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Apsley AT, Domico ER, Verbiest MA, Brogan CA, Buck ER, Burich AJ, Cardone KM, Stone WJ, Anisimova M, Vandenbergh DJ. A novel hypervariable variable number tandem repeat in the dopamine transporter gene ( SLC6A3). Life Sci Alliance 2023; 6:e202201677. [PMID: 36754567 PMCID: PMC9909461 DOI: 10.26508/lsa.202201677] [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: 08/17/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
The dopamine transporter gene, SLC6A3, has received substantial attention in genetic association studies of various phenotypes. Although some variable number tandem repeats (VNTRs) present in SLC6A3 have been tested in genetic association studies, results have not been consistent. VNTRs in SLC6A3 that have not been examined genetically were characterized. The Tandem Repeat Annotation Library was used to characterize the VNTRs of 64 unrelated long-read haplotype-phased SLC6A3 sequences. Sequence similarity of each repeat unit of the five VNTRs is reported, along with the correlations of SNP-SNP, SNP-VNTR, and VNTR-VNTR alleles across the gene. One of these VNTRs is a novel hyper-VNTR (hyVNTR) in intron 8 of SLC6A3, which contains a range of 3.4-133.4 repeat copies and has a consensus sequence length of 38 bp, with 82% G+C content. The 38-base repeat was predicted to form G-quadruplexes in silico and was confirmed by circular dichroism spectroscopy. In addition, this hyVNTR contains multiple putative binding sites for PRDM9, which, in combination with low levels of linkage disequilibrium around the hyVNTR, suggests it might be a recombination hotspot.
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Affiliation(s)
- Abner T Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
- The Molecular, Cellular and Integrative Biosciences Program, The Pennsylvania State University, State College, PA, USA
| | - Emma R Domico
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Max A Verbiest
- Institute of Computational Life Science, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Wädenswil, Switzerland
- Department of Molecular Life Sciences, Faculty of Science, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Carly A Brogan
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Evan R Buck
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Andrew J Burich
- Department of Information Science and Technologies - Applied Data Sciences, The Pennsylvania State University, State College, PA, USA
| | - Kathleen M Cardone
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Wesley J Stone
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Maria Anisimova
- Institute of Computational Life Science, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David J Vandenbergh
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
- The Molecular, Cellular and Integrative Biosciences Program, The Pennsylvania State University, State College, PA, USA
- Institute of the Neurosciences, The Pennsylvania State University, State College, PA, USA
- The Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
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Eslami Rasekh M, Hernández Y, Drinan SD, Fuxman Bass J, Benson G. Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. Nucleic Acids Res 2021; 49:4308-4324. [PMID: 33849068 PMCID: PMC8096271 DOI: 10.1093/nar/gkab224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/06/2021] [Accepted: 03/18/2021] [Indexed: 11/12/2022] Open
Abstract
Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.
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Affiliation(s)
| | - Yözen Hernández
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | | | - Juan I Fuxman Bass
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Gary Benson
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Computer Science, Boston University, Boston, MA 02215, USA
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Marshall JN, Lopez AI, Pfaff AL, Koks S, Quinn JP, Bubb VJ. Variable number tandem repeats - Their emerging role in sickness and health. Exp Biol Med (Maywood) 2021; 246:1368-1376. [PMID: 33794697 PMCID: PMC8239992 DOI: 10.1177/15353702211003511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Understanding the mechanisms regulating tissue specific and stimulus inducible
regulation is at the heart of understanding human biology and how this
translates to wellbeing, the ageing process, and disease progression.
Polymorphic DNA variation is superimposed as an extra layer of complexity in
such processes which underpin our individuality and are the focus of
personalized medicine. This review focuses on the role and action of repetitive
DNA, specifically variable number tandem repeats and
SINE-VNTR-Alu domains, highlighting their role in
modification of gene structure and gene expression in addition to their
polymorphic nature being a genetic modifier of disease risk and progression.
Although the literature focuses on their role in disease, it illustrates their
potential to be major contributors to normal physiological function. To date,
these elements have been under-reported in genomic analysis due to the
difficulties in their characterization with short read DNA sequencing methods.
However, recent advances in long read sequencing methods should resolve these
problems allowing for a greater understanding of their contribution to a host of
genomic and functional mechanisms underlying physiology and disease.
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Affiliation(s)
- Jack Ng Marshall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ana Illera Lopez
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
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A SINE-VNTR- Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus. Int J Mol Sci 2020; 21:ijms21228486. [PMID: 33187279 PMCID: PMC7697779 DOI: 10.3390/ijms21228486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
The hominid SINE-VNTR-Alu (SVA) retrotransposons represent a repertoire of genomic variation which could have significant effects on genome function. A human-specific SVA in the promoter region of the gene leucine-rich repeats and immunoglobulin-like domains 2 (LRIG2), which we termed SVA_LRIG2, is a common retrotransposon insertion polymorphism (RIP), defined as an element which is polymorphic for its presence or absence in the genome. We hypothesised that this RIP might be associated with differential levels of expression of LRIG2. The RIP genotype of SVA_LRIG2 was determined in a subset of frontal cortex DNA samples from the North American Brain Expression Consortium (NABEC) cohort and was imputed for a larger set of that cohort. Utilising available frontal cortex total RNA-seq and CpG methylation data for this cohort, we observed that increased allele dosage of SVA_LRIG2 was non-significantly associated with a decrease in transcription from the region and significantly associated with increased methylation of the CpG probe nearest to SVA_LRIG2, i.e., SVA_LRIG2 is a significant methylation quantitative trait loci (mQTL) at the LRIG2 locus. These data are consistent with SVA_LRIG2 being a transcriptional regulator, which in part may involve epigenetic modulation.
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Epigenetic variation at the SLC6A4 gene promoter in mother-child pairs with major depressive disorder. J Affect Disord 2019; 245:716-723. [PMID: 30447571 DOI: 10.1016/j.jad.2018.10.369] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/05/2018] [Accepted: 10/31/2018] [Indexed: 01/16/2023]
Abstract
BACKGROUND Genetic and epigenetic variations of the serotonin transporter gene (SLC6A4) have been related to the etiology of depression. The 5-HTTLPR polymorphism at the SLC6A4 promoter region has two variants, a short allele (S) and a long allele (L), in which the S allele results in lower gene transcription and has been associated with depression. The short S-allele of 5-HTTLPR polymorphism of this gene has been associated with depression. In addition to molecular mechanisms, exposure to early life risk factors such as maternal depression seems to affect the development of depression in postnatal life. The present study investigated the association of 5-HTTLPR polymorphism and CpG DNA methylation (5mC) levels of an AluJb repeat element at the SLC6A4 promoter region in mother-child pairs exposed to maternal depression. METHODS We analyzed DNA samples from 60 subjects (30 mother-child pairs) split into three groups, with and without major depression disorder (DSM-IV) among children and mothers. The genotyping of 5-HTTLPR polymorphism and quantification of 5mC levels was performed by qualitative PCR and methylation-sensitive restriction enzyme digestion, and real-time quantitative PCR (MSRED-qPCR), respectively. RESULTS The sample analyzed presented a higher frequency of S allele of 5-HTTLPR (67.5%). Despite the high frequency of this allele, we did not find statistically significant differences between individuals carrying at least one S allele between the depression and healthy control subjects, or among the mother-child pair groups with different patterns of occurrence of depression. In the group where the mother and child were both diagnosed with depression, we found a statistically significant decrease of the 5mC level at the SLC6A4 promoter region. LIMITATIONS The limitations are the relatively small sample size and lack of gene expression data available for comparison with methylation data. CONCLUSION In this study, we demonstrated a repeat element specific 5mC level reduction in mother-child pairs, concordant for the diagnosis of depression.
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Kõks G, Prans E, Tran HDT, Ngo NBT, Hoang LNN, Tran HMT, Cao Ngoc T, Doan Phuoc T, Ho XD, Ho Duy B, Lättekivi F, Quinn J, Kõks S. Genetic Interaction Between Two VNTRs in the SLC6A4 Gene Regulates Nicotine Dependence in Vietnamese Men. Front Pharmacol 2018; 9:1398. [PMID: 30559666 PMCID: PMC6287221 DOI: 10.3389/fphar.2018.01398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/13/2018] [Indexed: 11/29/2022] Open
Abstract
Nicotine dependence is an addiction to tobacco products and a global public health concern. Association between the SLC6A4 polymorphisms and nicotine dependence is controversial. Two variable number tandem repeat (VNTR) domains, termed HTTLPR and STin2, in the SLC6A4 gene are well characterized transcriptional regulatory elements. Their polymorphism in the copy number of the repeat correlates with the particular personality and psychiatric traits. We analyzed nicotine dependence in 1,804 participants from Central Vietnam. The Fagerström Test (FTND) was used to evaluate the nicotine dependence and PCR was used to determine the SLC6A4 HTTLPR and STin2 VNTRs. The HTTLPR VNTR was associated with difficulties to refrain from smoking in a prohibiting environment. The STIn2 10/10 genotype was associated with (1) years of smoking, (2) difficulties to quit the first cigarette, and (3) higher number of cigarettes smoked per day (CPD). Stratification analysis was used to find the genetic interaction between these two VNTRs in nicotine dependence as they may synergistically regulate the SLC6A4 expression. Smokers with the S/S HTTLPR genotypes showed a much stronger association between STin2 10/10 variant and CPD. This finding is consistent with the molecular evidence for the functional interaction between HTTLPR and STin2 in cell line models, where STin2 has described as a stronger expressional regulator. Similarly, we found that STin2 is a much stronger modifier of smoking with 10/10 genotype related to higher nicotine dependence. The present study supports genetic interaction between HTTLPR and STin2 VNTRs in the regulation of nicotine dependence with the dominance of the STin2 effects. This finding could be explained by their differential effect on the SLC6A4 expression.
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Affiliation(s)
- Gea Kõks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Ele Prans
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Ha Diep Thi Tran
- Public Health Faculty, Danang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Ngoc Bich Thi Ngo
- Public Health Faculty, Danang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Linh Nhat Nguyen Hoang
- Public Health Faculty, Danang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Hue Minh Thi Tran
- Public Health Faculty, Danang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Thanh Cao Ngoc
- College of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | | | - Xuan Dung Ho
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,College of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Binh Ho Duy
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,College of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Freddy Lättekivi
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - John Quinn
- Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Sulev Kõks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia.,The Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
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Quinn JP, Savage AL, Bubb VJ. Non-coding genetic variation shaping mental health. Curr Opin Psychol 2018; 27:18-24. [PMID: 30099302 PMCID: PMC6624474 DOI: 10.1016/j.copsyc.2018.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022]
Abstract
Gene expression determined by the genome mediating a response to cell environment. Genetic variation results in distinct individual response in gene expression. Non-coding DNA is an important site for such functional genetic variation. Gene expression is a major modulator of brain chemistry and thus behavior.
Over 98% of our genome is non-coding and is now recognised to have a major role in orchestrating the tissue specific and stimulus inducible gene expression pattern which underpins our wellbeing and mental health. The non-coding genome responds functionally to our environment at all levels, encompassing the span from psychological to physiological challenge. The gene expression pattern, termed the transcriptome, ultimately gives us our neurochemistry. Therefore a major modulator of mental wellbeing is how our genes are regulated in response to life experiences. Superimposed on the aforementioned non-coding DNA framework is a vast body of genetic variation in the elements that control response to challenges. These differences, termed polymorphisms, allow for a differential response from a specific DNA element to the same challenge thus potentially allowing ‘individuality’ in the modulation of our transcriptome. This review will focus on a fundamental mechanism defining our psychological and psychiatric wellbeing, namely how genetic variation can be correlated with differential gene expression in response to specific challenges, thus resulting in altered neurochemistry which consequently may shape behaviour.
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Affiliation(s)
- John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK.
| | - Abigail L Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
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Abstract
The monoamine oxidase A (MAOA) uVNTR (upstream variable number tandem repeat) is one of the most often cited examples of a gene by environment interaction (GxE) in relation to behavioral traits. However, MAOA possesses a second VNTR, 500 bp upstream of the uVNTR, which is termed d- or distal VNTR. Furthermore, genomic analysis indicates that there are a minimum of two transcriptional start sites (TSSs) for MAOA, one of which encompasses the uVNTR within the 5′ untranslated region of one of the isoforms. Through expression analysis in semi-haploid HAP1 cell lines genetically engineered in order to knockout (KO) either the uVNTR, dVNTR, or both VNTRs, we assessed the effect of the two MAOA VNTRs, either alone or in combination, on gene expression directed from the different TSSs. Complementing our functional analysis, we determined the haplotype variation of these VNTRs in the general population. The expression of the two MAOA isoforms was differentially modulated by the two VNTRs located in the promoter region. The most extensively studied uVNTR, previously considered a positive regulator of the MAOA gene, did not modulate the expression of what it is considered the canonical isoform, while we found that the dVNTR positively regulated this isoform in our model. In contrast, both the uVNTR and the dVNTR were found to act as negative regulators of the second less abundant MAOA isoform. The haplotype analysis for these two VNTRs demonstrated a bias against the presence of one of the potential variants. The uVNTR and dVNTR differentially affect expression of distinct MAOA isoforms, and thus, their combined profiling offers new insights into gene-regulation, GxE interaction, and ultimately MAOA-driven behavior.
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Clark SL, McClay JL, Adkins DE, Kumar G, Aberg KA, Nerella S, Xie L, Collins AL, Crowley JJ, Quackenbush CR, Hilliard CE, Shabalin AA, Vrieze SI, Peterson RE, Copeland WE, Silberg JL, McGue M, Maes H, Iacono WG, Sullivan PF, Costello EJ, van den Oord EJ. Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence. Alcohol Clin Exp Res 2017; 41:711-718. [PMID: 28196272 DOI: 10.1111/acer.13352] [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] [Received: 10/06/2016] [Accepted: 02/09/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Previous genomewide association studies (GWASs) have identified a number of putative risk loci for alcohol dependence (AD). However, only a few loci have replicated and these replicated variants only explain a small proportion of AD risk. Using an innovative approach, the goal of this study was to generate hypotheses about potentially causal variants for AD that can be explored further through functional studies. METHODS We employed targeted capture of 71 candidate loci and flanking regions followed by next-generation deep sequencing (mean coverage 78X) in 806 European Americans. Regions included in our targeted capture library were genes identified through published GWAS of alcohol, all human alcohol and aldehyde dehydrogenases, reward system genes including dopaminergic and opioid receptors, prioritized candidate genes based on previous associations, and genes involved in the absorption, distribution, metabolism, and excretion of drugs. We performed single-locus tests to determine if any single variant was associated with AD symptom count. Sets of variants that overlapped with biologically meaningful annotations were tested for association in aggregate. RESULTS No single, common variant was significantly associated with AD in our study. We did, however, find evidence for association with several variant sets. Two variant sets were significant at the q-value <0.10 level: a genic enhancer for ADHFE1 (p = 1.47 × 10-5 ; q = 0.019), an alcohol dehydrogenase, and ADORA1 (p = 5.29 × 10-5 ; q = 0.035), an adenosine receptor that belongs to a G-protein-coupled receptor gene family. CONCLUSIONS To our knowledge, this is the first sequencing study of AD to examine variants in entire genes, including flanking and regulatory regions. We found that in addition to protein coding variant sets, regulatory variant sets may play a role in AD. From these findings, we have generated initial functional hypotheses about how these sets may influence AD.
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Affiliation(s)
- Shaunna L Clark
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Joseph L McClay
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Daniel E Adkins
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Gaurav Kumar
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Srilaxmi Nerella
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Linying Xie
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Ann L Collins
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - James J Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Corey R Quackenbush
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Christopher E Hilliard
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andrey A Shabalin
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Scott I Vrieze
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado.,Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Roseann E Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - William E Copeland
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina
| | - Judy L Silberg
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Hermine Maes
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elizabeth J Costello
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina
| | - Edwin J van den Oord
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
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Iurescia S, Seripa D, Rinaldi M. Looking Beyond the 5-HTTLPR Polymorphism: Genetic and Epigenetic Layers of Regulation Affecting the Serotonin Transporter Gene Expression. Mol Neurobiol 2016; 54:8386-8403. [DOI: 10.1007/s12035-016-0304-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
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Duman EA, Canli T. Influence of life stress, 5-HTTLPR genotype, and SLC6A4 methylation on gene expression and stress response in healthy Caucasian males. BIOLOGY OF MOOD & ANXIETY DISORDERS 2015; 5:2. [PMID: 25995833 PMCID: PMC4438516 DOI: 10.1186/s13587-015-0017-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 04/27/2015] [Indexed: 12/14/2022]
Abstract
Background Previous research reported that individual differences in the stress response were moderated by an interaction between individuals’ life stress experience and the serotonin transporter-linked polymorphic region (5-HTTLPR), a common polymorphism located in the promoter region of the serotonin transporter gene (SLC6A4). Furthermore, this work suggested that individual differences in SLC6A4 DNA methylation could be one underlying mechanism by which stressful life events might regulate gene expression. The aim of this study was to understand the relation between early and recent life stress experiences, 5-HTTLPR genotype, and SLC6A4 methylation. In addition, we aimed to address how these factors influence gene expression and cortisol response to an acute psychosocial stressor, operationalized as the Trier Social Stress Test (TSST). In a sample of 105 Caucasian males, we collected early and recent life stress measures and blood samples to determine 5-HTTLPR genotype and SLC6A4 methylation. Furthermore, 71 of these participants provided blood and saliva samples before and after the TSST to measure changes in SLC6A4 and NR3C1 gene expression and cortisol response. Results Compared to S-group individuals, LL individuals responded with increased SLC6A4 mRNA levels to the TSST (t(66) = 3.71, P < .001) and also showed increased global methylation as a function of ELS (r (32) = .45, P = .008) and chronic stress (r (32) = .44, P = .010). Compared to LL individuals, S-group individuals showed reduced SLC6A4 mRNA levels (r (41) = −.31, P = .042) and increased F3 methylation (r (67) = .30, P = .015) as a function of ELS; as well as increased F1 methylation as a function of chronic stress and recent depressive symptoms (r = .41, P < .01), which correlated positively with NR3C1 expression (r (42) = .31, P = .040). Conclusions Both early and recent life stress alter DNA methylation as a function of 5-HTTLPR genotype. Some of these changes are also reflected in gene expression and cortisol response, differentially affecting individuals’ stress response in a manner that may confer susceptibility or resilience for psychopathology upon experiencing stressful life events. Electronic supplementary material The online version of this article (doi:10.1186/s13587-015-0017-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elif A Duman
- Integrative Neuroscience, Department of Psychology, Stony Brook University, Stony Brook, NY 11794-2500 USA ; Department of Psychology, Bogazici University, Bebek, 34342 Istanbul, Turkey ; Center for Life Sciences and Technologies, Bogazici University, Bebek, 34342 Istanbul, Turkey
| | - Turhan Canli
- Integrative Neuroscience, Department of Psychology, Stony Brook University, Stony Brook, NY 11794-2500 USA ; Department of Radiology, Stony Brook University, Stony Brook, NY 11794 USA ; Program in Neuroscience, Stony Brook University, Stony Brook, NY 11794 USA ; Program in Genetics, Stony Brook University, Stony Brook, NY 11794 USA
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12
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Warburton A, Breen G, Rujescu D, Bubb VJ, Quinn JP. Characterization of a REST-Regulated Internal Promoter in the Schizophrenia Genome-Wide Associated Gene MIR137. Schizophr Bull 2015; 41:698-707. [PMID: 25154622 PMCID: PMC4393679 DOI: 10.1093/schbul/sbu117] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MIR137 has been identified as a candidate gene for schizophrenia from genome-wide association studies via association with an intronic single nucleotide polymorphism (SNP), rs1625579. The location of the SNP suggests one mechanism in which transcriptional or posttranscriptional regulation of miR-137 expression could underlie schizophrenia. We identified and validated a novel promoter of the MIR137 gene adjacent to miR-137 itself which can direct the expression of distinct mRNA isoforms encoding miR-137. Analysis of both endogenous gene expression and reporter gene assays determined that this internal promoter is regulated by repressor element-1 silencing transcription factor (REST), which has previously been associated with pathways linked to schizophrenia. Distinct isoforms of REST mediate differential expression at this locus, suggesting the relative levels of these isoforms are important for miR-137 expression profiles. The internal promoter contains a variable number tandem repeat (VNTR) domain adjacent to the pre-miR-137 sequence. The reporter gene activity directed by this promoter was modified by the genotype of the VNTR. Differential expression was also observed in response to cocaine, which is known to regulate the REST pathway in SH-SY5Y cells. Our data support the hypothesis that a "gene × environment" interaction could modify the level of miR-137 expression via this internal promoter and that the genotype of the VNTR could modulate transcriptional responses. We demonstrate that this promoter region is not in disequilibrium with rs1625579 and therefore would supply a distinct pathway to potentially alter miR-137 levels in response to environmental cues.
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Affiliation(s)
- Alix Warburton
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK;
| | - Gerome Breen
- King’s College London, MRC Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, London, UK; ,National Institute for Health Research (NIHR), Biomedical Research Centre for Mental Health, South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King’s College London SE5 8DF, UK;
| | - Dan Rujescu
- Department of Psychiatry, University of Halle-Wittenberg, Halle, Germany
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK;
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK; ,*To whom correspondence should be addressed; Department of Molecular and Clinical Pharmacology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK; tel: +44-151-794-5498, fax: +44-151-794-5517, e-mail:
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Quinn JP, Bubb VJ. SVA retrotransposons as modulators of gene expression. Mob Genet Elements 2014; 4:e32102. [PMID: 25077041 PMCID: PMC4114917 DOI: 10.4161/mge.32102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/12/2022] Open
Abstract
Endogenous mobile genetic elements can give rise to de novo germline or somatic mutations that can have dramatic consequences for genome regulation both local and possibly more globally based on the site of integration. However if we consider them as "normal genetic" components of the reference genome then they are likely to modify local chromatin structure which would have an effect on gene regulation irrelevant of their ability to further transpose. As such they can be treated as any other domain involved in a gene × environment interaction. Similarly their evolutionary appearance in the reference genome would supply a driver for species specific responses/traits. Our recent data would suggest the hominid specific subset of retrotransposons, SINE-VNTR-Alu (SVA), can function as transcriptional regulatory domains both in vivo and in vitro when analyzed in reporter gene constructs. Of particular interest in the SVA element, were the variable number tandem repeat (VNTR) domains which as their name suggests can be polymorphic. We and others have previously shown that VNTRs can be both differential regulators and biomarkers of disease based on the genotype of the repeat. Here, we provide an overview of why polymorphism in the SVA elements, in particular the VNTRs, could alter gene expression patterns that could be mechanistically associated with different traits in evolution or disease progression in humans.
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Affiliation(s)
- John P Quinn
- Department of Molecular and Clinical Pharmacology; Institute of Translational Medicine; University of Liverpool; Liverpool, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology; Institute of Translational Medicine; University of Liverpool; Liverpool, UK
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Savage AL, Wilm TP, Khursheed K, Shatunov A, Morrison KE, Shaw PJ, Shaw CE, Smith B, Breen G, Al-Chalabi A, Moss D, Bubb VJ, Quinn JP. An evaluation of a SVA retrotransposon in the FUS promoter as a transcriptional regulator and its association to ALS. PLoS One 2014; 9:e90833. [PMID: 24608899 PMCID: PMC3946630 DOI: 10.1371/journal.pone.0090833] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 02/04/2014] [Indexed: 12/13/2022] Open
Abstract
Genetic mutations of FUS have been linked to many diseases including Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration. A primate specific and polymorphic retrotransposon of the SINE-VNTR-Alu (SVA) family is present upstream of the FUS gene. Here we have demonstrated that this retrotransposon can act as a classical transcriptional regulatory domain in the context of a reporter gene construct both in vitro in the human SK-N-AS neuroblastoma cell line and in vivo in a chick embryo model. We have also demonstrated that the SVA is composed of multiple distinct regulatory domains, one of which is a variable number tandem repeat (VNTR). The ability of the SVA and its component parts to direct reporter gene expression supported a hypothesis that this region could direct differential FUS expression in vivo. The SVA may therefore contribute to the modulation of FUS expression exhibited in and associated with neurological disorders including ALS where FUS regulation may be an important parameter in progression of the disease. As VNTRs are often clinical associates for disease progression we determined the extent of polymorphism within the SVA. In total 2 variants of the SVA were identified based within a central VNTR. Preliminary analysis addressed the association of these SVA variants within a small sporadic ALS cohort but did not reach statistical significance, although we did not include other parameters such as SNPs within the SVA or an environmental factor in this analysis. The latter may be particularly important as the transcriptional and epigenetic properties of the SVA are likely to be directed by the environment of the cell.
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Affiliation(s)
- Abigail L. Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Thomas P. Wilm
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Kejhal Khursheed
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Aleksey Shatunov
- Clinical Neuroscience, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Karen E. Morrison
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, University of Birmingham, Birmingham, United Kingdom; and Neurosciences Division, University Hospital Birmingham NHS Foundation Trust, Birmingham, West Midlands, United Kingdom
| | - Pamela J. Shaw
- Academic Unit of Neurology, Department of Neuroscience, Sheffield Institute for Translational Research, University of Sheffield, Sheffield, South Yorkshire, United Kingdom
| | - Christopher E. Shaw
- Clinical Neuroscience, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Bradley Smith
- Clinical Neuroscience, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Gerome Breen
- MRC Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, King's College London, London, United Kingdom; National Institute for Health Research Biomedical Research, Centre for Mental Health, South London, United Kingdom; and Maudsley NHS Foundation Trust and Institute of Psychiatry, King's College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Clinical Neuroscience, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Diana Moss
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
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Tristán-Noguero A, Fernàndez-Castillo N, Roncero C, Sánchez-Mora C, Ramos-Quiroga JA, Daigre C, Egido A, Alvarós J, Prat G, Casas M, Cormand B, Ribasés M. Lack of association between the LPR and VNTR polymorphisms of the serotonin transporter gene and cocaine dependence in a Spanish sample. Psychiatry Res 2013; 210:1287-9. [PMID: 24120036 DOI: 10.1016/j.psychres.2013.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/23/2013] [Accepted: 09/05/2013] [Indexed: 01/25/2023]
Abstract
We genotyped the LPR and VNTR polymorphisms of the serotonin transporter gene in 504 cocaine-dependent patients and 508 controls. No association was detected with either polymorphism or with any haplotype combination. This study provided no evidence that these polymorphisms confer susceptibility to cocaine dependence in our sample.
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Quinn JP, Warburton A, Myers P, Savage AL, Bubb VJ. Polymorphic variation as a driver of differential neuropeptide gene expression. Neuropeptides 2013; 47:395-400. [PMID: 24210140 DOI: 10.1016/j.npep.2013.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 11/15/2022]
Abstract
The regulation of neuropeptide gene expression and their receptors in a tissue specific and stimulus inducible manner will determine in part behaviour and physiology. This can be a dynamic process resulting from short term changes in response to the environment or long term modulation imposed by epigenetically determined mechanisms established during life experiences. The latter underpins what is termed 'nature and nurture, or 'gene×environment interactions'. Dynamic gene expression of neuropeptides or their receptors is a key component of signalling in the CNS and their inappropriate regulation is therefore a predicted target underpinning psychiatric disorders and neuropathological processes. Finding the regulatory domains within our genome which have the potential to direct gene expression is a difficult challenge as 98% of our genome is non-coding and, with the exception of proximal promoter regions, such elements can be quite distant from the gene that they regulate. This review will deal with how we can find such domains by addressing both the most conserved non-exonic regions in the genome using comparative genomics and the most recent or constantly evolving DNA such as repetitive DNA or retrotransposons. We shall also explore how polymorphic changes in such domains can be associated with CNS disorders by altering the appropriate gene expression patterns which maintain normal physiology.
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Affiliation(s)
- John P Quinn
- Neurogenetics in Wellbeing and Disease Section, Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Sherrington Building, Ashton Street, Liverpool L69 3GE, UK.
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Pramod AB, Foster J, Carvelli L, Henry LK. SLC6 transporters: structure, function, regulation, disease association and therapeutics. Mol Aspects Med 2013; 34:197-219. [PMID: 23506866 DOI: 10.1016/j.mam.2012.07.002] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/03/2012] [Indexed: 02/08/2023]
Abstract
The SLC6 family of secondary active transporters are integral membrane solute carrier proteins characterized by the Na(+)-dependent translocation of small amino acid or amino acid-like substrates. SLC6 transporters, which include the serotonin, dopamine, norepinephrine, GABA, taurine, creatine, as well as amino acid transporters, are associated with a number of human diseases and disorders making this family a critical target for therapeutic development. In addition, several members of this family are directly involved in the action of drugs of abuse such as cocaine, amphetamines, and ecstasy. Recent advances providing structural insight into this family have vastly accelerated our ability to study these proteins and their involvement in complex biological processes.
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Affiliation(s)
- Akula Bala Pramod
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, United States
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Sugawara H, Bundo M, Ishigooka J, Iwamoto K, Kato T. Epigenetic Regulation of Serotonin Transporter in Psychiatric Disorders. J Genet Genomics 2013; 40:325-9. [DOI: 10.1016/j.jgg.2012.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
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Savage AL, Bubb VJ, Breen G, Quinn JP. Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns. BMC Evol Biol 2013; 13:101. [PMID: 23692647 PMCID: PMC3667099 DOI: 10.1186/1471-2148-13-101] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/15/2013] [Indexed: 12/24/2022] Open
Abstract
Background Retrotransposons are a major component of the human genome constituting as much as 45%. The hominid specific SINE-VNTR-Alus are the youngest of these elements constituting 0.13% of the genome; they are therefore a practical and amenable group for analysis of both their global integration, polymorphic variation and their potential contribution to modulation of genome regulation. Results Consistent with insertion into active chromatin we have determined that SVAs are more prevalent in genic regions compared to gene deserts. The consequence of which, is that their integration has greater potential to have affects on gene regulation. The sequences of SVAs show potential for the formation of secondary structure including G-quadruplex DNA. We have shown that the human specific SVA subtypes (E-F1) show the greatest potential for forming G-quadruplexes within the central tandem repeat component in addition to the 5’ ‘CCCTCT’ hexamer. We undertook a detailed analysis of the PARK7 SVA D, located in the promoter of the PARK7 gene (also termed DJ-1), in a HapMap cohort where we identified 2 variable number tandem repeat domains and 1 tandem repeat within this SVA with the 5’ CCCTCT element being one of the variable regions. Functionally we were able to demonstrate that this SVA contains multiple regulatory elements that support reporter gene expression in vitro and further show these elements exhibit orientation dependency. Conclusions Our data supports the hypothesis that SVAs integrate preferentially in to open chromatin where they could modify the existing transcriptional regulatory domains or alter expression patterns by a variety of mechanisms.
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Affiliation(s)
- Abigail L Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
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Banerjee E, Banerjee D, Chatterjee A, Sinha S, Nandagopal K. Selective maternal inheritance of risk alleles and genetic interaction between serotonin receptor-1B (5-HTR1B) and serotonin transporter (SLC6A4) in ADHD. Psychiatry Res 2012; 200:1083-5. [PMID: 22575343 DOI: 10.1016/j.psychres.2012.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 02/19/2012] [Accepted: 04/05/2012] [Indexed: 11/15/2022]
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Funk-Keenan J, Sacco J, Wong YYA, Rasmussen S, Motsinger-Reif A, Trepanier LA. Evaluation of polymorphisms in the sulfonamide detoxification genes CYB5A and CYB5R3 in dogs with sulfonamide hypersensitivity. J Vet Intern Med 2012; 26:1126-33. [PMID: 22816446 DOI: 10.1111/j.1939-1676.2012.00965.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/09/2012] [Accepted: 05/22/2012] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Delayed hypersensitivity (HS) reactions to potentiated sulfonamide antimicrobials occur in both dogs and humans, and involve an intermediate hydroxylamine metabolite that is detoxified by cytochrome b(5) and NADH cytochrome b(5) reductase. HYPOTHESIS/OBJECTIVES We hypothesized that polymorphisms in the genes (CYB5A and CYB5R3) encoding these 2 enzymes would be associated with risk of sulfonamide HS in dogs. ANIMALS A total of 18 dogs with delayed HS to potentiated sulfonamide antimicrobials and 16 dogs that tolerated (TOL) a therapeutic course of these drugs without adverse effect. METHODS CYB5A and CYB5R3 were sequenced from canine liver, and the promoter, exons, and 3' untranslated regions of both genes were resequenced from genomic DNA obtained from all dogs. RESULTS Multiple polymorphisms were found in both genes. When controlled for multiple comparisons, the 729GG variant in CYB5R3 was significantly overrepresented in dogs with sulfonamide HS (78% of dogs), compared to TOL dogs (31%; P = .003). CONCLUSIONS AND CLINICAL IMPORTANCE The CYB5R3 729GG variant may contribute to the risk of sulfonamide HS in dogs. Functional characterization of this polymorphism, as well as genotyping in a larger number of HS and TOL dogs, is warranted.
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Affiliation(s)
- J Funk-Keenan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706-1102, USA
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Haddley K, Bubb VJ, Breen G, Parades-Esquivel UM, Quinn JP. Behavioural genetics of the serotonin transporter. Curr Top Behav Neurosci 2012; 12:503-535. [PMID: 22261701 DOI: 10.1007/7854_2011_186] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The serotonin transporter is a key regulator of the bioavailability of serotonin and therefore any modulation in the expression or action of the transporter would be expected to have consequences on behaviour. The transporter has therefore become a target for pharmaceutical intervention in behavioural and mood disorders. The search for polymorphic variants in the transporter that would associate with neurological disorders has been extensive but has become focused on two domains which are both termed variable number tandem repeat (VNTR)polymorphisms. Both of these VNTRs are in non-coding DNA and therefore proposed to be mechanistically involved in a disorder through their ability to modulate transcriptional or post-transcriptional regulation of the transporter. The most extensively studied is in the promoter and is a bi-allelic insertion/deletion found in the 50 promoter region of the gene 1.2 kb upstream of the transcriptional start site. This VNTR, termed, 5-HTTLPR was initially identified as two variants containing either, 14 (short/deletion) or 16 (long/insertion) copies of a 22 bp repeat. A second widely studied VNTR found in the non-coding region of the transporter is located within intron 2 and comprises 9, 10 or 12 copies of a16–17 bp repeat termed, STin2.9, STin2.10 and STin2.12, respectively. These VNTR polymorphisms have been associated with a range of behavioural and psychiatric disorders including depression, OCD, anxiety and schizophrenia, however often the lack of reproducibility in different cohorts has led to debate on the actual association of the polymorphisms with this extensive range of neurological conditions. Here we review these two polymorphic VNTRs in depth and relate that to pharmaceutical response, their ability to regulate differential transporter expression, their core involvement in gene-environment interaction and their genetic association with specific disorders.
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Jost KL, Rottach A, Milden M, Bertulat B, Becker A, Wolf P, Sandoval J, Petazzi P, Huertas D, Esteller M, Kremmer E, Leonhardt H, Cardoso MC. Generation and characterization of rat and mouse monoclonal antibodies specific for MeCP2 and their use in X-inactivation studies. PLoS One 2011; 6:e26499. [PMID: 22140431 PMCID: PMC3225355 DOI: 10.1371/journal.pone.0026499] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 09/28/2011] [Indexed: 11/23/2022] Open
Abstract
Methyl CpG binding protein 2 (MeCP2) binds DNA, and has a preference for methylated CpGs and, hence, in cells, it accumulates in heterochromatin. Even though it is expressed ubiquitously MeCP2 is particularly important during neuronal maturation. This is underscored by the fact that in Rett syndrome, a neurological disease, 80% of patients carry a mutation in the MECP2 gene. Since the MECP2 gene lies on the X chromosome and is subjected to X chromosome inactivation, affected patients are usually chimeric for wild type and mutant MeCP2. Here, we present the generation and characterization of the first rat monoclonal MeCP2 specific antibodies as well as mouse monoclonal antibodies and a rabbit polyclonal antibody. We demonstrate that our antibodies are suitable for immunoblotting, (chromatin) immunoprecipitation and immunofluorescence of endogenous and ectopically expressed MeCP2. Epitope mapping revealed that most of the MeCP2 monoclonal antibodies recognize the C-terminal domain and one the N-terminal domain of MeCP2. Using slot blot analysis, we determined a high sensitivity of all antibodies, detecting amounts as low as 1 ng of MeCP2 protein. Moreover, the antibodies recognize MeCP2 from different species, including human, mouse, rat and pig. Lastly, we have validated their use by analyzing and quantifying X chromosome inactivation skewing using brain tissue of MeCP2 heterozygous null female mice. The new MeCP2 specific monoclonal antibodies described here perform well in a large variety of immunological applications making them a very valuable set of tools for studies of MeCP2 pathophysiology in situ and in vitro.
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Affiliation(s)
- K. Laurence Jost
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Andrea Rottach
- Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Manuela Milden
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Bianca Bertulat
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Annette Becker
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Patricia Wolf
- Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Paolo Petazzi
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Dori Huertas
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Elisabeth Kremmer
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Molecular Immunology, Munich, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
- * E-mail:
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