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Guo X, Lan G, Jiang Q, Guo Y, Ouyang Y, Liang J, Zhang M. Expression mechanisms of mir-486-5p and its host gene sANK1 in porcine muscle. Mol Biol Rep 2024; 51:840. [PMID: 39042282 DOI: 10.1007/s11033-024-09773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/01/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND MiR-486-5p has been identified as a crucial regulator of the PI3K/AKT signalling pathway, which plays a significant role in skeletal muscle development. Its host gene, sANK1, is also essential for skeletal muscle development. However, the understanding of porcine miR-486-5p and sANK1 has been limited. METHODS AND RESULTS In this study, PCR analyses revealed a positive correlation between the expression of miR-486-5p and sANK1 in the longissimus dorsi muscle of the Bama mini-pig and Landrace-pig, as well as during myoblast differentiation. Furthermore, the expression of miR-486-5p/sANK1 was higher in the Bama mini-pig compared to the Landrace-pig. There was a total of 18 single nucleotide polymorphisms (SNP) present in the sANK1 promoter region. Among these SNPs, 14 of them resulted in alterations in transcription factor binding sites (TFBs). Additionally, the promoter fluorescence assay demonstrated that the activity of the sANK1 promoter derived from the Bama mini-pig was significantly higher compared to Landrace-pig. It is worth noting that ten regulatory SNPs have the potential to influence the activity of the sANK1 promoter. A nuclear mutation A-G located at position - 401 (relative to the transcription start site) in the Bama mini-pig was identified, which creates a putative TFB motif for MyoD. CONCLUSIONS The findings presented in this study offer fundamental molecular knowledge and expression patterns of miR-486-5p/sANK1, which can be valuable for gaining a deeper understanding of the gene's involvement in porcine skeletal muscle development, and meat quality.
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Affiliation(s)
- Xiaoping Guo
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Qinyang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yafen Guo
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yiqiang Ouyang
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Mingyuan Zhang
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Life Science Institute, Guangxi Medical University, Nanning, 530021, China.
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2
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Majocha MR, Jackson DE, Ha NH, Amin R, Pangrácová M, Ross CR, Yang HH, Lee MP, Hunter KW. Resf1 is a compound G4 quadruplex-associated tumor suppressor for triple negative breast cancer. PLoS Genet 2024; 20:e1011236. [PMID: 38722825 PMCID: PMC11081379 DOI: 10.1371/journal.pgen.1011236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/27/2024] [Indexed: 05/13/2024] Open
Abstract
Patients with ER-negative breast cancer have the worst prognosis of all breast cancer subtypes, often experiencing rapid recurrence or progression to metastatic disease shortly after diagnosis. Given that metastasis is the primary cause of mortality in most solid tumors, understanding metastatic biology is crucial for effective intervention. Using a mouse systems genetics approach, we previously identified 12 genes associated with metastatic susceptibility. Here, we extend those studies to identify Resf1, a poorly characterized gene, as a novel metastasis susceptibility gene in ER- breast cancer. Resf1 is a large, unstructured protein with an evolutionarily conserved intron-exon structure, but with poor amino acid conservation. CRISPR or gene trap mouse models crossed to the Polyoma Middle-T antigen genetically engineered mouse model (MMTV-PyMT) demonstrated that reduction of Resf1 resulted in a significant increase in tumor growth, a shortened overall survival time, and increased incidence and number of lung metastases, consistent with patient data. Furthermore, an analysis of matched tail and primary tissues revealed loss of the wildtype copy in tumor tissue, consistent with Resf1 being a tumor suppressor. Mechanistic analysis revealed a potential role of Resf1 in transcriptional control through association with compound G4 quadruplexes in expressed sequences, particularly those associated with ribosomal biogenesis. These results suggest that loss of Resf1 enhances tumor progression in ER- breast cancer through multiple alterations in both transcriptional and translational control.
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Affiliation(s)
- Megan R. Majocha
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Devin E. Jackson
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Ngoc-Han Ha
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ruhul Amin
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marie Pangrácová
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christina R. Ross
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Howard H. Yang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maxwell P. Lee
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kent W. Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Hurabielle C, LaFlam TN, Gearing M, Ye CJ. Functional genomics in inborn errors of immunity. Immunol Rev 2024; 322:53-70. [PMID: 38329267 PMCID: PMC10950534 DOI: 10.1111/imr.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Inborn errors of immunity (IEI) comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.
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Affiliation(s)
- Charlotte Hurabielle
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Taylor N LaFlam
- Division of Pediatric Rheumatology, Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, UCSF, San Francisco, California, USA
- Institute of Computational Health Sciences, UCSF, San Francisco, California, USA
- Gladstone Genomic Immunology Institute, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, UCSF, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, California, USA
- Arc Institute, Palo Alto, California, USA
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4
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Fallahi M, Masoudi AA, Torshizi RV. Genetic variants in the TAC1 transcriptional regulatory region affect on trainability and excitability levels in Belgian Malinois dogs. Vet Med Sci 2024; 10:e1346. [PMID: 38227710 PMCID: PMC10790320 DOI: 10.1002/vms3.1346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 11/12/2023] [Accepted: 12/10/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Trainability in dogs is affected by learning aptitude and memory capacity. While this trait has a heritable basis in canines, the specific genetic loci responsible for it remain unknown. Our previous results suggested that the BDNF, CCK and TAC1 genes are associated with learning and memory in canines. Experimental validation is crucial to confirm the effects of these candidate genes on trainability. Understanding the genetic foundation of this trait would offer insight into the inheritance pattern of complex behavioural characteristics. OBJECTIVE This study aimed to assess the genetic variations within candidate genes and explore their potential associations with behavioural phenotypes in dogs. METHODS The behavioural characteristics of 123 male Belgian Malinois dogs were assessed using a customised questionnaire. Target regions of candidate genes were screened for genetic variation by single-strand conformational polymorphism (SSCP). Following that, SSCP banding patterns were sequenced, and putative transcription factor binding sites were predicted using bioinformatics tools. Quantitative association analysis between identified genetic variants and behavioural trait scores was performed using the general linear model (GLM). RESULTS Sequencing the coding and flanking regions revealed three mutations (c.-89C>T, c.-162G>C and c.*33T>A) in the dog TAC1 gene. Bioinformatics analysis predicted two single nucleotide polymorphisms (SNPs) were located within the putative TAC1 promoter and could disrupt transcription factor binding sites. Statistical tests revealed that the c.-89C>T was significantly associated with excitability (p < 0.01), while the c.-162G>C was significantly associated with trainability level (p < 0.05). CONCLUSION In summary, we identified two regulatory SNPs in the 5'-UTR promoter region of the TAC1 gene that are associated with excitability and trainability in Belgian Malinois dogs. These genetic variations have the potential to alter the binding sites of transcription factors NRF1 and OTX1, consequently influencing TAC1 expression and related behavioural characteristics. Our findings implicate TAC1 polymorphisms as candidates influencing breed-specific behavioural characteristics in canines. Further studies on diverse breeds of dogs are necessary to validate these SNPs' effects.
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Affiliation(s)
- Mohammad Fallahi
- Faculty of AgricultureDepartment of Animal ScienceTarbiat Modares UniversityTehranIran
| | - Ali Akbar Masoudi
- Faculty of AgricultureDepartment of Animal ScienceTarbiat Modares UniversityTehranIran
| | - Rasoul Vaez Torshizi
- Faculty of AgricultureDepartment of Animal ScienceTarbiat Modares UniversityTehranIran
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Zhu XB, Niu ZH, Fan WM, Sheng CS, Chen Q. Type 2 diabetes mellitus and the risk of male infertility: a Mendelian randomization study. Front Endocrinol (Lausanne) 2023; 14:1279058. [PMID: 38152129 PMCID: PMC10752377 DOI: 10.3389/fendo.2023.1279058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023] Open
Abstract
Objective To assess the causal effect of type 2 diabetes mellitus (T2DM) on male infertility (MI) and erectile dysfunction (ED) by Mendelian randomization (MR) analysis. Methods Data for T2DM, MI, and ED were obtained from genome-wide association studies (GWAS) involving 298, 957, 73, 479, and 223, 805 Europeans, respectively. We performed univariate MR analysis using MR Egger, Weighted median (WM) and Inverse variance weighted (IVW) methods to assess causal effects among the three. Through the Genotype Tissue Expression (GTEx) database, single-nucleotide polymorphisms (SNPs) that affect the expression levels of T2DM-related genes were located using expression quantitative trait loci (eQTL). Results MR analysis showed a significant causal relationship between T2DM and ED (WM, OR: 1.180, 95%CI: 1.010-1.378, P = 0.037; IVW, OR: 1.190, 95%CI: 1.084-1.300, P < 0.001). There is also a significant causal relationship between T2DM and MI (MR Egger, OR: 0.549, 95%CI: 0.317-0.952, P = 0.037; WM, OR: 0.593, 95%CI: 0.400, P = 0.010; IVW, OR: 0.767, 95%CI: 0.600-0.980, P = 0.034). ED may not cause MI (P > 0.05). We also found that rs6585827 corresponding to the PLEKHA1 gene associated with T2DM is an eQTL variant affecting the expression of this gene. Conclusion T2DM has a direct causal effect on ED and MI. The level of PLEKHA1 expression suppressed by rs6585827 is potentially associated with a lower risk of T2DM.
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Affiliation(s)
- Xiao-Bin Zhu
- Department of Gynecology and Obstetrics, Reproductive Medical Center, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Hong Niu
- Department of Gynecology and Obstetrics, Reproductive Medical Center, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei-Min Fan
- Department of Gynecology and Obstetrics, Reproductive Medical Center, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang-Sheng Sheng
- Department of Cardiovascular Medicine, Center for Epidemiological Studies and Clinical Trials and Center for Vascular Evaluation, Shanghai Key Lab of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qian Chen
- Department of Gynecology and Obstetrics, Reproductive Medical Center, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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Fox E. Polygenic scores, and the genome-wide association studies they derive from, will have difficulty identifying genes that predispose one to develop a social behavioral trait. Behav Brain Sci 2023; 46:e214. [PMID: 37694986 DOI: 10.1017/s0140525x22002370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Polygenic scores (PGSs) have several limitations. They are confounded with environmental effects on behavior and cannot be used to study how mutations affect brain function and behavior. For this, mutations with large effects, which often arise in only one geographical population are needed. Genome-wide association studies (GWASs), commonly used for identifying mutations, have difficulty detecting these mutations. A strategy that overcomes this challenge is discussed.
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Affiliation(s)
- Edward Fox
- Department of Psychological Science, Purdue University, West Lafayette, IN, USA https://www.purdue.edu/hhs/psy/directory/faculty/Fox_Edward.html
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7
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Tourkochristou E, Tsounis EP, Tzoupis H, Aggeletopoulou I, Tsintoni A, Lourida T, Diamantopoulou G, Zisimopoulos K, Kafentzi T, de Lastic AL, Rodi M, Tselios T, Thomopoulos K, Mouzaki A, Triantos C. The Influence of Single Nucleotide Polymorphisms on Vitamin D Receptor Protein Levels and Function in Chronic Liver Disease. Int J Mol Sci 2023; 24:11404. [PMID: 37511164 PMCID: PMC10380285 DOI: 10.3390/ijms241411404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) gene have been associated with chronic liver disease. We investigated the role of VDR SNPs on VDR protein levels and function in patients with chronic liver disease. VDR expression levels were determined in peripheral T lymphocytes (CD3+VDR+), monocytes (CD14+VDR+), and plasma from patients (n = 66) and healthy controls (n = 38). Genotyping of SNPs and the determination of expression of VDR/vitamin D-related genes were performed by using qPCR. The effect of FokI SNP on vitamin D-binding to VDR was investigated by molecular dynamics simulations. CD14+VDR+ cells were correlated with the MELD score. The ApaI SNP was associated with decreased CD3+VDR+ levels in cirrhotic patients and with higher liver stiffness in HCV patients. The BsmI and TaqI SNPs were associated with increased VDR plasma concentrations in cirrhotic patients and decreased CD14+VDR+ levels in HCV patients. The FokI SNP was associated with increased CD3+VDR+ levels in cirrhotic patients and controls. VDR polymorphisms were significantly related to the expression of genes critical for normal hepatocyte function and immune homeostasis. VDR expression levels were related to the clinical severity of liver disease. VDR SNPs may be related to the progression of chronic liver disease by affecting VDR expression levels.
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Affiliation(s)
- Evanthia Tourkochristou
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, 26504 Patras, Greece
| | - Efthymios P Tsounis
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
| | | | - Ioanna Aggeletopoulou
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, 26504 Patras, Greece
| | - Aggeliki Tsintoni
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
| | - Theoni Lourida
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
| | - Georgia Diamantopoulou
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
| | - Konstantinos Zisimopoulos
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
| | - Theodora Kafentzi
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
| | - Anne-Lise de Lastic
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, 26504 Patras, Greece
| | - Maria Rodi
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, 26504 Patras, Greece
| | - Theodore Tselios
- Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Konstantinos Thomopoulos
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
| | - Athanasia Mouzaki
- Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, 26504 Patras, Greece
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, 26504 Patras, Greece
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Yao S, Li L, Guan X, He Y, Jouaux A, Xu F, Guo X, Zhang G, Zhang L. Pooled resequencing of larvae and adults reveals genomic variations associated with Ostreid herpesvirus 1 resistance in the Pacific oyster Crassostrea gigas. Front Immunol 2022; 13:928628. [PMID: 36059443 PMCID: PMC9437489 DOI: 10.3389/fimmu.2022.928628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022] Open
Abstract
The Ostreid herpesvirus 1 (OsHV-1) is a lethal pathogen of the Pacific oyster (Crassostrea gigas), an important aquaculture species. To understand the genetic architecture of the defense against the pathogen, we studied genomic variations associated with herpesvirus-caused mortalities by pooled whole-genome resequencing of before and after-mortality larval samples as well as dead and surviving adults from a viral challenge. Analysis of the resequencing data identified 5,271 SNPs and 1,883 genomic regions covering 3,111 genes in larvae, and 18,692 SNPs and 28,314 regions covering 4,863 genes in adults that were significantly associated with herpesvirus-caused mortalities. Only 1,653 of the implicated genes were shared by larvae and adults, suggesting that the antiviral response or resistance in larvae and adults involves different sets of genes or differentiated members of expanded gene families. Combined analyses with previous transcriptomic data from challenge experiments revealed that transcription of many mortality-associated genes was also significantly upregulated by herpesvirus infection confirming their importance in antiviral response. Key immune response genes especially those encoding antiviral receptors such as TLRs and RLRs displayed strong association between variation in regulatory region and herpesvirus-caused mortality, suggesting they may confer resistance through transcriptional modulation. These results point to previously undescribed genetic mechanisms for disease resistance at different developmental stages and provide candidate polymorphisms and genes that are valuable for understanding antiviral immune responses and breeding for herpesvirus resistance.
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Affiliation(s)
- Shanshan Yao
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Li Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, College of Marine Science, Beijing, China
| | - Xudong Guan
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yan He
- Ministry of Education (MOE) Key Laboratory of Molecular Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Aude Jouaux
- UMR BOREA, “Biologie des Organismes et Ecosystèmes Aquatiques”, MNHN, UPMC, UCBN, CNRS-7208, IRD, Université de Caen Basse-Normandie, Esplanade de la Paix, Caen, France
| | - Fei Xu
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ, United States
- *Correspondence: Ximing Guo, ; Guofan Zhang, ; Linlin Zhang,
| | - Guofan Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, College of Marine Science, Beijing, China
- *Correspondence: Ximing Guo, ; Guofan Zhang, ; Linlin Zhang,
| | - Linlin Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, College of Marine Science, Beijing, China
- *Correspondence: Ximing Guo, ; Guofan Zhang, ; Linlin Zhang,
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9
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Demographic pattern of A1/A2 beta casein variants indicates conservation of A2 type haplotype across native cattle breeds (Bos indicus) of India. 3 Biotech 2022; 12:167. [PMID: 35845115 PMCID: PMC9276908 DOI: 10.1007/s13205-022-03232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 06/17/2022] [Indexed: 11/30/2022] Open
Abstract
Genetic variations of the beta casein gene hold importance because of their probable association with human health. Comparative sequence analysis of β-casein gene across Indian native, crossbred and exotic breeds in India revealed 15 SNPs and 4 INDELs corresponding to 14 haplotypes. The frequency of A2 type haplotype was maximum (0.941) across all Indian native breeds. Among the 15 variants reported for taurine breeds, only three (A1, A2 and B) were observed in analysed populations. Allelic profiling of A1/A2 β-casein variants in ~ 4000 animals belonging to three cattle types and breeding bulls also revealed the predominance of A2 allele (0.95) in Indian cattle. The high proportion of A2 allele/haplotype indicates that Indian native cattle are the best suited to meet the demands for A2 milk globally. However, a higher percentage of heterozygous genotype (A1A2) in breeding bulls warrants the need to screen sire lines so as to drift the herd towards A2. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03232-0.
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Ashraf MF, Hou D, Hussain Q, Imran M, Pei J, Ali M, Shehzad A, Anwar M, Noman A, Waseem M, Lin X. Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance. Int J Mol Sci 2022; 23:651. [PMID: 35054836 PMCID: PMC8775971 DOI: 10.3390/ijms23020651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists' emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants' genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.
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Affiliation(s)
- Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Muhammad Imran
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Mohsin Ali
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Aamar Shehzad
- Maize Research Station, AARI, Faisalabad 38000, Pakistan;
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38000, Pakistan;
| | - Muhammad Waseem
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
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11
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Wei H, Li Z, Liu F, Wang Y, Ding S, Chen Y, Liu J. The Role of FTO in Tumors and It's Research Progress. Curr Med Chem 2021; 29:924-933. [PMID: 34269659 DOI: 10.2174/0929867328666210714153046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND A malignant tumor is a disease that seriously threatens human health. At present, more and more research results show that the pathogenesis of different tumors is very complicated, and the methods of clinical treatment are also diverse. This review analyzes and summarizes the role of fat mass and obesity-associated (FTO) genes in different tumors and provides a reference value for research and drug treatment methods. METHOD We conducted a comprehensive literature search using the database. According to the article's primary purpose, irrelevant articles were excluded from the research summary and included in the relevant articles. Finally, the relevant information of the article was summarized. RESULT In this article, the relationship between malignant tumors and FTO is introduced by citing many documents. In addition, the inhibitors that act on FTO are listed. CONCLUSION This article has shown that FTO protein is a demethylase that can regulate N6-methyladenosine (m6A) levels in mRNA and plays a crucial role in the progression and resistance of various tumors such as leukemia, breast cancer, and lung cancer.
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Affiliation(s)
- Hao Wei
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Zhen Li
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Fang Liu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Yang Wang
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Shi Ding
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Ye Chen
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Ju Liu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
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12
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He J, Lin X, Yang H, Tian Y, Zhao Y, Zhang L, Wei W, Chen J. UBXN1 is a strong candidate gene in regulation of pork water-holding capacity. Arch Anim Breed 2021; 64:109-118. [PMID: 34084909 PMCID: PMC8162240 DOI: 10.5194/aab-64-109-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/15/2021] [Indexed: 11/15/2022] Open
Abstract
The UBX domain containing protein 1-like gene (UBXN1) promotes the degradation of
myofibrillar proteins during meat maturation, which affects meat water-holding capacity (WHC). This study aims to identify functional mutations in
UBXN1 promoter region, which affects the transcription activity and therefore the
WHC. Firstly, we confirmed that the UBXN1 expression level was positively
associated with WHC. Individuals with high and low WHC (n=16 per
group) were selected from 168 Duroc × Large White × Yorkshire (D × L × Y) crossbred pigs. The UBXN1 promoter region
was comparatively sequenced using DNA pools from these two groups, and a
mutation ca. -379T > G was revealed that had reverse allele distribution.
The single nucleotide polymorphism (SNP) was then genotyped in the abovementioned population. TT genotype individuals exhibited higher UBXN1 mRNA level
and higher WHC compared with GG genotype ones. Further luciferase assay
confirmed that TT genotype promoter had higher activity. Moreover, the
degradation of cytoskeletal framework proteins of muscle cells like
desmin, synemin, dystrophin, and vinculin was higher in TT genotype individuals than GG ones. In
conclusion, we identified a SNP in the UBXN1 gene promoter that contributes to
WHC improvement and pork quality. And UBXN1 is a strong candidate gene in
regulation of pork WHC.
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Affiliation(s)
- Jiawen He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiangsheng Lin
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Haoxin Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ye Tian
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yuelei Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wei Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jie Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
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13
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Sequence and haplotypes of ankyrin 1 gene (ANK1) and their association with carcass and meat quality traits in yak. Mamm Genome 2021; 32:104-114. [PMID: 33655403 DOI: 10.1007/s00335-021-09861-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Abstract
Ankyrin 1 (ANK1) gene has been demonstrated to be a functional candidate gene for meat quality that helps to constitute and maintain the structure of the cell skeleton. In this study, three contiguous ANK1 regions from yak were analyzed using polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP). As a result, nine single-nucleotide polymorphisms (SNPs) were identified, four of them in the coding region and three (c.179 C/A, c.250 G/C, and c.313 C/T) putatively resulting in amino acid changes (p. Ala 60 Glu, p. Asp 84 His, and p. Pro 105 Ser). Some SNPs in promoter region were located within or nearby the putative transcription factor binding sites, such as Sp1 and GATA, which might have an impact on the expression of the yak ANK1 gene. The presence of C1-D3 and C1-A3 were associated with an increased hot carcass weight (p = 0.0045) and a decreased drip loss rate (p = 0.0046). The presence of B1-B3, C1-A3 and C1-D3 had decreased Warner-Bratzler shear force (p = 0.0066, p = 0.0343 and p = 0.0004). The presence of one and two copies of B1-B3 and C1-A3 had decreased Warner-Bratzler shear force (p = 0.0005 and p = 0.0443), and C1-A3 had also decreased drip loss rate (p = 0.0164). These findings indicated that genetic variations of the ANK1 gene would be a preferable biomarker for the improvement of yak meat quality.
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14
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Owen KA, Price A, Ainsworth H, Aidukaitis BN, Bachali P, Catalina MD, Dittman JM, Howard TD, Kingsmore KM, Labonte AC, Marion MC, Robl RD, Zimmerman KD, Langefeld CD, Grammer AC, Lipsky PE. Analysis of Trans-Ancestral SLE Risk Loci Identifies Unique Biologic Networks and Drug Targets in African and European Ancestries. Am J Hum Genet 2020; 107:864-881. [PMID: 33031749 PMCID: PMC7675009 DOI: 10.1016/j.ajhg.2020.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder with a prominent genetic component. Individuals of African ancestry (AA) experience the disease more severely and with an increased co-morbidity burden compared to European ancestry (EA) populations. We hypothesize that the disparities in disease prevalence, activity, and response to standard medications between AA and EA populations is partially conferred by genomic influences on biological pathways. To address this, we applied a comprehensive approach to identify all genes predicted from SNP-associated risk loci detected with the Immunochip. By combining genes predicted via eQTL analysis, as well as those predicted from base-pair changes in intergenic enhancer sites, coding-region variants, and SNP-gene proximity, we were able to identify 1,731 potential ancestry-specific and trans-ancestry genetic drivers of SLE. Gene associations were linked to upstream and downstream regulators using connectivity mapping, and predicted biological pathways were mined for candidate drug targets. Examination of trans-ancestral pathways reflect the well-defined role for interferons in SLE and revealed pathways associated with tissue repair and remodeling. EA-dominant genetic drivers were more often associated with innate immune and myeloid cell function pathways, whereas AA-dominant pathways mirror clinical findings in AA subjects, suggesting disease progression is driven by aberrant B cell activity accompanied by ER stress and metabolic dysfunction. Finally, potential ancestry-specific and non-specific drug candidates were identified. The integration of all SLE SNP-predicted genes into functional pathways revealed critical molecular pathways representative of each population, underscoring the influence of ancestry on disease mechanism and also providing key insight for therapeutic selection.
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MESH Headings
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Black People
- Bortezomib/therapeutic use
- DNA, Intergenic/genetics
- DNA, Intergenic/immunology
- Enhancer Elements, Genetic
- Gene Expression
- Gene Ontology
- Gene Regulatory Networks
- Genetic Predisposition to Disease
- Genome, Human
- Genome-Wide Association Study
- Heterocyclic Compounds/therapeutic use
- Humans
- Interferons/genetics
- Interferons/immunology
- Isoquinolines/therapeutic use
- Lactams
- Lupus Erythematosus, Systemic/drug therapy
- Lupus Erythematosus, Systemic/ethnology
- Lupus Erythematosus, Systemic/genetics
- Lupus Erythematosus, Systemic/immunology
- Molecular Sequence Annotation
- Polymorphism, Single Nucleotide
- Protein Array Analysis
- Quantitative Trait Loci
- Quantitative Trait, Heritable
- White People
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Affiliation(s)
| | - Andrew Price
- AMPEL BioSolutions LLC, Charlottesville, VA 22902, USA
| | | | | | | | | | | | | | | | | | | | - Robert D Robl
- AMPEL BioSolutions LLC, Charlottesville, VA 22902, USA
| | - Kip D Zimmerman
- Wake Forest School of Medicine, Winston-Salem, NC 27109, USA
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15
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Coates BS, Hohenstein JD, Giordano R, Donthu RK, Michel AP, Hodgson EW, O'Neal ME. Genome scan detection of selective sweeps among biotypes of the soybean aphid, Aphis glycines, with differing virulence to resistance to A. glycines (Rag) traits in soybean, Glycine max. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 124:103364. [PMID: 32360957 DOI: 10.1016/j.ibmb.2020.103364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/22/2019] [Accepted: 03/18/2020] [Indexed: 05/12/2023]
Abstract
Multiple biotypes of soybean aphid, Aphis glycines, occur in North America adapted for survival (virulence) on soybean, Glycine max, with one or more different resistance to A. glycines (Rag) traits. The degree of genome-wide variance between biotypes and the basis of virulence remains unknown, but the latter is hypothesized to involve secreted effector proteins. Between 167,249 and 217,750 single nucleotide polymorphisms (SNPs) were predicted from whole genome re-sequencing of A. glycines avirulent biotype 1 (B1) and virulent B2, B3 and B4 colony-derived iso-female lines when compared to the draft B1 genome assembly, Ag_bt1_v6.0. Differences in nucleotide diversity indices (π) estimated within 1000 bp sliding windows demonstrated that 226 of 353 (64.0%) regions most differentiated between B1 and ≥ 2 virulent biotypes, representing < 0.1% of the 308 Mb assembled genome size, are located on 15 unordered scaffolds. Furthermore, these 226 intervals were coincident and show a significant association with 326 of 508 SNPs with significant locus-by-locus FST estimates between biotype populations (r = 0.6271; F1,70 = 45.36, P < 0.001) and genes showing evidence of directions selection (πN/πS > 2.0; r = 0.6233; F1,70 = 50.20, P < 0.001). A putative secreted effector glycoprotein is encoded in proximity to genome intervals of low estimated π (putative selective sweep) within avirulent B1 compared to all three virulent biotypes. Additionally, SNPs are clustered in or in proximity to genes putatively involved in intracellular protein cargo transport and the regulation of secretion. Results of this study indicate that factors on a small number of scaffolds of the A. glycines genome may contribute to variance in virulence towards Rag traits in G. max.
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Affiliation(s)
- Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, 50011, USA.
| | | | - Rosanna Giordano
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, 00927, USA; Know Your Bee Inc., San Juan, PR, 00927, USA
| | - Ravi Kiran Donthu
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, 00927, USA; Know Your Bee Inc., San Juan, PR, 00927, USA
| | - Andrew P Michel
- The Ohio State University, Department of Entomology, and Center for Applied Plant Sciences Wooster, OH, 44691, USA
| | - Erin W Hodgson
- Iowa State University, Department of Entomology, Ames, IA, 50011, USA
| | - Matthew E O'Neal
- Iowa State University, Department of Entomology, Ames, IA, 50011, USA
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16
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Okamoto M, Watanabe M, Inoue N, Ogawa K, Hidaka Y, Iwatani Y. Gene polymorphisms of VEGF and VEGFR2 are associated with the severity of Hashimoto's disease and the intractability of Graves' disease, respectively. Endocr J 2020; 67:545-559. [PMID: 32074519 DOI: 10.1507/endocrj.ej19-0480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Vascular endothelial growth factor (VEGF) is one of main regulators of angiogenesis that functions by binding to its receptors, including VEGF receptor (VEGFR) 2. There are few data available regarding the association between VEGF and VEGFR polymorphisms and the susceptibility to and prognosis of autoimmune thyroid diseases (AITDs). To elucidate this association, we genotyped four functional VEGF and two VEGFR2 polymorphisms and measured serum VEGF levels. In the four functional VEGF polymorphisms, the frequencies of the I carrier and I allele of VEGF -2549 I/D, which has lower activity, were higher in patients with severe HD than in those with mild HD. In the two functional VEGFR2 polymorphisms, the frequency of the rs2071559 CC genotype, which has higher activity, was higher in patients with intractable GD than in controls, and the proportion of GD patients with larger goiters was higher in those with the CC genotype. Moreover, the frequency of the rs1870377 TT genotype with higher activity was higher in patients with intractable GD than in those with GD in remission. Combinations of VEGF and VEGFR2 polymorphisms with stronger interactions were associated with the intractability of GD. Serum VEGF levels were higher in HD and AITD patients than those in controls. In conclusion, VEGF polymorphisms with lower activity were associated with the severity of HD, while VEGFR2 polymorphisms and the combinations of VEGF and VEGFR2 polymorphisms, which have stronger interactions, were associated with the intractability of GD. VEGF and VEGFR2 polymorphisms were associated with HD severity and GD intractability, respectively.
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Affiliation(s)
- Mami Okamoto
- Department of Biomedical Informatics, Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Mikio Watanabe
- Department of Biomedical Informatics, Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Naoya Inoue
- Department of Biomedical Informatics, Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
- Laboratory for Clinical Investigation, Osaka University Hospital, Osaka 565-0871, Japan
| | - Kazane Ogawa
- Department of Biomedical Informatics, Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Yoh Hidaka
- Laboratory for Clinical Investigation, Osaka University Hospital, Osaka 565-0871, Japan
| | - Yoshinori Iwatani
- Department of Biomedical Informatics, Division of Health Sciences, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
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17
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Moradifard S, Saghiri R, Ehsani P, Mirkhani F, Ebrahimi‐Rad M. A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites. Mol Genet Genomic Med 2020; 8:e1219. [PMID: 32155318 PMCID: PMC7216802 DOI: 10.1002/mgg3.1219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/25/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND In the human genome, the transcription factors (TFs) and transcription factor-binding sites (TFBSs) network has a great regulatory function in the biological pathways. Such crosstalk might be affected by the single-nucleotide polymorphisms (SNPs), which could create or disrupt a TFBS, leading to either a disease or a phenotypic defect. Many computational resources have been introduced to predict the TFs binding variations due to SNPs inside TFBSs, sTRAP being one of them. METHODS A literature review was performed and the experimental data for 18 TFBSs located in 12 genes was provided. The sequences of TFBS motifs were extracted using two different strategies; in the size similar with synthetic target sites used in the experimental techniques, and with 60 bp upstream and downstream of the SNPs. The sTRAP (http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) was applied to compute the binding affinity scores of their cognate TFs in the context of reference and mutant sequences of TFBSs. The alternative bioinformatics model used in this study was regulatory analysis of variation in enhancers (RAVEN; http://www.cisreg.ca/cgi-bin/RAVEN/a). The bioinformatics outputs of our study were compared with experimental data, electrophoretic mobility shift assay (EMSA). RESULTS In 6 out of 18 TFBSs in the following genes COL1A1, Hb ḉᴪ, TF, FIX, MBL2, NOS2A, the outputs of sTRAP were inconsistent with the results of EMSA. Furthermore, no p value of the difference between the two scores of binding affinity under the wild and mutant conditions of TFBSs was presented. Nor, were any criteria for preference or selection of any of the measurements of different matrices used for the same analysis. CONCLUSION Our preliminary study indicated some paradoxical results between sTRAP and experimental data. However, to link the data of sTRAP to the biological functions, its optimization via experimental procedures with the integration of expanded data and applying several other bioinformatics tools might be required.
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Affiliation(s)
| | - Reza Saghiri
- Biochemistry DepartmentPasteur Institute of IranTehranIran
| | - Parastoo Ehsani
- Molecular Biology DepartmentPasteur Institute of IranTehranIran
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18
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Martins Trevisan C, Naslavsky MS, Monfardini F, Wang J, Zatz M, Peluso C, Pellegrino R, Mafra F, Hakonarson H, Ferreira FM, Nakaya H, Christofolini DM, Montagna E, Crandall KA, Barbosa CP, Bianco B. Variants in the Kisspeptin-GnRH Pathway Modulate the Hormonal Profile and Reproductive Outcomes. DNA Cell Biol 2020; 39:1012-1022. [PMID: 32352843 DOI: 10.1089/dna.2019.5165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Kisspeptin has been identified as a key regulatory protein in the release of gonadotropin-releasing hormone (GnRH), which subsequently increases gonadotropin secretion during puberty to establish reproductive function and regulate the hypothalamic-pituitary-gonadal axis. The effects of variants in the KISS1, KISS1R, and GNRHR genes and their possible association with assisted reproduction outcomes remain to be elucidated. In this study, we used next-generation sequencing to investigate the associations of the genetic diversity at the candidate loci for KISS1, KISS1R, and GNRHR with the hormonal profiles and reproductive outcomes in 86 women who underwent in vitro fertilization treatments. Variants in the KISS1 and KISS1R genes were associated with luteinizing hormone (rs35431622:T>C), anti-Mullerian hormone (rs71745629delT), follicle-stimulating hormone (rs73507529:C>A), and estradiol (rs73507527:G>A, rs350130:A>G, and rs73507529:C>A) levels, as well as with reproductive outcomes such as the number of oocytes retrieved (s35431622:T>C), metaphasis II oocytes (rs35431622:T>C), and embryos (rs1132506:G>C). Additionally, variants in the GNRHR UTR3' (rs1038426:C>A, rs12508464:A>C, rs13150734:C>A, rs17635850:A>G, rs35683646:G>A, rs35610027:C>G, rs35845954:T>C, rs17635749:C>T, and rs7666201:C>T) were associated with low prolactin levels. A conjoint analysis of clinical, hormonal, and genetic variables using a generalized linear model identified two variants of the KISS1 gene (rs71745629delT and rs1132506:G>C) that were significantly associated with hormonal variations and reproductive outcomes. The findings suggest that variants in KISS1, KISS1R, and GNRHR genes can modulate hormone levels and reproductive outcomes.
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Affiliation(s)
- Camila Martins Trevisan
- Discipline of Sexual and Reproductive Health and Populational Genetics, Department of Collective Health, Centro Universitário Saúde ABC, FMABC, Santo André, São Paulo, Brazil
| | - Michel Satya Naslavsky
- Human Genome and Stem Cell Research Center, Biosciences Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Frederico Monfardini
- Human Genome and Stem Cell Research Center, Biosciences Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline Wang
- Human Genome and Stem Cell Research Center, Biosciences Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Biosciences Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Carla Peluso
- Discipline of Sexual and Reproductive Health and Populational Genetics, Department of Collective Health, Centro Universitário Saúde ABC, FMABC, Santo André, São Paulo, Brazil
| | - Renata Pellegrino
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Fernanda Mafra
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frederico Moraes Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Helder Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Denise Maria Christofolini
- Discipline of Sexual and Reproductive Health and Populational Genetics, Department of Collective Health, Centro Universitário Saúde ABC, FMABC, Santo André, São Paulo, Brazil
| | - Erik Montagna
- Postgraduation Program in Health Sciences, Research and Innovation, Centro Universitário Saúde ABC, FMABC, Santo André, São Paulo, Brazil
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Caio Parente Barbosa
- Discipline of Sexual and Reproductive Health and Populational Genetics, Department of Collective Health, Centro Universitário Saúde ABC, FMABC, Santo André, São Paulo, Brazil
| | - Bianca Bianco
- Discipline of Sexual and Reproductive Health and Populational Genetics, Department of Collective Health, Centro Universitário Saúde ABC, FMABC, Santo André, São Paulo, Brazil
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19
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Höher G, Rodrigues MMDO, Waskow G, Agnes G, Von Burg PV, Onsten T, Fiegenbaum M, Almeida S. Identification of ACKR1 variants associated with altered Duffy phenotype expression in blood donors from southern Brazil. Transfus Apher Sci 2020; 59:102768. [PMID: 32276863 DOI: 10.1016/j.transci.2020.102768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 11/18/2022]
Abstract
The atypical chemokine receptor 1 gene (ACKR1) is responsible for the clinically significant Duffy blood group. The main antigens of this system, Fya and Fyb, can be related to a null or weak expression of the DARC protein. In the present work, we aimed to identify ACKR1 gene variants in blood donors from southern Brazil based on discrepancies between their serological and molecular typing results. Then, we analyzed the association of these variants with the expression of the Duffy phenotype. The Fy antigen types were determined via hemagglutination and real-time PCR (c.125 G > A, c.265C > T and c.-67T > C SNPs) tests in a sample composed of 382 regular repetitive voluntary blood donors to the Blood Bank of Hospital de Clínicas de Porto Alegre. An inconclusive correlation between phenotype-genotype analyses was found in 11 (2.88 %) donors, and the entire ACKR1 gene was sequenced in these samples. Our investigation found 11 genetic variants, four of which (c.-541C > T, c.21 + 150C > T, c.22-58A > G, and c.298 G > A SNPs) seem to have putative functional effects on the structure and expression of DARC undertaken for in silico analysis (SIFT, PolyPhen-2 and RegulomeDB). Molecular events can result in apparent discrepancies between red cell genotypes and phenotypes. Our findings provided insight into the molecular background of FY antigens to improve technical approaches for red cell genotyping.
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Affiliation(s)
- Gabriela Höher
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | | | - Gabriela Waskow
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Grasiela Agnes
- Laboratório de Biologia Molecular, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Pâmela Victoria Von Burg
- Laboratório de Biologia Molecular, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Tor Onsten
- Hospital de Clínicas de Porto Alegre - HCPA, Porto Alegre, Brazil
| | - Marilu Fiegenbaum
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Silvana Almeida
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil.
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20
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Genetic polymorphisms influence gene expression of human periodontal ligament fibroblasts in the early phases of orthodontic tooth movement. Odontology 2019; 108:493-502. [PMID: 31741103 DOI: 10.1007/s10266-019-00475-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 10/31/2019] [Indexed: 11/27/2022]
Abstract
Genetic polymorphisms could be involved in the individual rate of OTM (orthodontic tooth movement) corresponding to the clinical phenomenon of "slow movers" and "fast movers". This study evaluated, if genetic polymorphisms in RANK, RANKL, OPG, COX2 and IL6 are associated with the expression of RANKL, OPG, COX2 and IL6 by human periodontal ligament (hPDL) fibroblasts during OTM. Primary hPDL fibroblasts from periodontal connective tissue of teeth extracted from 57 human subjects for medical reasons were collected, isolated, cultivated and characterized. To simulate orthodontic forces in PDL pressure areas, a physiological compressive force of 2 g/cm2 was applied to the hPDL fibroblasts under cell culture conditions at 70% confluency for 48 h, using a glass disc. Thereafter we analysed relative expression of RANKL, OPG, COX2 and IL6 by RT-qPCR. We also performed genotyping analysis of seven genetic polymorphisms in RANK, RANKL, OPG, COX2 and IL6. Relative gene expression was compared among the genotypes. The genotype TT in polymorphism rs9594738 (RANKL) had a higher RANKL expression in the recessive model (p = 0.021; TT vs. CT + CC). For polymorphism rs9594738 (RANKL), in the recessive model, TT was associated with a higher RANKL/OPG expression ratio (p = 0.013; TT vs. CT + CC). In the dominant model, GG genotype in rs5275 (COX2) was associated with a lower gene expression of COX2 (p = 0.04; GG vs. AA + AG). Genetic polymorphisms in genes associated with OTM affect the relative force-induced upregulation of these genes in hPDL fibroblasts.
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Bartholomew ES, Black K, Feng Z, Liu W, Shan N, Zhang X, Wu L, Bailey L, Zhu N, Qi C, Ren H, Liu X. Comprehensive Analysis of the Chitinase Gene Family in Cucumber ( Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum. Int J Mol Sci 2019; 20:E5309. [PMID: 31731414 PMCID: PMC6861899 DOI: 10.3390/ijms20215309] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022] Open
Abstract
Chitinases, a subgroup of pathogenesis-related proteins, are responsible for catalyzing the hydrolysis of chitin. Accumulating reports indicate that chitinases play a key role in plant defense against chitin-containing pathogens and are therefore good targets for defense response studies. Here, we undertook an integrated bioinformatic and expression analysis of the cucumber chitinases gene family to identify its role in defense against Fusarium oxysporum f. sp. cucumerinum. A total of 28 putative chitinase genes were identified in the cucumber genome and classified into five classes based on their conserved catalytic and binding domains. The expansion of the chitinase gene family was due mainly to tandem duplication events. The expression pattern of chitinase genes was organ-specific and 14 genes were differentially expressed in response to F. oxysporum challenge of fusarium wilt-susceptible and resistant lines. Furthermore, a class I chitinase, CsChi23, was constitutively expressed at high levels in the resistant line and may play a crucial role in building a basal defense and activating a rapid immune response against F. oxysporum. Whole-genome re-sequencing of both lines provided clues for the diverse expression patterns observed. Collectively, these results provide useful genetic resource and offer insights into the role of chitinases in cucumber-F. oxysporum interaction.
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Affiliation(s)
- Ezra S. Bartholomew
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Kezia Black
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Zhongxuan Feng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Wan Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Nan Shan
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Xiao Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Licai Wu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Latoya Bailey
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Ning Zhu
- Changping Agricultural Technology Service Center, Beijing 102200, China; (N.Z.); (C.Q.)
| | - Changhong Qi
- Changping Agricultural Technology Service Center, Beijing 102200, China; (N.Z.); (C.Q.)
| | - Huazhong Ren
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Xingwang Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
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Yang JH, Chen WT, Lee MC, Fang WH, Hsu YJ, Chin-Lin, Chen HC, Chang HL, Chen CF, Tu MY, Kuo CW, Lin YH, Hsiao PJ, Su SL. Investigation of the variants at the binding site of inflammatory transcription factor NF-κB in patients with end-stage renal disease. BMC Nephrol 2019; 20:300. [PMID: 31382928 PMCID: PMC6683452 DOI: 10.1186/s12882-019-1471-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background A chronic inflammatory state is a prominent feature in patients with end-stage renal disease (ESRD). Nuclear factor-kappa B (NF-κB) is a transcription factor that regulates the expression of genes involved in inflammation. Some genetic studies have demonstrated that the NF-κB genetic mutation could cause kidney injury and kidney disease progression. However, the association of a gene polymorphism in the transcription factor binding site of NF-κB with kidney disease is not clear. Methods We used the Taiwan Biobank database, the University of California, Santa Cruz, reference genome, and a chromatin immunoprecipitation sequencing database to find single nucleotide polymorphisms (SNPs) at potential binding sites of NF-κB. In addition, we performed a case–control study and genotyped 847 patients with ESRD and 846 healthy controls at Tri-Service General Hospital from 2015 to 2016. Furthermore, we used the ChIP assay to identify the binding activity of different genotypes and used Luciferase reporter assay to examine the function of the rs9395890 polymorphism. Result The results of biometric screening in the databases revealed 15 SNPs with the potential binding site of NF-κB. Genotype distributions of rs9395890 were significantly different in ESRD cases and healthy controls (P = 0.049). The ChIP assay revealed an approximately 1.49-fold enrichment of NF-κB of the variant type TT when compared to that of the wild-type GG in rs9395890 (P = 0.027; TT = 3.20 ± 0.16, GT = 2.81 ± 0.20, GG = 1.71 ± 0.18). The luciferase reporter assay showed that the NF-κB binding site activity in T allele was slightly higher than that in G allele, though it is not significant. Conclusions Our findings indicate that rs9395890 is associated with susceptibility to ESRD in Taiwan population. Electronic supplementary material The online version of this article (10.1186/s12882-019-1471-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jia-Hwa Yang
- School of Public Health and Graduate institute of Life Sciences, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 114, Taiwan, Republic of China.,Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan, Republic of China
| | - Wei-Teing Chen
- Division of Chest Medicine, Department of Medicine, Cheng Hsin General Hospital, Taipei, Taiwan, Republic of China.,Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Meng-Chang Lee
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Wen-Hui Fang
- Department of Family and Community Medicine, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - Yu-Juei Hsu
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - Chin-Lin
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hsiang-Cheng Chen
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hsueh-Lu Chang
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chien-Fu Chen
- Department of Orthopedics, Taichung Armed Forces General Hospital, Taichung, Taiwan, Republic of China
| | - Min-Yu Tu
- Department of Orthopedics, Kaohsiung Armed Forces General Hospital, Gangshan Branch, Kaohsiung, Taiwan, Republic of China
| | - Chien-Wei Kuo
- Division of Nephrology Dialysis, Shih-Kang Clinic, New Taipei City, Taiwan, Republic of China
| | - Yuan-Hau Lin
- Division of Nephrology Dialysis, Yuan-Lin Clinic, Taipei, Taiwan, Republic of China
| | - Po-Jen Hsiao
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan, Republic of China. .,Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan City, Taiwan, Republic of China. .,Big Data Research Center, Fu-Jen Catholic University, Taipei, Taiwan, Republic of China. .,Department of Life Sciences, National Central University, Taoyuan City, Taiwan, Republic of China.
| | - Sui-Lung Su
- School of Public Health and Graduate institute of Life Sciences, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 114, Taiwan, Republic of China. .,School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China.
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23
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Huang X, An Y, Li X, Wang D, Tan H, Lei J. Genetic variants in DICER1, DROSHA, RAN, and XPO5 genes and risk of pregnancy-induced hypertension. Pregnancy Hypertens 2019; 16:161-166. [DOI: 10.1016/j.preghy.2019.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/01/2019] [Accepted: 04/15/2019] [Indexed: 12/14/2022]
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24
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Dhillon BK, Chopra G, Jamwal M, Chandak GR, Duseja A, Malhotra P, Chawla YK, Garewal G, Das R. Adult onset hereditary hemochromatosis is associated with a novel recurrent Hemojuvelin (HJV) gene mutation in north Indians. Blood Cells Mol Dis 2018; 73:14-21. [DOI: 10.1016/j.bcmd.2018.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/26/2022]
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25
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Genetic variants with gene regulatory effects are associated with diisocyanate-induced asthma. J Allergy Clin Immunol 2018; 142:959-969. [PMID: 29969634 DOI: 10.1016/j.jaci.2018.06.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/01/2018] [Accepted: 06/08/2018] [Indexed: 11/23/2022]
Abstract
BACKGROUND Isocyanates are major causes of occupational asthma, but susceptibility and mechanisms of diisocyanate-induced asthma (DA) remain uncertain. OBJECTIVE The aim of this study was to identify DA-associated functional genetic variants through next-generation sequencing (NGS), bioinformatics, and functional assays. METHODS NGS was performed in 91 workers with DA. Fourteen loci with known DA-associated single nucleotide polymorphisms (SNPs) were sequenced and compared with data from 238 unexposed subjects. Ranking of DA-associated SNPs based on their likelihood to affect gene regulatory mechanisms in the lung yielded 21 prioritized SNPs. Risk and nonrisk oligonucleotides were tested for binding of nuclear extracts from A549, BEAS-2B, and IMR-90 lung cell lines by using electrophoretic mobility shift assays. DNA constructs were cloned into a pGL3 promoter vector for luciferase gene reporter assays. RESULTS NGS detected 130 risk variants associated with DA (3.1 × 10-6 to 6.21 × 10-4), 129 of which were located in noncoding regions. The 21 SNPs prioritized by using functional genomic data sets were in or proximal to 5 genes: cadherin 17 (CDH17; n = 10), activating transcription factor 3 (ATF3; n = 7), family with sequence similarity, member A (FAM71A; n = 2), tachykinin receptor 1 (TACR1; n = 1), and zinc finger and BTB domain-containing protein 16 (ZBTB16; n = 1). Electrophoretic mobility shift assays detected allele-dependent nuclear protein binding in A549 cells for 8 of 21 variants. In the luciferase assay 4 of the 21 SNPs exhibited allele-dependent changes in gene expression. DNA affinity precipitation and mass spectroscopy of rs147978008 revealed allele-dependent binding of H1 histones, which was confirmed by using Western blotting. CONCLUSIONS We identified 5 DA-associated potential regulatory SNPs. Four variants exhibited effects on gene regulation (ATF rs11571537, CDH17 rs2446824 and rs2513789, and TACR1 rs2287231). A fifth variant (FAM71A rs147978008) showed nonrisk allele preferential binding to H1 histones. These results demonstrate that many DA-associated genetic variants likely act by modulating gene regulation.
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Gao L, Uzun Y, Gao P, He B, Ma X, Wang J, Han S, Tan K. Identifying noncoding risk variants using disease-relevant gene regulatory networks. Nat Commun 2018; 9:702. [PMID: 29453388 PMCID: PMC5816022 DOI: 10.1038/s41467-018-03133-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/22/2018] [Indexed: 02/01/2023] Open
Abstract
Identifying noncoding risk variants remains a challenging task. Because noncoding variants exert their effects in the context of a gene regulatory network (GRN), we hypothesize that explicit use of disease-relevant GRNs can significantly improve the inference accuracy of noncoding risk variants. We describe Annotation of Regulatory Variants using Integrated Networks (ARVIN), a general computational framework for predicting causal noncoding variants. It employs a set of novel regulatory network-based features, combined with sequence-based features to infer noncoding risk variants. Using known causal variants in gene promoters and enhancers in a number of diseases, we show ARVIN outperforms state-of-the-art methods that use sequence-based features alone. Additional experimental validation using reporter assay further demonstrates the accuracy of ARVIN. Application of ARVIN to seven autoimmune diseases provides a holistic view of the gene subnetwork perturbed by the combinatorial action of the entire set of risk noncoding mutations. Current methods for prioritization of non-coding genetic risk variants are based on sequence and chromatin features. Here, Gao et al. develop ARVIN, which predicts causal regulatory variants using disease-relevant gene-regulatory networks, and validate this approach in reporter gene assays.
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Affiliation(s)
- Long Gao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yasin Uzun
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Peng Gao
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Bing He
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Xiaoke Ma
- School of Computer Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, China
| | - Jiahui Wang
- The Jackson Laboratory, Farmington, CT, 06032, USA
| | - Shizhong Han
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Kai Tan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Cell & Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Yao Y, Fang Z, Yang S, Zhao H, Chen Y, Jin Y, Zhao X, Zhu L, Tian Y, Shen C. Evaluation of genetic effect of NOS3 and G×E interaction on the variability of serum bilirubin in a Han Chinese population. Nitric Oxide 2017; 70:25-30. [PMID: 28797660 DOI: 10.1016/j.niox.2017.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 07/25/2017] [Accepted: 08/05/2017] [Indexed: 11/28/2022]
Abstract
Bilirubin was shown to be related to the generation and functional exertion of endothelial nitric oxide synthase (eNOS) whilst the genetic effect of NOS3 on bilirubin variability was rarely reported. Herein we assessed the associations of three single nucleotide polymorphisms (SNPs) of NOS3 (rs4496877, rs1808593, and rs3918186) with bilirubin elevation in 2077 adults. The results showed that rs1808593 was significantly associated with bilirubin elevation, and odds ratios (ORs) of dominant model for the elevation of total bilirubin (TBIL), direct bilirubin (DBIL), and indirect bilirubin (IDBIL) were 0.837, 0.821 and 0.754, respectively (P < 0.05 for all). Stratification analysis indicated that rs3918186 was significantly associated with the elevation of TBIL and IDBIL in the males, and ORs of dominant model were 1.505 and 1.440 with P < 0.05 for all. In the smoking group, significant associations of rs4496877, rs1808593, and rs3918186 with TBIL elevation were observed, and ORs of dominant model were 1.739, 0.758 and 1.626 (P < 0.05 for all). rs4496877 and rs3918186 were both associated with TBIL elevation in the drinking group, and ORs were 1.557 and 1.769 with P < 0.05 for all. In the ≥55 year-old group, rs4496877 and rs1808593 were significantly associated with DBIL and IDBIL elevations, and ORs were 1.340 and 0.790 (P < 0.05). Meanwhile, rs4496877, rs1808593, rs3918186, smoking, and drinking were shown to have a notable interaction effects on the TBIL elevation. Our findings supported that NOS3 harbors the genetic susceptibility to the bilirubin elevation. Age, gender, smoking, and drinking could be involved in the genetic modification of NOS3 on the bilirubin variability.
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Affiliation(s)
- Yingshui Yao
- Department of Epidemiology and Biostatistics, School of Public Health, Wannan Medical College, Wuhu 241001, China
| | - Zhengmei Fang
- Department of Epidemiology and Biostatistics, School of Public Health, Wannan Medical College, Wuhu 241001, China
| | - Song Yang
- Department of Cardiology, Affiliated Yixing People's Hospital of Jiangsu University, People's Hospital of Yixing City, Yixing 214200, China
| | - Hailong Zhao
- Central Laboratory, Affiliated Yixing People's Hospital of Jiangsu University, People's Hospital of Yixing City, Yixing 214200, China
| | - Yanchun Chen
- Department of Cardiology, Affiliated Yixing People's Hospital of Jiangsu University, People's Hospital of Yixing City, Yixing 214200, China
| | - Yuelong Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Wannan Medical College, Wuhu 241001, China
| | - Xianghai Zhao
- Department of Cardiology, Affiliated Yixing People's Hospital of Jiangsu University, People's Hospital of Yixing City, Yixing 214200, China
| | - Lijun Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Wannan Medical College, Wuhu 241001, China
| | - Yuanrui Tian
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chong Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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Wang G, Liao J, Tang M, Yu S. Genetic variation in the MITF promoter affects skin colour and transcriptional activity in black-boned chickens. Br Poult Sci 2017; 59:21-27. [PMID: 28891677 DOI: 10.1080/00071668.2017.1379053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
1. Microphthalmia-associated transcription factor (MITF) plays a pivotal role in melanocyte development by regulating the transcription of major pigmentation enzymes (e.g. TYR, TYRP1 and DCT). A single-nucleotide polymorphism (SNP), c.-638T>C, was identified in the MITF promoter, and genotyping of a population (n = 426) revealed that SNP c.-638T>C was associated with skin colour in black-boned chickens. 2. Individuals with genotypes CC and TC exhibited greater MTIF expression than those with genotype TT. Luciferase assays also revealed that genotype CC and TC promoters had higher activity levels than genotype TT. Expression of melanogenesis-related gene (TYR) was higher in the skin of chickens with the CC and CT genotype compared to TT chickens (P < 0.05). 3. Transcription factor-binding site analyses showed that the c.-638C allele contains a putative binding site for transcription factor sterol regulatory element-binding transcription factor 2, aryl hydrocarbon receptor nuclear translocator, transcription factor binding to IGHM enhancer 3 and upstream transcription factor 2. In contrast, the c.-638T allele contains binding sites for Sp3 transcription factor and Krüppel-like factor 1. 4. It was concluded that MITF promoter polymorphisms affected chicken skin colour. SNP c.-638T>C could be used for the marker-assisted selection of skin colour in black-boned chicken breeding.
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Affiliation(s)
- G Wang
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - J Liao
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - M Tang
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - S Yu
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
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29
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Buroker NE, Ning XH, Zhou ZN, Li K, Cen WJ, Wu XF, Zhu WZ, Scott CR, Chen SH. SNPs, linkage disequilibrium, and chronic mountain sickness in Tibetan Chinese. HYPOXIA 2017; 5:67-74. [PMID: 28770234 PMCID: PMC5529112 DOI: 10.2147/hp.s117967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chronic mountain sickness (CMS) is estimated at 1.2% in Tibetans living at the Qinghai-Tibetan Plateau. Eighteen single-nucleotide polymorphisms (SNPs) from nine nuclear genes that have an association with CMS in Tibetans have been analyzed by using pairwise linkage disequilibrium (LD). The SNPs included are the angiotensin-converting enzyme (rs4340), the angiotensinogen (rs699), and the angiotensin II type 1 receptor (AGTR1) (rs5186) from the renin-angiotensin system. A low-density lipoprotein apolipoprotein B (rs693) SNP was also included. From the hypoxia-inducible factor oxygen signaling pathway, the endothetal Per-Arnt-Sim domain protein 1 (EPAS1) and the egl nine homolog 1 (ENGL1) (rs480902) SNPs were included in the study. SNPs from the vascular endothelial growth factor (VEGF) signaling pathway included are the v-akt murine thymoma viral oncogene homolog 3 (rs4590656 and rs2291409), the endothelial cell nitric oxide synthase 3 (rs1007311 and rs1799983), and the (VEGFA) (rs699947, rs34357231, rs79469752, rs13207351, rs28357093, rs1570360, rs2010963, and rs3025039). An increase in LD occurred in 40 pairwise comparisons, whereas a decrease in LD was found in 55 pairwise comparisons between the controls and CMS patients. These changes were found to occur within and between signaling pathways, which suggests that there is an interaction between SNP alleles from different areas of the genome that affect CMS.
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Affiliation(s)
| | - Xue-Han Ning
- Department of Pediatrics, University of Washington.,Division of Cardiology, Seattle Children's Hospital Research Foundation, Seattle, WA, USA
| | - Zhao-Nian Zhou
- Laboratory of Hypoxia Physiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kui Li
- Lhasa People Hospital, Lhasa, Tibet
| | | | - Xiu-Feng Wu
- Laboratory of Hypoxia Physiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei-Zhong Zhu
- Center for Cardiovascular Biology and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Shi-Han Chen
- Department of Pediatrics, University of Washington
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30
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Xue B, Lipps D, Devineni S. Integrated Strategy Improves the Prediction Accuracy of miRNA in Large Dataset. PLoS One 2016; 11:e0168392. [PMID: 28002428 PMCID: PMC5176297 DOI: 10.1371/journal.pone.0168392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/29/2016] [Indexed: 01/08/2023] Open
Abstract
MiRNAs are short non-coding RNAs of about 22 nucleotides, which play critical roles in gene expression regulation. The biogenesis of miRNAs is largely determined by the sequence and structural features of their parental RNA molecules. Based on these features, multiple computational tools have been developed to predict if RNA transcripts contain miRNAs or not. Although being very successful, these predictors started to face multiple challenges in recent years. Many predictors were optimized using datasets of hundreds of miRNA samples. The sizes of these datasets are much smaller than the number of known miRNAs. Consequently, the prediction accuracy of these predictors in large dataset becomes unknown and needs to be re-tested. In addition, many predictors were optimized for either high sensitivity or high specificity. These optimization strategies may bring in serious limitations in applications. Moreover, to meet continuously raised expectations on these computational tools, improving the prediction accuracy becomes extremely important. In this study, a meta-predictor mirMeta was developed by integrating a set of non-linear transformations with meta-strategy. More specifically, the outputs of five individual predictors were first preprocessed using non-linear transformations, and then fed into an artificial neural network to make the meta-prediction. The prediction accuracy of meta-predictor was validated using both multi-fold cross-validation and independent dataset. The final accuracy of meta-predictor in newly-designed large dataset is improved by 7% to 93%. The meta-predictor is also proved to be less dependent on datasets, as well as has refined balance between sensitivity and specificity. This study has two folds of importance: First, it shows that the combination of non-linear transformations and artificial neural networks improves the prediction accuracy of individual predictors. Second, a new miRNA predictor with significantly improved prediction accuracy is developed for the community for identifying novel miRNAs and the complete set of miRNAs. Source code is available at:https://github.com/xueLab/mirMeta
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Affiliation(s)
- Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida, United States of America
- * E-mail:
| | - David Lipps
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida, United States of America
| | - Sree Devineni
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida, United States of America
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Deplancke B, Alpern D, Gardeux V. The Genetics of Transcription Factor DNA Binding Variation. Cell 2016; 166:538-554. [PMID: 27471964 DOI: 10.1016/j.cell.2016.07.012] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 12/23/2022]
Abstract
Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-DNA binding motifs. Variable TF-DNA interactions are therefore increasingly considered as key drivers of phenotypic variation. However, recent genome-wide studies revealed that the majority of variable TF-DNA binding events are not driven by sequence alterations in the motif of the studied TF. This observation implies that the molecular mechanisms underlying TF-DNA binding variation and, by extrapolation, inter-individual phenotypic variation are more complex than originally anticipated. Here, we summarize the findings that led to this important paradigm shift and review proposed mechanisms for local, proximal, or distal genetic variation-driven variable TF-DNA binding. In addition, we discuss the biomedical implications of these findings for our ability to dissect the molecular role(s) of non-coding genetic variants in complex traits, including disease susceptibility.
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Affiliation(s)
- Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Daniel Alpern
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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D'Amico F, Skarmoutsou E, Lo LJ, Granata M, Trovato C, Rossi GA, Bellocchi C, Marchini M, Scorza R, Mazzarino MC, Keinan A. Association between rs2294020 in X-linked CCDC22 and susceptibility to autoimmune diseases with focus on systemic lupus erythematosus. Immunol Lett 2016; 181:58-62. [PMID: 27888057 DOI: 10.1016/j.imlet.2016.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 12/12/2022]
Abstract
Autoimmune diseases often share common susceptibility genes. Most genetic variants associated with susceptibility to systemic lupus erythematosus are also associated with other autoimmune diseases. The X-linked variant rs2294020 is positioned in exon 7 of the CCDC22 gene. The encoded protein functions in the regulation of NF-κB, a master regulator in immune response. The aim of this study is to investigate whether the rs2294020 polymorphism may be a general susceptibility factor for autoimmunity. We evaluated case-control association between the occurrence of rs2294020 and different autoimmune diseases, including new data for systemic lupus erythematosus and previous genome-wide association studies (GWAS) (though most did not analyse the X chromosome) of psoriasis, celiac disease, Crohn's disease, ulcerative colitis, multiple sclerosis, vitiligo, type-1 diabetes, rheumatoid arthritis, and ankylosing spondylitis. Cases from patients affected by amyotrophic lateral sclerosis and type-2 diabetes were also included in the study. We detected nominal significant associations of rs2294020 with systemic lupus erythematosus (additive model test: p=0.01), vitiligo (p=0.016), psoriasis (p=0.038), and in only one of two studies of multiple sclerosis (p=0.03). Our results suggest that rs2294020 is associated with the risk of several autoimmune diseases in European populations, specifically with diseases that present themselves, among else, in the skin.
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Affiliation(s)
- Fabio D'Amico
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Androne 83, I-95124 Catania, Italy.
| | - Evangelia Skarmoutsou
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Androne 83, I-95124 Catania, Italy
| | - Lauren J Lo
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Mariagrazia Granata
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Androne 83, I-95124 Catania, Italy
| | - Chiara Trovato
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Androne 83, I-95124 Catania, Italy
| | - Giulio A Rossi
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Androne 83, I-95124 Catania, Italy
| | - Chiara Bellocchi
- Referral Center for Systemic Autoimmune Diseases, University of Milan and Fondazione IRCCS Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Via Pace 9, I-20122 Milan, Italy
| | - Maurizio Marchini
- Referral Center for Systemic Autoimmune Diseases, University of Milan and Fondazione IRCCS Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Via Pace 9, I-20122 Milan, Italy
| | - Raffaella Scorza
- Referral Center for Systemic Autoimmune Diseases, University of Milan and Fondazione IRCCS Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Via Pace 9, I-20122 Milan, Italy
| | - Maria Clorinda Mazzarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Androne 83, I-95124 Catania, Italy
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
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Jin Y, Cai H, Liu J, Lin F, Qi X, Bai Y, Lei C, Chen H, Lan X. The 10 bp duplication insertion/deletion in the promoter region within paired box 7 gene is associated with growth traits in cattle. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-469-2016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Abstract. Paired box 7 (Pax7) gene, a member of the paired box gene family, plays a critical role in animal growth and muscle development, especially in cell proliferation and self-renewal. The aim of this study was to detect the 10 base pair (bp) duplication insertion/deletion (indel) in the promoter region within the bovine Pax7 gene as well as its association with growth traits. Herein, a total of 718 individuals from five Chinese cattle breeds were sampled and detected. The 10 bp duplication indel was found in these cattle breeds and there were three genotypes: II (insertion/insertion), ID (insertion/deletion), and DD (deletion/deletion). Moreover, this indel was significantly associated with the body weight in Xianan cattle (P = 0.006), the body height in Jinjiang cattle (P = 0.046), and the hip width in Pi'nan cattle (P = 0.020). Consistently, the individuals with II genotype showed better phenotypic traits than those with the other genotypes in these five breeds. These findings suggest that the 10 bp duplication indel within the bovine Pax7 gene could be considered as an effective DNA molecular marker that provides valuable theoretical basis for marker-assisted selection (MAS) in beef cattle in the future.
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Buroker NE. Identifying changes in punitive transcriptional factor binding sites from regulatory single nucleotide polymorphisms that are significantly associated with disease or sickness. World J Hematol 2016; 5:75-87. [DOI: 10.5315/wjh.v5.i4.75] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/14/2016] [Accepted: 08/15/2016] [Indexed: 02/05/2023] Open
Abstract
AIM To identify punitive transcriptional factor binding sites (TFBS) from regulatory single nucleotide polymorphisms (rSNPs) that are significantly associated with disease.
METHODS The genome-wide association studies have provided us with nearly 6500 disease or trait-predisposing SNPs where 93% are located within non-coding regions such as gene regulatory or intergenic areas of the genome. In the regulatory region of a gene, a SNP can change the DNA sequence of a transcriptional factor (TF) motif and in turn may affect the process of gene regulation. SNP changes that affect gene expression and impact gene regulatory sequences such as promoters, enhancers, and silencers are known as rSNPs. Computational tools can be used to identify unique punitive TFBS created by rSNPs that are associated with disease or sickness. Computational analysis was used to identify punitive TFBS generated by the alleles of these rSNPs.
RESULTS rSNPs within nine genes that have been significantly associated with disease or sickness were used to illustrate the tremendous diversity of punitive unique TFBS that can be generated by their alleles. The genes studied are the adrenergic, beta, receptor kinase 1, the v-akt murine thymoma viral oncogene homolog 3, the activating transcription factor 3, the type 2 demodkinase gene, the endothetal Per-Arnt-Sim domain protein 1, the lysosomal acid lipase A, the signal Transducer and Activator of Transcription 4, the thromboxane A2 receptor and the vascular endothelial growth factor A. From this sampling of SNPs among the nine genes, there are 73 potential unique TFBS generated by the common alleles compared to 124 generated by the minor alleles indicating the tremendous diversity of potential TFs that are capable of regulating these genes.
CONCLUSION From the diversity of unique punitive binding sites for TFs, it was found that some TFs play a role in the disease or sickness being studied.
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Safari MR, Ghafouri-Fard S, Noroozi R, Sayad A, Omrani MD, Komaki A, Eftekharian MM, Taheri M. FOXP3 gene variations and susceptibility to autism: A case-control study. Gene 2016; 596:119-122. [PMID: 27751813 DOI: 10.1016/j.gene.2016.10.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 09/27/2016] [Accepted: 10/13/2016] [Indexed: 12/11/2022]
Abstract
Autism Spectrum Disorders (ASD) are a group of heterogeneous neurodevelopmental disorders associated with immune system dysregulation. There are supporting evidences for the role of Forkhead Box P3 (FOXP3) gene as a lineage specification factor of regulatory T cells in the pathogenesis of ASD. The aim of this study was to explore possible relationship between genetic variants rs2232365 and rs3761548 of FOXP3 and ASD in 523 ASD patients versus 472 control individuals. Allele frequency analyses showed significant overpresentation of rs2232365-G allele in cases versus controls. In addition, rs2232365 GG genotype was associated with ASD in dominant inheritance model. Haplotype analysis revealed no significant association of any estimated block of rs2232365/rs3761548 with ASD. Our study indicated that rs2232365 is associated with ASD.
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Affiliation(s)
- Mohammad Reza Safari
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rezvan Noroozi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arezou Sayad
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Komaki
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Mohammad Taheri
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Donmez C, Konac E, Aydogan BT, Bilen CY. Might E-cadherin promoter polymorphisms of rs16260 and rs5030625 associate with the risk of nephrolithiasis? SPRINGERPLUS 2016; 5:1673. [PMID: 27733975 PMCID: PMC5040654 DOI: 10.1186/s40064-016-3363-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/22/2016] [Indexed: 12/30/2022]
Abstract
Purpose To study whether −160 C > A (rs16260) and −347 G > GA (rs5030625) single nucleotide polymorphisms of the regulatory region (rSNPs) of CDH1 gene modulate the risk of nephrolithiasis. Methods Genomic DNA of 101 patients with calcium oxalate nephrolithiasis and 114 healthy controls were screened for both polymorphisms, using polymerase chain reaction-restriction fragments length polymorphism method (PCR-RLFP). Haplotype frequencies were also analyzed. To determine the association of rSNPs of CDH1 gene with the clinicopathological features of nephrolithiasis, nearly all possible etiological factors were documented. These factors were family history, gender, age, body mass index, liquid consumption, eating habits, tea–coffee and meat (oxalate rich) consumption, adequate physical activity, and all serum and urine levels—the serum levels of Na, K, Cl, phosphate, Ca, Mg, uric acid, albumin, blood urea nitrogen (BUN), creatinine and serum parathyroid hormone (PTH) as well as 24 h urine excretions of creatinine, Na, K, Cl, phosphate, Ca, Mg, citrate, oxalate, uric acid, albumin and BUN. Results Significant differences were found between rs16260 and the risk of nephrolithiasis. Patients having CA genotype of rs16260 CDH1 polymorphism were associated with an almost trifold increased risk for developing kidney stone than those with the AA genotype (95 % CI 1.08–7.28, OR 2.8, P = 0.033). We also found that non-A allele carriers (CC) had significantly higher nephrolithiasis risk associated with the clinicopathological characteristics including serum calcium (P = 0.027) and 24 h urinary magnesium level (P = 0.042). Moreover, we did find a directly proportional relationship between the CA genotype and serum calcium levels (P = 0.041). There was no significant difference between patients and controls in terms of the distribution of rs5030625 genotypes and alleles (P > 0.05). Likewise, no associations between the rs16260 and rs5030625 haplotypes and susceptibility to kidney stone were observed (P > 0.05). Conclusion Regulatory variants of rs16260 of the CDH1 gene may confer susceptibility to nephrolithiasis. This may have important implications for understanding the pathophysiological mechanisms of the disease and suggesting novel targets for drug treatment.
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Affiliation(s)
- Cigdem Donmez
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University, Besevler, 06510 Ankara, Turkey
| | - Ece Konac
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University, Besevler, 06510 Ankara, Turkey
| | - Batuhan T Aydogan
- Department of Urology, Faculty of Medicine, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
| | - Cenk Y Bilen
- Department of Urology, Faculty of Medicine, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
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Yeh SI, Fang WF, Huang CJ, Wang TM, Yang JT. The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform. J Vis Exp 2016. [PMID: 27768033 DOI: 10.3791/54424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A simple and visual method to detect multi-nucleotide polymorphism (MNP) was performed on a pneumatic droplet manipulation platform on an open surface. This approach to colorimetric DNA detection was based on the hybridization-mediated growth of gold nanoparticle probes (AuNP probes). The growth size and configuration of the AuNP are dominated by the number of DNA samples hybridized with the probes. Based on the specific size- and shape-dependent optical properties of the nanoparticles, the number of mismatches in a sample DNA fragment to the probes is able to be discriminated. The tests were conducted via droplets containing reagents and DNA samples respectively, and were transported and mixed on the pneumatic platform with the controlled pneumatic suction of the flexible PDMS-based superhydrophobic membrane. Droplets can be delivered simultaneously and precisely on an open-surface on the proposed pneumatic platform that is highly biocompatible with no side effect of DNA samples inside the droplets. Combining the two proposed methods, the multi-nucleotide polymorphism can be detected at sight on the pneumatic droplet manipulation platform; no additional instrument is required. The procedure from installing the droplets on the platform to the final result takes less than 5 min, much less than with existing methods. Moreover, this combined MNP detection approach requires a sample volume of only 10 µl in each operation, which is remarkably less than that of a macro system.
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Affiliation(s)
- Szu-I Yeh
- Department of Mechanical Engineering, National Taiwan University
| | - Wei-Feng Fang
- Department of Mechanical Engineering, National Taiwan University
| | - Chao-Jyun Huang
- Department of Mechanical Engineering, National Taiwan University
| | - Tzu-Ming Wang
- Department of Mechanical Engineering, National Taiwan University
| | - Jing-Tang Yang
- Department of Mechanical Engineering, National Taiwan University;
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38
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Peterson TA, Mort M, Cooper DN, Radivojac P, Kann MG, Mooney SD. Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants. Hum Mutat 2016; 37:1137-1143. [PMID: 27406314 DOI: 10.1002/humu.23049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022]
Abstract
In silico methods for detecting functionally relevant genetic variants are important for identifying genetic markers of human inherited disease. Much research has focused on protein-coding variants since coding regions have well-defined physicochemical and functional properties. However, many bioinformatics tools are not applicable to variants outside coding regions. Here, we increase the classification performance of our regulatory single-nucleotide variant predictor (RSVP) for variants that cause regulatory abnormalities from an AUC of 0.90-0.97 by incorporating genomic regions identified by the ENCODE project into RSVP. RSVP is comparable to a recently published tool, Genome-Wide Annotation of Variants (GWAVA); both RSVP and GWAVA perform better on regulatory variants than a traditional variant predictor, combined annotation-dependent depletion (CADD). However, our method outperforms GWAVA on variants located at similar distances to the transcription start site as the positive set (AUC: 0.96) as compared with GWAVA (AUC: 0.71). Much of this disparity is due to RSVP's incorporation of features pertaining to the nearest gene (expression, GO terms, etc.), which are not included in GWAVA. Our findings hold out the promise of a framework for the assessment of all functional regulatory variants, providing a means to predict which rare or de novo variants are of pathogenic significance.
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Affiliation(s)
- Thomas A Peterson
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana
| | - Maricel G Kann
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington.
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Dai L, Chu X, Lu F, Xu R. Detection of four polymorphisms in 5' upstream region of PNPLA2 gene and their associations with economic traits in pigs. Mol Biol Rep 2016; 43:1305-1313. [PMID: 27565982 DOI: 10.1007/s11033-016-4068-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/22/2016] [Indexed: 12/16/2022]
Abstract
As an important triglyceride hydrolase in mammalian cells, patatin-like phospholipase domain-containing 2 (PNPLA2) predominantly performs the first step in triglyceride hydrolysis. The objective of this study was to detect and evaluate the effects of mutations in the 5' upstream region of porcine PNPLA2 gene with fat deposition and carcass traits. Four single nuclear polymorphisms were identified, including g.161969 T>C, g.161962 A>G, g.161953 C>G and g.161904 G>T, and subsequently genotyped in five pure breeds. Three haplotypes were constructed, including H1(CGGT), H2(TACG) and H3(CACT), which were the most abundant haplotypes in Duroc (0.75), Landrace (0.78) and Chinese indigenous breeds (>0.73), respectively. Duroc individuals with the H1H1 diplotype always exhibited the lowest feed conversion ratio (FCR) (P < 0.05), while H2H2 had the thickest backfat thickness (P < 0.05). Landrace individuals with H2H3 had lower backfat thickness (P < 0.05), higher muscle thickness (P < 0.05) and estimated lean meat percentage (P < 0.05) than those with diplotype H2H2 and H3H3. Luciferase assay indicated pGL3-basic-H2 had the highest activity and pGL3-basic-H1 had the lowest activity in driving reporter gene transcription in HEK293 cells in vitro. In H1 haplotype, two GR binding sites and an ERα binding site were predicted to be introduced. While in H2 and H3, there were other transcriptional factor binding sites predicted in H2 and H3, such as Sp1, AP-2 and CAC-binding proteins, which were broadly expressed transcription factors and capable of contributing to basal promoter activity. The reduced basal promoter activity of H1 may be due to the lack of inducement for GR and ERα binding sites in HEK293 cells. The identified functional polymorphisms provide new evidence of PNPLA2 as an important candidate gene for fat deposition and carcass traits in pigs.
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Affiliation(s)
- Lihe Dai
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Xiaohong Chu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Fuzeng Lu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Ruhai Xu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.
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Yang H, He J, Wei W, Chu W, Yu S, Tian Y, Peng F, Liu H, Zhang Z, Chen J. The c.-360 T>C mutation affects PGAM2 transcription activity and is linked with the water holding capacity of the longissimus lumborum muscle in pigs. Meat Sci 2016; 122:139-144. [PMID: 27538264 DOI: 10.1016/j.meatsci.2016.07.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022]
Abstract
The phosphoglycerate mutase 2 (PGAM2) gene encodes a key enzyme in the glycolytic process. This study examined a functional mutation in the PGAM2 gene and evaluated its relationship with water holding capacity (WHC). RT-qPCR analysis showed the PGAM2 mRNA level was significantly higher in the low-WHC group than in the high-WHC group (P<0.05). The c.-360 T>C mutation was identified through sequencing and found to have opposite allele distributions in the two groups. The allele was further genotyped in 170 Duroc×Large White×Yorkshire crossbred pigs using allele-specific PCR. The CC genotype was associated with lower WHC and higher PGAM2 mRNA levels, whereas the TT genotype corresponded to a higher WHC and lower PGAM2 mRNA levels (P<0.05). A luciferase activity assay also showed that the CC-genotype promoter had higher activity than the TT-genotype promoter (P<0.05). In conclusion, we discovered the c.-360 T>C mutation in the PGAM2 gene, which is a promising marker for improving pork WHC.
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Affiliation(s)
- Haoxin Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiawen He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wei Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Weiwei Chu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shigang Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ye Tian
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Fengyi Peng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hongcheng Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zengkai Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jie Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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Ding X, Hu J, Zhang H, Xu Y. Genetic Variants in the STMN1 Transcriptional Regulatory Region Affect Promoter Activity and Fear Behavior in English Springer Spaniels. PLoS One 2016; 11:e0158756. [PMID: 27390866 PMCID: PMC4938412 DOI: 10.1371/journal.pone.0158756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/21/2016] [Indexed: 01/14/2023] Open
Abstract
Stathmin 1 (STMN1) is a neuronal growth-associated protein that is involved in microtubule dynamics and plays an important role in synaptic outgrowth and plasticity. Given that STMN1 affects fear behavior, we hypothesized that genetic variations in the STMN1 transcriptional regulatory region affect gene transcription activity and control fear behavior. In this study, two single nucleotide polymorphisms (SNPs), g. -327 A>G and g. -125 C>T, were identified in 317 English Springer Spaniels. A bioinformatics analysis revealed that both were loci located in the canine STMN1 putative promoter region and affected transcription factor binding. A statistical analysis revealed that the TT genotype at g.-125 C>T produced a significantly greater fear level than that of the CC genotype (P < 0.05). Furthermore, the H4H4 (GTGT) haplotype combination was significantly associated with canine fear behavior (P < 0.01). Using serially truncated constructs of the STMN1 promoters and the luciferase reporter, we found that a 395 bp (-312 nt to +83 nt) fragment constituted the core promoter region. The luciferase assay also revealed that the H4 (GT) haplotype promoter had higher activity than that of other haplotypes. Overall, our results suggest that the two SNPs in the canine STMN1 promoter region could affect canine fear behavior by altering STMN1 transcriptional activity.
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Affiliation(s)
- Xiaolin Ding
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, People’s Republic of China
| | - Jin Hu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, People’s Republic of China
| | - Hanying Zhang
- Pharmacology Department, R&D center, Nanjing Sanhome Pharmaceutical Co. LTD, Nanjing, Jiangsu Province, People’s Republic of China
| | - Yinxue Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, People’s Republic of China
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Cui X, Sun Y, Wang X, Yang C, Ju Z, Jiang Q, Zhang Y, Huang J, Zhong J, Yin M, Wang C. A g.-1256 A>C in the promoter region of CAPN1 is associated with semen quality traits in Chinese Holstein bulls. Reproduction 2016; 152:101-9. [PMID: 27107033 DOI: 10.1530/rep-15-0535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/21/2016] [Indexed: 02/04/2023]
Abstract
The micromolar calcium-activated neutral protease gene (CAPN1) is a physiological candidate gene for sperm motility. However, the molecular mechanisms involved in regulating the expression of the CAPN1 gene in bulls remain unknown. In this study, we investigated the expression pattern of CAPN1 in testis, epididymis, and sperm at the RNA and protein levels by qRT-PCR, western blot, immunohistochemistry, and immunofluorescence assay. Results revealed that the expression of CAPN1 levels was higher in the sperm head compared with that in other tissues. Moreover, we identified a novel single-nucleotide polymorphism (g.-1256 A>C, ss 1917715340) in the noncanonical core promoter of the CAPN1 gene between base g.-1306 and g.-1012. Additionally, we observed greater sperm motility in bulls with the genotype CC than in those with the genotype AA (P<0.01), indicating that different genotypes were associated with the bovine semen trait. Furthermore, a higher fluorescence intensity of the C allele than that of the A allele at g. -1256 A>C was revealed by transient transfection in MLTC-1 cells and luciferase report assay. Finally, CAPN1 was highly expressed in the spermatozoa with the CC genotype compared with that with the AA genotype by qRT-PCR. This study is the first report on genetic variant g.-1256 A>C in the promoter region of CAPN1 gene association with the semen quality of Chinese Holstein bulls by influencing its expression. g.-1256 A>C can be a functional molecular marker in cattle breeding.
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Affiliation(s)
- Xiaohui Cui
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China College of Life ScienceShandong Normal University, Jinan, People's Republic of China
| | - Yan Sun
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Chunhong Yang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Zhihua Ju
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Qiang Jiang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Yan Zhang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Jinming Huang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Jifeng Zhong
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Miao Yin
- College of Life ScienceShandong Normal University, Jinan, People's Republic of China
| | - Changfa Wang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
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Misra MK, Mishra A, Pandey SK, Kapoor R, Sharma RK, Agrawal S. Association of functional genetic variants of transcription factor Forkhead Box P3 and Nuclear Factor-κB with end-stage renal disease and renal allograft outcome. Gene 2016; 581:57-65. [DOI: 10.1016/j.gene.2016.01.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/30/2015] [Accepted: 01/16/2016] [Indexed: 12/19/2022]
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Cohen-Zinder M, Asher A, Lipkin E, Feingersch R, Agmon R, Karasik D, Brosh A, Shabtay A. FABP4 is a leading candidate gene associated with residual feed intake in growing Holstein calves. Physiol Genomics 2016; 48:367-76. [PMID: 26993365 DOI: 10.1152/physiolgenomics.00121.2015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/09/2016] [Indexed: 01/08/2023] Open
Abstract
Ecological and economic concerns drive the need to improve feed utilization by domestic animals. Residual feed intake (RFI) is one of the most acceptable measures for feed efficiency (FE). However, phenotyping RFI-related traits is complex and expensive and requires special equipment. Advances in marker technology allow the development of various DNA-based selection tools. To assimilate these technologies for the benefit of RFI-based selection, reliable phenotypic measures are prerequisite. In the current study, we identified single nucleotide polymorphisms (SNPs) associated with RFI phenotypic consistency across different ages and diets (named RFI 1-3), using DNA samples of high or low RFI ranked Holstein calves. Using targeted sequencing of chromosomal regions associated with FE- and RFI-related traits, we identified 48 top SNPs significantly associated with at least one of three defined RFIs. Eleven of these SNPs were harbored by the fatty acid binding protein 4 (FABP4). While 10 significant SNPs found in FABP4 were common for RFI 1 and RFI 3, one SNP (FABP4_5; A<G substitution), in the promoter region of the gene, was significantly associated with all three RFIs. As the three RFI classes reflect changing diets and ages with concomitant RFI phenotypic consistency, the above polymorphisms and in particular FABP4_5, might be considered possible markers for RFI-based selection for FE in the Holstein breed, following a larger-scale validation.
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Affiliation(s)
- Miri Cohen-Zinder
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel;
| | - Aviv Asher
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel; Israeli Center for Interdisciplinary Research in Chronobiology, University of Haifa, Haifa, Israel
| | - Ehud Lipkin
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel; and
| | - Roi Feingersch
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Rotem Agmon
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - David Karasik
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Arieh Brosh
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Ariel Shabtay
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
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45
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Barr CL, Misener VL. Decoding the non-coding genome: elucidating genetic risk outside the coding genome. GENES, BRAIN, AND BEHAVIOR 2016; 15:187-204. [PMID: 26515765 PMCID: PMC4833497 DOI: 10.1111/gbb.12269] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/19/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Current evidence emerging from genome-wide association studies indicates that the genetic underpinnings of complex traits are likely attributable to genetic variation that changes gene expression, rather than (or in combination with) variation that changes protein-coding sequences. This is particularly compelling with respect to psychiatric disorders, as genetic changes in regulatory regions may result in differential transcriptional responses to developmental cues and environmental/psychosocial stressors. Until recently, however, the link between transcriptional regulation and psychiatric genetic risk has been understudied. Multiple obstacles have contributed to the paucity of research in this area, including challenges in identifying the positions of remote (distal from the promoter) regulatory elements (e.g. enhancers) and their target genes and the underrepresentation of neural cell types and brain tissues in epigenome projects - the availability of high-quality brain tissues for epigenetic and transcriptome profiling, particularly for the adolescent and developing brain, has been limited. Further challenges have arisen in the prediction and testing of the functional impact of DNA variation with respect to multiple aspects of transcriptional control, including regulatory-element interaction (e.g. between enhancers and promoters), transcription factor binding and DNA methylation. Further, the brain has uncommon DNA-methylation marks with unique genomic distributions not found in other tissues - current evidence suggests the involvement of non-CG methylation and 5-hydroxymethylation in neurodevelopmental processes but much remains unknown. We review here knowledge gaps as well as both technological and resource obstacles that will need to be overcome in order to elucidate the involvement of brain-relevant gene-regulatory variants in genetic risk for psychiatric disorders.
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Affiliation(s)
- C. L. Barr
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - V. L. Misener
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
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Duan Z, He M, Zhang J, Chen K, Li B, Wang J. Assessment of functional tag single nucleotide polymorphisms within the DRD2 gene as risk factors for post-traumatic stress disorder in the Han Chinese population. J Affect Disord 2015; 188:210-7. [PMID: 26363619 DOI: 10.1016/j.jad.2015.08.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/10/2015] [Accepted: 08/28/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Gene variations related to the dopaminergic pathway have been implicated in a number of neuropsychiatric disorders, including post-traumatic stress disorder (PTSD). Dopamine D2 receptor (DRD2) has been shown to significantly contribute to neuropsychiatric disorders and may specifically contribute to predisposition to PTSD. This study aimed to evaluate the association of polymorphisms within the entire DRD2 gene with PTSD in a case-control study. MATERIALS AND METHODS A total of 834 unrelated Han Chinese adults, including 497 healthy volunteers and 337 patients with PTSD, were used in this study. Fifteen tag single-nucleotide polymorphisms (tSNPs) were selected spanning the entire DRD2 gene through the construction of haplotype bins. Genotypes were gathered using an improved multiplex ligation detection reaction (iMLDR) technique. Allelic frequencies and clinical characteristics were compared in two independent Han Chinese populations. Moreover, the functionality of the rs2075652 and rs7131056 polymorphisms were assessed by measuring transcriptional enhancer activities. RESULTS Fifteen tag SNPs were identified in the Han Chinese population and all were common SNPs. Among 15 tSNPs, two of them (rs2075652 and rs7131056) significantly associated with PTSD. PTSD individuals were more likely to carry the rs2075652A and rs7131056A allele compared to the controls (P<0.05). The haplotype GTGATCGCGCAGGCG, had a risk effect on PTSD occurrence (OR=1.75, 95% CI: 1.24-2.48, P=0.002). Additionally, the rs2075652 polymorphism contained intronic enhancer activities. CONCLUSIONS The rs2075652 and rs7131056 polymorphisms, and the haplotype GTGATCGCGCAGGCG within the DRD2 gene, may be potential markers to predict susceptibility to PTSD.
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Affiliation(s)
- Zhaoxia Duan
- Department 6 of Research Institute of Surgery, Daping Hospital, Third Military Medical University, State Key Laboratory of Trauma, Burns and Combined Injury, Daping, Chongqing 400042, China.
| | - Mei He
- Department of Clinical Psychology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Jieyuan Zhang
- Department 6 of Research Institute of Surgery, Daping Hospital, Third Military Medical University, State Key Laboratory of Trauma, Burns and Combined Injury, Daping, Chongqing 400042, China
| | - Kuijun Chen
- Department 6 of Research Institute of Surgery, Daping Hospital, Third Military Medical University, State Key Laboratory of Trauma, Burns and Combined Injury, Daping, Chongqing 400042, China
| | - Bingcang Li
- Department 6 of Research Institute of Surgery, Daping Hospital, Third Military Medical University, State Key Laboratory of Trauma, Burns and Combined Injury, Daping, Chongqing 400042, China
| | - Jianmin Wang
- Department 6 of Research Institute of Surgery, Daping Hospital, Third Military Medical University, State Key Laboratory of Trauma, Burns and Combined Injury, Daping, Chongqing 400042, China
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Gu W, Gurguis CI, Zhou JJ, Zhu Y, Ko EA, Ko JH, Wang T, Zhou T. Functional and Structural Consequence of Rare Exonic Single Nucleotide Polymorphisms: One Story, Two Tales. Genome Biol Evol 2015; 7:2929-40. [PMID: 26454016 PMCID: PMC4684694 DOI: 10.1093/gbe/evv191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 01/01/2023] Open
Abstract
Genetic variation arising from single nucleotide polymorphisms (SNPs) is ubiquitously found among human populations. While disease-causing variants are known in some cases, identifying functional or causative variants for most human diseases remains a challenging task. Rare SNPs, rather than common ones, are thought to be more important in the pathology of most human diseases. We propose that rare SNPs should be divided into two categories dependent on whether the minor alleles are derived or ancestral. Derived alleles are less likely to have been purified by evolutionary processes and may be more likely to induce deleterious effects. We therefore hypothesized that the rare SNPs with derived minor alleles would be more important for human diseases and predicted that these variants would have larger functional or structural consequences relative to the rare variants for which the minor alleles are ancestral. We systematically investigated the consequences of the exonic SNPs on protein function, mRNA structure, and translation. We found that the functional and structural consequences are more significant for the rare exonic variants for which the minor alleles are derived. However, this pattern is reversed when the minor alleles are ancestral. Thus, the rare exonic SNPs with derived minor alleles are more likely to be deleterious. Age estimation of rare SNPs confirms that these potentially deleterious SNPs are recently evolved in the human population. These results have important implications for understanding the function of genetic variations in human exonic regions and for prioritizing functional SNPs in genome-wide association studies of human diseases.
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Affiliation(s)
- Wanjun Gu
- Research Center for Learning Sciences, Southeast University, Nanjing, Jiangsu, China
| | | | - Jin J Zhou
- Department of Epidemiology and Biostatistics, The University of Arizona
| | - Yihua Zhu
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China College of Information Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Eun-A Ko
- Department of Pharmacology, The University of Nevada School of Medicine, Reno
| | - Jae-Hong Ko
- Department of Physiology, College of Medicine, Chung-Ang University, Seoul, South Korea
| | - Ting Wang
- Department of Medicine, The University of Arizona
| | - Tong Zhou
- Department of Medicine, The University of Arizona
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Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data. Int J Genomics 2015; 2015:260159. [PMID: 26417590 PMCID: PMC4568383 DOI: 10.1155/2015/260159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/29/2015] [Indexed: 12/15/2022] Open
Abstract
The expression level of each gene is controlled by its regulatory regions, which determine the precise regulation in a tissue-specific manner, according to the developmental stage of the body and the necessity of a response to external stimuli. Nucleotide substitutions in regulatory gene regions may modify the affinity of transcription factors to their specific DNA binding sites, affecting the transcription rates of genes. In our previous research, we found that genes controlling the sensory perception of smell and genes involved in antigen processing and presentation were overrepresented significantly among genes with high SNP contents in their promoter regions. The goal of our study was to reveal functional features of human genes containing extremely small numbers of SNPs in promoter regions. Two functional groups were found to be overrepresented among genes whose promoters did not contain SNPs: (1) genes involved in gene-specific transcription and (2) genes controlling chromatin organization. We revealed that the 5′-regulatory regions of genes encoding transcription factors and chromatin-modifying proteins were characterized by reduced genetic variability. One important exception from this rule refers to genes encoding transcription factors with zinc-coordinating DNA-binding domains (DBDs), which underwent extensive expansion in vertebrates, particularly, in primate evolution. Hence, we obtained new evidence for evolutionary forces shaping variability in 5′-regulatory regions of genes.
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Lapitan LDS, Guo Y, Zhou D. Nano-enabled bioanalytical approaches to ultrasensitive detection of low abundance single nucleotide polymorphisms. Analyst 2015; 140:3872-87. [PMID: 25785914 PMCID: PMC4456783 DOI: 10.1039/c4an02304h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A survey of the recent, significant developments on nanomaterials enabled ultrasensitive DNA and gene mutation assays is presented.
Single nucleotide polymorphisms (SNPs) constitute the most common types of genetic variations in the human genome. A number of SNPs have been linked to the development of life threatening diseases including cancer, cardiovascular diseases and neurodegenerative diseases. The ability for ultrasensitive and accurate detection of low abundant disease-related SNPs in bodily fluids (e.g. blood, serum, etc.) holds a significant value in the development of non-invasive future biodiagnostic tools. Over the past two decades, nanomaterials have been utilized in a myriad of biosensing applications due to their ability of detecting extremely low quantities of biologically important biomarkers with high sensitivity and accuracy. Of particular interest is the application of such technologies in the detection of SNPs. The use of various nanomaterials, coupled with different powerful signal amplification strategies, has paved the way for a new generation of ultrasensitive SNP biodiagnostic assays. Over the past few years, several ultrasensitive SNP biosensors capable of detecting specific targets down to the ultra-low regimes (ca. aM and below) and therefore holding great promises for early clinical diagnosis of diseases have been developed. This mini review will highlight some of the most recent, significant advances in nanomaterial-based ultrasensitive SNP sensing technologies capable of detecting specific targets on the attomolar (10–18 M) regime or below. In particular, the design of novel, powerful signal amplification strategies that hold the key to the ultrasensitivity is highlighted.
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Affiliation(s)
- Lorico D S Lapitan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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Yang J, Zhang J, Wang X, Wang C, Chen J, Qian Y, Duan Z. Identification of functional tag single nucleotide polmorphisms within the entire CAT gene and their clinical relevance in patients with noise-induced hearing loss. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:2852-2863. [PMID: 26045794 PMCID: PMC4440103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/21/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVES Noise-induced hearing loss (NIHL) is an important occupational disease which results from an interaction between genetic and environmental factors. More and more evidences suggested that Catalase (CAT) gene polymorphism plays an important role in the development of NIHL. The aim of this study was to investigate the association of CAT gene polymorphisms with NIHL in a case-control study. DESIGN A total of 719 unrelated adult Chinese Han population, including 225 healthy volunteers and 494 noise-exposed workers were recruited in this study. Six tag single-nucleotide polymorphisms (tSNPs) were genotyped using an improved multiplex ligation detection reaction technique. Subsequently, the interaction between noise exposure level and genotypes and their effect on NIHL were analyzed using logistic regression. RESULTS Among six tSNPs, two of them (rs208679 and rs769217) were significantly associated with noise exposure level. For rs208679 recessive effect, GG genotype had a significantly increased of NIHL risk in the exposure level of <85 dB; and for rs769217 dominant effect, the combined genotypes TT/TC had a significantly increased of NIHL risk in the exposure level of 85 dB~92 dB; and the haplotype A-G-T-C-A-C had a risk effect on the NIHL in the exposure level of 85 dB~92 dB. In addition, the rs769217 polymorphism could enhance the transcription activities of the CAT gene. CONCLUSIONS This study identified CAT is a NIHL susceptibility gene when noise exposure levels are taken into account. Rs208679 and rs769217 polymorphisms might be used as relevant risk estimates for the development of NIHL in population with different noise exposure levels.
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Affiliation(s)
- Junhui Yang
- Department of Otolaryngology Head and Neck Surgery, Daping Hospital, Third Military Medical UniversityChongqing 400042, China
| | - Jieyuan Zhang
- Department 6 of Research Institute of Surgery, Daping Hospital, Third Military Medical University, State Key Laboratory of Trauma, Burns and Combined InjuryChongqing 400042, China
| | - Xiaoming Wang
- Prevention and Control Center of Disease of Chongqing FulingChongqing 408000, China
| | - Chaoyong Wang
- Chongqing Fuling Central HospitalChongqing 408000, China
| | - Jichuan Chen
- Department of Otolaryngology Head and Neck Surgery, Daping Hospital, Third Military Medical UniversityChongqing 400042, China
| | - Yu Qian
- Department of Otolaryngology Head and Neck Surgery, Daping Hospital, Third Military Medical UniversityChongqing 400042, China
| | - Zhaoxia Duan
- Department 6 of Research Institute of Surgery, Daping Hospital, Third Military Medical University, State Key Laboratory of Trauma, Burns and Combined InjuryChongqing 400042, China
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