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http://dx.doi.org/10.5352/JLS.2021.31.6.568

The Association of Long Noncoding RNA LOC105372577 with Endoplasmic Reticulum Protein 29 Expression: A Genome-wide Association Study  

Lee, Soyeon (School of Systems Biomedical Science, College of Natural Sciences, Soongsil University)
Kwon, Kiang (Department of Clinical Laboratory Science, Wonkwang Health Science University)
Ko, Younghwa (Department of Anatomy & Cell Biology, College of Medicine, Chungnam National University)
Kwon, O-Yu (Department of Anatomy & Cell Biology, College of Medicine, Chungnam National University)
Publication Information
Journal of Life Science / v.31, no.6, 2021 , pp. 568-573 More about this Journal
Abstract
This study identified genomic factors associated with endoplasmic reticulum protein (ERp)29 gene expression in a genome-wide association study (GWAS) of genetic variants, including single-nucleotide polymorphisms (SNPs). In total, 373 European genes from the 1000 Genomes Project were analyzed. SNPs with an allelic frequency of less than or more than 5% were removed, resulting in 5,913,563 SNPs including in the analysis. The following expression quantitative trait loci (eQTL) from the long noncoding RNA LOC105372577 were strongly associated with ERp29 expression: rs6138266 (p<4.172e10), rs62193420 (p<1.173e10), and rs6138267 (p<2.041e10). These were strongly expressed in the testis and in the brain. The three eQTL were identified through a transcriptome-wide association study (TWAS) and showed a significant association with ERp29 and osteosarcoma amplified 9 (OS9) expression. Upstream sequences of rs6138266 were recognized by ChIP-seq data, while HaploReg was used to demonstrate how its regulatory DNA binds upstream of transcription factor 1 (USF1). There were no changes in the expression of OS9 or USF1 following ER stress.
Keywords
Endoplasmic reticulum protein (ERp)29; expression quantitative trait loci (eQTL); genome-wide association study (GWAS); osteosarcoma amplified 9 (OS9); single-nucleotide polymorphisms (SNPs);
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