◽  
Jia Liu ◽  
Ruokun Yi ◽  
...  
Keyword(s):  
Bone Formation ◽  
Bone Biology ◽  
Potential Therapeutic Target ◽  
Osteoporosis Therapy ◽  
Genomic Variations ◽  
Functional Polymorphisms ◽  
Target Sites ◽  
Specific Manner ◽  
Allele Specific ◽  
Osteoporosis Risk

MicroRNAs (miRNAs) play essential roles in regulating bone formation and homeostasis. Genomic variations within miRNA target sites may therefore be important sources of genetic differences in osteoporosis risk. The function of CCDC170 in bone biology is still unclear. To verify the function of CCDC170, we knocked down CCDC170 in cells and mice and searched for miRNA recognition sites within CCDC170 using the TargetScan, miRNASNP, and miRBase databases. In this study, our results demonstrated that CCDC170 plays an important role in the positive regulation of bone formation. MiR-153-3p, miR-374b-3p, miR-4274, miR-572 and miR-2964a-5p inhibited CCDC170 expression in an allele-specific manner by binding GWAS lead SNPs rs6932603, rs3757322 and rs3734806. These findings may improve our understanding of the association between CCDC170, miRNAs, GWAS lead SNPs, and osteoporosis pathogenesis and may provide a potential therapeutic target for osteoporosis therapy.

scholarly journals Association between miRNA Target Sites and Incidence of Primary Osteoarthritis in Women from Volga-Ural Region of Russia: A Case-Control Study

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1222
Author(s):  
Anton Tyurin ◽  
Daria Shapovalova ◽  
Halida Gantseva ◽  
Valentin Pavlov ◽  
Rita Khusainova
Keyword(s):  
Ethnic Groups ◽  
Mirna Target ◽  
Ural Region ◽  
Specific Pcr ◽  
Target Sites ◽  
Allele Specific ◽  
Polymorphic Variants ◽  
Allele Specific Pcr ◽  
Volga Ural Region ◽  
Control Study

Over the past decades, numerous studies on the genetic markers of osteoarthritis (OA) have been conducted. MiRNA targets sites are a promising new area of research. In this study, we analyzed the polymorphic variants in 3′ UTR regions of COL1A1, COL11A1, ADAMTS5, MMP1, MMP13, SOX9, GDF5, FGF2, FGFR1, and FGFRL1 genes to examine the association between miRNA target site alteration and the incidence of OA in women from the Volga-Ural region of Russia using competitive allele-specific PCR. The T allele of the rs9659030 was associated with generalized OA (OR = 2.0), whereas the C allele of the rs229069 was associated with total OA (OR = 1.43). The T allele of the rs13317 was associated with the total OA (OR = 1.67). After Benjamini-Hochberg correction, only rs13317 remained statistically significant. According to ethnic heterogeneity, associations between the T allele (rs1061237) with OA in women of Russian descent (OR = 1.77), the G allele (rs6854081) in women of Tatar descent (OR = 4.78), the C allele (rs229069) and the T allele (rs73611720) in women of mixed descent and other ethnic groups (OR = 2.25 and OR = 3.02, respectively) were identified. All associations remained statistically significant after Benjamini-Hochberg correction. Together, this study identified miRNA target sites as a genetic marker for the development of OA in various ethnic groups.

scholarly journals Investigation of TAGAP gene polymorphism (rs1738074) in Turkish pediatric celiac patients

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Melek Pehlivan ◽  
Tülay K. Ayna ◽  
Maşallah Baran ◽  
Mustafa Soyöz ◽  
Aslı Ö. Koçyiğit ◽  
...  
Keyword(s):  
Pediatric Patients ◽  
Disease Risk ◽  
Polymerase Chain Reaction Method ◽  
Control Group ◽  
Healthy Children ◽  
Single Nucleotide ◽  
Significant Difference ◽  
Allele Specific ◽  
And Control

Abstract Objectives There are several hypotheses on the effects of the rs1738074 T/C single nucleotide polymorphism in the TAGAP gene; however, there has been no study on Turkish pediatric patients. We aimed to investigate the association of celiac disease (CD) and type 1 diabetes mellitus (T1DM) comorbidity with the polymorphism in the TAGAP gene of Turkish pediatric patients. Methods Totally, 127 pediatric CD patients and 100 healthy children were included. We determined the polymorphism by the allele-specific polymerase chain reaction method. We used IBM SPSS Statistics version 25.0 and Arlequin 3.5.2 for the statistical analyses. The authors have no conflict of interest. Results It was determined that 72% (n=154) of only CD patients had C allele, whereas 28% (n=60) had T allele. Of the patients with celiac and T1DM, 42.5% (n=17) and 57.5% (n=23) had T and C alleles, respectively. Of the individuals in control group, 67% (n=134) had C allele, whereas 33% (n=66) had T allele. Conclusions There was no significant difference in the genotype and allele frequencies between the patient and control groups (p>0.05). There was no significant association between the disease risk and the polymorphism in our study group.

scholarly journals MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 661 ◽  
Author(s):  
Chenxing Liu ◽  
Fuquan Zhang ◽  
Tingting Li ◽  
Ming Lu ◽  
Lifang Wang ◽  
...  
Keyword(s):  
Mirna Target ◽  
Gwas Snps ◽  
Target Sites

scholarly journals Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

2021 ◽  
Vol 12 ◽  
Author(s):  
Pengfei Xu ◽  
Yantao Zhu ◽  
Yanfeng Zhang ◽  
Jianxia Jiang ◽  
Liyong Yang ◽  
...  
Keyword(s):  
Mirna Target ◽  
Target Genes ◽  
Rare Variants ◽  
Agronomic Traits ◽  
Global Analysis ◽  
Variant Calling ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
A Genome ◽  
Target Sites

MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.

scholarly journals An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation

2018 ◽  
Vol 102 (5) ◽  
pp. 776-793 ◽  
Author(s):  
Xiao-Feng Chen ◽  
Dong-Li Zhu ◽  
Man Yang ◽  
Wei-Xin Hu ◽  
Yuan-Yuan Duan ◽  
...  
Keyword(s):  
Long Range ◽  
Loop Formation ◽  
Allele Specific ◽  
Osteoporosis Risk

Bioinformatics Methods for Studying MicroRNA and ARE-Mediated Regulation of Post-Transcriptional Gene Expression

2010 ◽  
Vol 1 (3) ◽  
pp. 97-112 ◽  
Author(s):  
Richipal Singh Bindra ◽  
Jason T. L. Wang ◽  
Paramjeet Singh Bagga
Keyword(s):  
Mirna Target ◽  
Target Prediction ◽  
Untranslated Regions ◽  
Regulatory Rna ◽  
Rna Motifs ◽  
Protein Coding ◽  
Rna Molecules ◽  
Cellular Processes ◽  
Target Sites ◽  
Transcriptional Gene Regulation

MicroRNAs (miRNAs) are short single-stranded RNA molecules with 21-22 nucleotides known to regulate post-transcriptional expression of protein-coding genes involved in most of the cellular processes. Prediction of miRNA targets is a challenging bioinformatics problem. AU-rich elements (AREs) are regulatory RNA motifs found in the 3’ untranslated regions (UTRs) of mRNAs, and they play dominant roles in the regulated decay of short-lived human mRNAs via specific interactions with proteins. In this paper, the authors review several miRNA target prediction tools and data sources, as well as computational methods used for the prediction of AREs. The authors discuss the connection between miRNA and ARE-mediated post-transcriptional gene regulation. Finally, a data mining method for identifying the co-occurrences of miRNA target sites in ARE containing genes is presented.

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