Functional Analysis of Deep Intronic SNP rs13438494 in Intron 24 of PCLO Gene

Seo, Sang‐Woo; Takayama, K.; Uno, Kyosuke; Ohi, Kazutaka; Hashimoto, Ryota; Nishizawa, Daisuke; Ikeda, Kazutaka; Ozaki, Norio; Nabeshima, Toshitaka; Miyamoto, Yukio; Nitta, Atsumi

doi:10.1371/journal.pone.0076960

Cited by 54 publications

(33 citation statements)

References 21 publications

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“…The polymorphisms selected for this study are located within the introns of the TIMP2 gene and do not affect the protein structure. They may indirectly affect the level of transcription by altering the structure of the DNA‐binding site of regulatory proteins or the effect on mRNA stability or lead to DNA‐histone binding strength alternations, but such relationships have not yet been described in the literature for any of the assessed SNPs.…”

Section: Discussionmentioning

confidence: 99%

TIMP2 Polymorphisms Association With Curve Initiation and Progression of Thoracic Idiopathic Scoliosis in the Caucasian Females

Andrusiewicz

Harasymczuk

Janusz

et al. 2019

Journal Orthopaedic Research

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Idiopathic scoliosis (IS) etiology remains unclear, but strong genetic background is suggested. Previously reported TIMP2 study indicates an association of genic rs8179090 with IS progression in a Han Chinese population. However, there has been a lack of investigation into intragenic TIMP2 polymorphisms in IS patients. We recruited 100 Caucasian females with IS and 100 controls. Patients were subdivided accordingly to: progression rate, curve severity, joint mobility, and curve pattern. Allele‐specific‐polymerase chain reaction based on fluorescence resonance energy transfer was applied to evaluate nine TIMP2 polymorphisms. Distribution of genotype and allele frequency in only one polymorphism (rs11658743) differed in case–control study. Four of the polymorphisms (rs2277700, rs11077401, rs2376999, and rs4789934) showed non‐equal distributions either in genotype or/and allele distributions in the patients of different progression rates. The rs11077401 was related to curve severity patients distinction and the rs8179090 distinguished patients with different joint mobility level. Two polymorphisms either differed statistically in case of curve patterns subgrouping (rs8068674 and rs8179090) or showed a slight tendency toward significance in the recessive model of allele distributions (rs9916809 and rs8179090). The remaining two polymorphisms (rs2377005, rs11658743) showed no association with either clinical or radiographic IS characteristics. The influence of the G allele of the rs8179090 on the clinical course of IS has not yet been confirmed. We identified four TIMP2 polymorphisms (rs11077401, rs2376999, rs2277700, and rs4789934) that were associated with a higher risk of the progressive IS form. Further genetic association studies based on suggested clinical criteria would be necessary to validate TIMP2 polymorphisms associated with the curve progression. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:2217–2225, 2019

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Section: Discussionmentioning

confidence: 99%

TIMP2 Polymorphisms Association With Curve Initiation and Progression of Thoracic Idiopathic Scoliosis in the Caucasian Females

Andrusiewicz

Harasymczuk

Janusz

et al. 2019

Journal Orthopaedic Research

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“…The analysis of the SNP–SNP interactions showed a strong interaction between these SNPs regarding susceptibility to lung cancer. Several studies provided increasing evidence to support that intronic SNPs confer susceptibilities by affecting the binding of transcription factor binds and/or RNA splicing (Seo et al, ; D. Wang & Sadee, ; Zhao et al, ). However, the mechanisms on the biological function of these SNPs in IL1R2 are unknown and need more functional studies to explore.…”

Section: Discussionmentioning

confidence: 99%

Association between IL‐1R2 polymorphisms and lung cancer risk in the Chinese Han population: A case–control study

Wang

Zhang

et al. 2019

Molec Gen & Gen Med

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Background Interleukin‐1 receptor 2 (IL‐1R2), as an anti‐inflammatory cytokine, is involved in the pathogenesis and progression of lung cancer. However, the role of IL‐1R2 polymorphisms in patients with lung cancer has yet to be fully elucidated. Methods Six single‐nucleotide polymorphisms (SNPs) in IL‐1R2 were genotyped in 259 patients and 346 healthy controls. We used the chi‐squared test, genetic model analysis, Haploview analysis, and multifactor dimensionality reduction (MDR) to evaluate the potential association between IL‐1R2 polymorphisms and lung cancer susceptibility. Bioinformatics analyses were conducted to analyze the expression level of IL‐1R2 and its association with the overall survival of lung cancer. Results Our results found that rs3218977‐GG was associated with a decreased risk of lung cancer (odds ratio [OR] = 0.39; 95% confidence interval [CI]: 0.17–0.87; p = 0.023), and rs2072472 had a significant risk‐increasing effect in the dominant model (AG + GG vs. AA: OR = 1.54; 95% CI: 1.09–2.20; p = 0.015). The MDR model also revealed that rs2072472 is the most influential risk factor of lung cancer (testing accuracy = 0.543; cross‐validation consistency = 10/10; p = 0.032). In addition, our results indicated that the IL‐1R2 mRNA level was downregulated in lung cancer patients, whereas the high expression of IL‐1R2 was related to a poor prognosis in lung cancer. Conclusions Our results suggest that genetic variants of IL‐1R2 may play a role in lung cancer susceptibility. Further population and functional validations of our findings are warranted.

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“…Huang et al reported that the variation (T4127G) in intron2 of CYP3A4 exists in the human liver, which could significantly decreases the hepatic microsomal testosterone 6-hydroxylase activity of cytochrome P450, family 3, subfamily A (CYP3A) [25] . Seo et al [26] demonstrated that intronic SNP rs13438494 alters splicing efficient creating or disrupting a splicing motif, which may ultimately result in bipolar disorder in affected people. In Holsteins, Wang et al [27] detected a SNP (c. 1033 + 2184 C>T) in intron 8 of CD46 molecule (CD46), which results in CD46-transcript GUI, WANG, JIA ZHANG, CHEN, HOU [28] showed that a point variation in intron1 (A3481C) of fatty acid binding protein 4, adipocyte (A-FABP) had strong effect on intramuscular fat content in Junmu No.…”

Section: Discussionmentioning

confidence: 99%

IGF-1 Gen Polimorfizmi Çin Qinchuan Sığırında Büyüme Özelliklerini Etkiler

Gui¹,

Wang²,

Jia³

et al. 2018

Kafkas Univ Vet Fak Derg

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Insulin-like growth factor I (IGF-1) influences gonadotrophin-releasing hormone (GnRH) neurons during puberty, and plays an important role in muscle growth in farm animals. The objective of this study was to estimate the genotype frequencies of the polymorphisms of IGF-1 and to determine associations between these polymorphisms and growth traits in Chinese Qinchuan cattle breeds. Five single nucleotide polymorphisms (SNPs), including one in intron 2 (g.5172T>G) and four in intron 3 (g.56495C>A, g.56501C>T, g.56801C>T and g.71090T>G) were identified according to the sequencing results of 487 individual of a Qinchuan cattle population. The chi-square test showed g.5172T>G, g.56495C>A and g.56801C>T were in Hardy-Weinberg equilibrium in all the samples. Six different haplotypes were identified, of which two major haplotypes had a frequency of 48.2% (-TCTTT-) and 16.3% (-TCCTT-). The single marker association analysis showed that the three polymorphisms (g.5172T>G, g.56501C>T and g.71090T>G) were significantly associated with growth traits (at P<0.01 or P<0.05). In conclusion, our results suggest that some polymorphisms in IGF-1 may play a role in determining one of the important genetic factors that influence growth traits in Chinese Qinchuan cattle.

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Functional Analysis of Deep Intronic SNP rs13438494 in Intron 24 of PCLO Gene

Cited by 54 publications

References 21 publications

TIMP2 Polymorphisms Association With Curve Initiation and Progression of Thoracic Idiopathic Scoliosis in the Caucasian Females

TIMP2 Polymorphisms Association With Curve Initiation and Progression of Thoracic Idiopathic Scoliosis in the Caucasian Females

Association between IL‐1R2 polymorphisms and lung cancer risk in the Chinese Han population: A case–control study

IGF-1 Gen Polimorfizmi Çin Qinchuan Sığırında Büyüme Özelliklerini Etkiler

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