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Wu WJ, Liu KQ, Li BJ, Dong C, Zhang ZK, Li PH, Huang RH, Wei W, Chen J, Liu HL. Identification of an (AC)n microsatellite in the Six1 gene promoter and its effect on production traits in Pietrain × Duroc × Landrace × Yorkshire pigs. J Anim Sci 2018; 96:17-26. [PMID: 29432614 DOI: 10.1093/jas/skx024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 02/05/2018] [Indexed: 12/22/2022] Open
Abstract
The Sine oculis homeobox 1 (Six1) gene is important for skeletal muscle growth and fiber specification; therefore, it is considered as a promising candidate gene that may influence porcine growth and meat quality traits. Nevertheless, the association of Six1 with these processes and the mechanisms regulating its expression remain unclear. The objectives of this study were to identify variant sites of Six1 in different pig breeds, conduct association analysis to evaluate the relationship between polymorphisms of these variants and porcine production traits in Pietrain × Duroc × Landrace × Yorkshire commercial pigs, and explore the potential regulatory mechanisms of Six1 affecting production traits. A total of 12 variants were identified, including 10 single- nucleotide variations (SNVs), 1 insertion- deletion (Indel), and 1 (AC)n microsatellite. Association analysis demonstrated that the SNV, g.1595A>G, was significantly associated with meat color (redness, a*); individuals with the G allele had greater a* values (P < 0.05). Moreover, our results demonstrated that the (AC)n polymorphism in the Six1 promoter was significantly associated with weaning weight (P < 0.05), carcass weight (P < 0.05), and thoracic and lumbar back fat (P < 0.01).In addition, we found that the (AC)n variant was closely related with Six1 expression levels and demonstrated this polymorphism on promoter activity by in vitro experiments. Overall, this study provides novel evidence for elucidating the effects of Six1 on porcine production traits as promising candidate and describes two variants with these traits, which are potential reference markers for pig molecular breeding. In addition, our data on the relationship between porcine Six1 expression and the polymorphic (AC)n microsatellite in its promoter may facilitate similar studies in other species.
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Affiliation(s)
- W J Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - K Q Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - B J Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - C Dong
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Z K Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - P H Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - R H Huang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - W Wei
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - J Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - H L Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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52
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Press MO, McCoy RC, Hall AN, Akey JM, Queitsch C. Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana. Genome Res 2018; 28:1169-1178. [PMID: 29970452 PMCID: PMC6071631 DOI: 10.1101/gr.231753.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 06/26/2018] [Indexed: 11/24/2022]
Abstract
Short tandem repeat (STR) mutations may comprise more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assessed this contribution across a collection of 96 strains of Arabidopsis thaliana, genotyping 2046 STR loci each, using highly parallel STR sequencing with molecular inversion probes. We found that 95% of examined STRs are polymorphic, with a median of six alleles per STR across these strains. STR expansions (large copy number increases) are found in most strains, several of which have evident functional effects. These include three of six intronic STR expansions we found to be associated with intron retention. Coding STRs were depleted of variation relative to noncoding STRs, and we detected a total of 56 coding STRs (11%) showing low variation consistent with the action of purifying selection. In contrast, some STRs show hypervariable patterns consistent with diversifying selection. Finally, we detected 133 novel STR-phenotype associations under stringent criteria, most of which could not be detected with SNPs alone, and validated some with follow-up experiments. Our results support the conclusion that STRs constitute a large, unascertained reservoir of functionally relevant genomic variation.
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Affiliation(s)
- Maximilian O Press
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Rajiv C McCoy
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Ashley N Hall
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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53
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Yu C, Baune BT, Wong ML, Licinio J. Investigation of short tandem repeats in major depression using whole-genome sequencing data. J Affect Disord 2018; 232:305-309. [PMID: 29501989 DOI: 10.1016/j.jad.2018.02.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/02/2018] [Accepted: 02/16/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Major depressive disorder (MDD) is a leading contributor to global disease burden. Recent studies have shown that genetic factors play significant roles in the susceptibility to this condition; however, the underlying genetic basis currently remains largely unknown. Short tandem repeat (STR) has been proposed as an explanatory factor in the "missing heritability" of complex diseases or traits. METHODS We investigated STR variations from 15 MDD patients and 10 ethnically matched healthy controls based on their deep whole-genome sequencing (WGS) data. The lobSTR software was used to computationally determine STRs. RESULTS The results of the Mexican-American sample showed that STRs are significantly richer in healthy controls than in MDD cases on each of the 23 chromosomes (all false discovery rates, FDR P-values < 0.0062); while for the Australian of European-ancestry sample, there was no statistically significant STRs difference between MDD cases and controls. LIMITATIONS High quality WGS costs limited obtaining larger datasets. CONCLUSIONS This preliminary work is the first study that STR variations are applied to investigate MDD based on WGS data. The results on Mexican-American population may imply that within the same ancestry, targeted sequencing on a specific chromosome or region of genome would be sufficient for examining the relationship between STR and MDD. Further studies should examine larger sequencing datasets on other ethnic groups.
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Affiliation(s)
- Chenglong Yu
- Robinson Research Institute, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Bedford Park, SA 5042, Australia.
| | - Bernhard T Baune
- Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ma-Li Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Bedford Park, SA 5042, Australia; Department of Psychiatry, College of Medicine, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA
| | - Julio Licinio
- Department of Psychiatry, College of Medicine, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA; Departments of Pharmacology and Medicine, College of Medicine, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA
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Hannan AJ. Tandem Repeats and Repeatomes: Delving Deeper into the 'Dark Matter' of Genomes. EBioMedicine 2018; 31:3-4. [PMID: 29665999 PMCID: PMC6013752 DOI: 10.1016/j.ebiom.2018.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 11/17/2022] Open
Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia; Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria, Australia.
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Lee JK, Conrad A, Epping E, Mathews K, Magnotta V, Dawson JD, Nopoulos P. Effect of Trinucleotide Repeats in the Huntington's Gene on Intelligence. EBioMedicine 2018; 31:47-53. [PMID: 29685790 PMCID: PMC6013750 DOI: 10.1016/j.ebiom.2018.03.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 12/05/2022] Open
Abstract
Background Huntington's Disease (HD) is caused by an abnormality in the HTT gene. This gene includes trinucleotide repeats ranging from 10 to 35, and when expanded beyond 39, causes HD. We previously reported that CAG repeats in the normal range had a direct and beneficial effect on brain development with higher repeats being associated with higher cognitive function. The current study now expands this line of inquiry to evaluate the effects of CAG repeat throughout the entire spectrum of repeats from 15 to 58. Methods We evaluated brain function in children ages 6–18 years old. DNA samples were processed to quantify the number of CAG repeats within HTT. Linear regression was used to determine if number of CAG repeats predicted measures of brain function. Findings The number of repeats in HTT, had a non-linear effect on a measure of general intelligence with an inverted U shape pattern. Increasing repeat length was associated with higher GAI scores up until roughly 40–41 repeats. After this peak, increasing repeat length was associated with declining GAI scores. Interpretation HTT may confer an advantage or a disadvantage depending upon the repeat length, playing a key role in the determination of intelligence, or causing a uniquely human brain disease. The HTT gene includes trinucleotide repeats ranging from 10 to 35 in the normal population. Huntington’s disease is caused when the trinucleotide repeats in the HTT gene expand beyond the normal range. The gene is vital for brain growth in which each repeat contributes to the development of brain function, measured as intelligence. Increasing repeats are beneficial to a certain point, then becomes detrimental to intelligence, forming an inverted U relationship.
A Faustian Bargain: Could the key to the evolution of the human brain be found in a dreadful disease? Huntington's Disease is a fatal progressive brain disease caused by a single gene. Results from the current study show that the same gene is important for brain development and intelligence. Therefore, this gene may have a simultaneous advantage and disadvantage: a role in the evolution of a superior human brain, yet the disadvantage of a uniquely human brain disease.
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Affiliation(s)
- Jessica K Lee
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Amy Conrad
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Eric Epping
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Kathy Mathews
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, United States; Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Vincent Magnotta
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Jeffrey D Dawson
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Peg Nopoulos
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, United States; Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, United States; Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA, United States.
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56
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Zavodna M, Bagshaw A, Brauning R, Gemmell NJ. The effects of transcription and recombination on mutational dynamics of short tandem repeats. Nucleic Acids Res 2018; 46:1321-1330. [PMID: 29300948 PMCID: PMC5814968 DOI: 10.1093/nar/gkx1253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 11/27/2017] [Accepted: 12/27/2017] [Indexed: 01/07/2023] Open
Abstract
Short tandem repeats (STR) are ubiquitous components of the genomic architecture of most living organisms. Recent work has highlighted the widespread functional significance of such repeats, particularly around gene regulation, but the mutational processes underlying the evolution of these highly abundant and highly variable sequences are not fully understood. Traditional models assume that strand misalignment during replication is the predominant mechanism, but empirical data suggest the involvement of other processes including recombination and transcription. Despite this evidence, the relative influences of these processes have not previously been tested experimentally on a genome-wide scale. Using deep sequencing, we identify mutations at >200 microsatellites, across 700 generations in replicated populations of two otherwise identical sexual and asexual Saccharomyces cerevisiae strains. Using generalized linear models, we investigate correlates of STR mutability including the nature of the mutation, STR composition and contextual factors including recombination, transcription and replication origins. Sexual capability was not a significant predictor of microsatellite mutability, but, intriguingly, we identify transcription as a significant positive predictor. We also find that STR density is substantially increased in regions neighboring, but not within, recombination hotspots.
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Affiliation(s)
- Monika Zavodna
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Andrew Bagshaw
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Rudiger Brauning
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin 9054, New Zealand
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Abstract
Accumulating evidence suggests that many classes of DNA repeats exhibit attributes that distinguish them from other genetic variants, including the fact that they are more liable to mutation; this enables them to mediate genetic plasticity. The expansion of tandem repeats, particularly of short tandem repeats, can cause a range of disorders (including Huntington disease, various ataxias, motor neuron disease, frontotemporal dementia, fragile X syndrome and other neurological disorders), and emerging data suggest that tandem repeat polymorphisms (TRPs) can also regulate gene expression in healthy individuals. TRPs in human genomes may also contribute to the missing heritability of polygenic disorders. A better understanding of tandem repeats and their associated repeatome, as well as their capacity for genetic plasticity via both germline and somatic mutations, is needed to transform our understanding of the role of TRPs in health and disease.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne.,Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria, Australia
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58
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Gardiner SL, van Belzen MJ, Boogaard MW, van Roon-Mom WMC, Rozing MP, van Hemert AM, Smit JH, Beekman ATF, van Grootheest G, Schoevers RA, Oude Voshaar RC, Roos RAC, Comijs HC, Penninx BWJH, van der Mast RC, Aziz NA. Huntingtin gene repeat size variations affect risk of lifetime depression. Transl Psychiatry 2017; 7:1277. [PMID: 29225330 PMCID: PMC5802693 DOI: 10.1038/s41398-017-0042-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/29/2017] [Accepted: 09/15/2017] [Indexed: 11/23/2022] Open
Abstract
Huntington disease (HD) is a severe neuropsychiatric disorder caused by a cytosine-adenine-guanine (CAG) repeat expansion in the HTT gene. Although HD is frequently complicated by depression, it is still unknown to what extent common HTT CAG repeat size variations in the normal range could affect depression risk in the general population. Using binary logistic regression, we assessed the association between HTT CAG repeat size and depression risk in two well-characterized Dutch cohorts─the Netherlands Study of Depression and Anxiety and the Netherlands Study of Depression in Older Persons─including 2165 depressed and 1058 non-depressed persons. In both cohorts, separately as well as combined, there was a significant non-linear association between the risk of lifetime depression and HTT CAG repeat size in which both relatively short and relatively large alleles were associated with an increased risk of depression (β = -0.292 and β = 0.006 for the linear and the quadratic term, respectively; both P < 0.01 after adjustment for the effects of sex, age, and education level). The odds of lifetime depression were lowest in persons with a HTT CAG repeat size of 21 (odds ratio: 0.71, 95% confidence interval: 0.52 to 0.98) compared to the average odds in the total cohort. In conclusion, lifetime depression risk was higher with both relatively short and relatively large HTT CAG repeat sizes in the normal range. Our study provides important proof-of-principle that repeat polymorphisms can act as hitherto unappreciated but complex genetic modifiers of depression.
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Affiliation(s)
- Sarah L. Gardiner
- 0000000089452978grid.10419.3dDepartments of Neurology, Leiden University Medical Centre, Leiden, The Netherlands ,0000000089452978grid.10419.3dDepartments of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Martine J. van Belzen
- 0000000089452978grid.10419.3dDepartments of Clinical Genetics, and Leiden University Medical Centre, Leiden, The Netherlands
| | - Merel W. Boogaard
- 0000000089452978grid.10419.3dDepartments of Neurology, Leiden University Medical Centre, Leiden, The Netherlands ,0000000089452978grid.10419.3dDepartments of Clinical Genetics, and Leiden University Medical Centre, Leiden, The Netherlands
| | - Willeke M. C. van Roon-Mom
- 0000000089452978grid.10419.3dDepartments of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maarten P. Rozing
- 0000 0001 0674 042Xgrid.5254.6Department of Public Health, Section of Social Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Albert M. van Hemert
- 0000000089452978grid.10419.3dDepartments of Psychiatry, Leiden University Medical Centre, Leiden, The Netherlands
| | - Johannes H. Smit
- 0000 0001 0686 3219grid.466632.3Department of Psychiatry, and EMGO Institute for Health and Care Research and Neuroscience Campus Amsterdam, VU University Medical Center/GGZ inGeest, Amsterdam, The Netherlands
| | - Aartjan T. F. Beekman
- 0000 0001 0686 3219grid.466632.3Department of Psychiatry, and EMGO Institute for Health and Care Research and Neuroscience Campus Amsterdam, VU University Medical Center/GGZ inGeest, Amsterdam, The Netherlands
| | - Gerard van Grootheest
- 0000 0001 0686 3219grid.466632.3Department of Psychiatry, and EMGO Institute for Health and Care Research and Neuroscience Campus Amsterdam, VU University Medical Center/GGZ inGeest, Amsterdam, The Netherlands
| | - Robert A. Schoevers
- 0000 0000 9558 4598grid.4494.dDepartment of Psychiatry, University Medical Centre Groningen, Groningen, The Netherlands
| | - Richard C. Oude Voshaar
- 0000 0000 9558 4598grid.4494.dDepartment of Psychiatry, University Medical Centre Groningen, Groningen, The Netherlands
| | - Raymund A. C. Roos
- 0000000089452978grid.10419.3dDepartments of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hannie C. Comijs
- 0000 0001 0686 3219grid.466632.3Department of Psychiatry, and EMGO Institute for Health and Care Research and Neuroscience Campus Amsterdam, VU University Medical Center/GGZ inGeest, Amsterdam, The Netherlands
| | - Brenda W. J. H. Penninx
- 0000 0001 0686 3219grid.466632.3Department of Psychiatry, and EMGO Institute for Health and Care Research and Neuroscience Campus Amsterdam, VU University Medical Center/GGZ inGeest, Amsterdam, The Netherlands
| | - Roos C. van der Mast
- 0000000089452978grid.10419.3dDepartments of Psychiatry, Leiden University Medical Centre, Leiden, The Netherlands ,0000 0001 0790 3681grid.5284.b Department of Psychiatry, Collaborative Antwerp Psychiatric Research Institute (CAPRI), University of Antwerp, Antwerp, Belgium
| | - N. Ahmad Aziz
- 0000000089452978grid.10419.3dDepartments of Neurology, Leiden University Medical Centre, Leiden, The Netherlands ,0000000121901201grid.83440.3bDepartment of Neurodegenerative Disease, UCL Huntington’s Disease Centre, University College London Institute of Neurology, London, United Kingdom
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Kamsaeng P, Tassanakajon A, Somboonwiwat K. Regulation of antilipopolysaccharide factors, ALFPm3 and ALFPm6, in Penaeus monodon. Sci Rep 2017; 7:12694. [PMID: 28978934 PMCID: PMC5627258 DOI: 10.1038/s41598-017-12137-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/01/2017] [Indexed: 12/28/2022] Open
Abstract
ALFPm6, a member of antimicrobial peptide in the antilipopolysaccharide factor (ALF) family from Penaeus monodon, plays important roles in shrimp immunity against pathogens. However, its antimicrobial activity and underlying mechanism have not been reported. The synthetic cyclic ALFPm6#29–52 peptide (cALFPm6#29–52) corresponding to the ALFPm6 LPS-binding domain can agglutinate and exhibited bacterial killing activity toward a Gram-negative bacterium, Escherichia coli 363 and Gram-positive bacteria, Bacillus megaterium, Aerococcus viridans, and Micrococcus luteus, with MIC values of 25–50 μM. Specifically, ALFPm6 and ALFPm3, the most abundant ALF isoforms, are different in terms of gene expression patterns upon pathogen infections. Herein, the regulation of ALFPm3 and ALFPm6 gene expression was studied. The 5′-upstream and promoter sequences were identified and the putative transcription factor (TF)-binding sites were predicted. The narrow down assay indicated that the ALFPm3 promoter and partial promoter of the ALFPm6 active regions were located at nucleotide positions (−814/+302) and (−282/+85), respectively. Mutagenesis of selected TF-binding sites revealed that Rel/NF-κB (−280/−270) of ALFPm3 and C/EBPβ (−88/−78) and Sp1 (−249/−238) sites of ALFPm6 were the activator-binding sites. Knockdown of the PmMyD88 and PmRelish genes in V. harveyi-infected shrimp suggested that the ALFPm3 gene was regulated by Toll and IMD pathways, while the ALFPm6 gene was regulated by the Toll pathway.
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Affiliation(s)
- Pitchayanan Kamsaeng
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, 10330, Thailand
| | - Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, 10330, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, 10330, Thailand.
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Large normal-range TBP and ATXN7 CAG repeat lengths are associated with increased lifetime risk of depression. Transl Psychiatry 2017; 7:e1143. [PMID: 28585930 PMCID: PMC5534943 DOI: 10.1038/tp.2017.116] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 04/20/2017] [Indexed: 01/27/2023] Open
Abstract
Depression is one of the most prevalent and debilitating psychiatric disorders worldwide. Recently, we showed that both relatively short and relatively long cytosine-adenine-guanine (CAG) repeats in the huntingtin gene (HTT) are associated with an increased risk of lifetime depression. However, to what extent the variations in CAG repeat length in the other eight polyglutamine disease-associated genes (PDAGs) are associated with depression is still unknown. We determined the CAG repeat sizes of ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, TBP, ATN1 and AR in two well-characterized Dutch cohorts-the Netherlands Study of Depression and Anxiety and the Netherlands Study of Depression in Older Persons-including 2165 depressed and 1058 non-depressed individuals-aged 18-93 years. The association between PDAG CAG repeat size and the risk for depression was assessed via binary logistic regression. We found that the odds ratio (OR) for lifetime depression was significantly higher for individuals with >10, compared with subjects with ≤10, CAG repeats in both ATXN7 alleles (OR=1.90, confidence interval (CI) 1.26-2.85). For TBP we found a similar association: A CAG repeat length exceeding the median in both alleles was associated with an increased risk for lifetime depression (OR=1.33, CI 1.00-1.76). In conclusion, we observed that carriers of either ATXN7 or TBP alleles with relatively large CAG repeat sizes in both alleles had a substantially increased risk of lifetime depression. Our findings provide critical evidence for the notion that repeat polymorphisms can act as complex genetic modifiers of depression.
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Dias C, Giordano M, Frechette R, Bellone S, Polychronakos C, Legault L, Deal CL, Goodyer CG. Genetic variations at the human growth hormone receptor (GHR) gene locus are associated with idiopathic short stature. J Cell Mol Med 2017; 21:2985-2999. [PMID: 28557176 PMCID: PMC5661101 DOI: 10.1111/jcmm.13210] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
GH plays an essential role in the growing child by binding to the growth hormone receptor (GHR) on target cells and regulating multiple growth promoting and metabolic effects. Mutations in the GHR gene coding regions result in GH insensitivity (dwarfism) due to a dysfunctional receptor protein. However, children with idiopathic short stature (ISS) show growth impairment without GH or GHR defects. We hypothesized that decreased expression of the GHR gene may be involved. To test this, we investigated whether common genetic variants (microsatellites, SNPs) in regulatory regions of the GHR gene region were associated with the ISS phenotype. Genotyping of a GT‐repeat microsatellite in the GHR 5′UTR in a Montreal ISS cohort (n = 37 ISS, n = 105 controls) revealed that the incidence of the long/short (L/S) genotype was 3.3× higher in ISS children than controls (P = 0.04, OR = 3.85). In an Italian replication cohort (n = 143 ISS, n = 282 controls), the medium/short (M/S) genotype was 1.9× more frequent in the male ISS than controls (P = 0.017, OR = 2.26). In both ISS cohorts, logistic regression analysis of 27 SNPs showed an association of ISS with rs4292454, while haplotype analysis revealed specific risk haplotypes in the 3′ haploblocks. In contrast, there were no differences in GT genotype frequencies in a cohort of short stature (SS) adults versus controls (CARTaGENE: n = 168 SS, n = 207 controls) and the risk haplotype in the SS cohort was located in the most 5′ haploblock. These data suggest that the variants identified are potentially genetic markers specifically associated with the ISS phenotype.
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Affiliation(s)
- Christel Dias
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Mara Giordano
- Laboratory of Human Genetics, Department of Health Science, University of Eastern Piedmont, Novara, Italy
| | | | - Simonetta Bellone
- Division of Pediatrics, Department of Health Science, University of Eastern Piedmont, Novara, Italy
| | - Constantin Polychronakos
- Departments of Experimental Medicine, Human Genetics and Pediatrics, McGill University, Montreal, QC, Canada
| | - Laurent Legault
- Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Cheri L Deal
- CHU Ste-Justine Research Centre and Department of Pediatrics, Université de Montréal, Montreal, QC, Canada
| | - Cynthia Gates Goodyer
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada.,Departments of Experimental Medicine and Pediatrics, McGill University, Montreal, QC, Canada
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Malik N, Agarwal P, Tyagi A. Emerging functions of multi-protein complex Mediator with special emphasis on plants. Crit Rev Biochem Mol Biol 2017; 52:475-502. [DOI: 10.1080/10409238.2017.1325830] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Akhilesh Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Shin G, Grimes SM, Lee H, Lau BT, Xia LC, Ji HP. CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis. Nat Commun 2017; 8:14291. [PMID: 28169275 PMCID: PMC5309709 DOI: 10.1038/ncomms14291] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 12/15/2016] [Indexed: 11/09/2022] Open
Abstract
Microsatellites are multi-allelic and composed of short tandem repeats (STRs) with individual motifs composed of mononucleotides, dinucleotides or higher including hexamers. Next-generation sequencing approaches and other STR assays rely on a limited number of PCR amplicons, typically in the tens. Here, we demonstrate STR-Seq, a next-generation sequencing technology that analyses over 2,000 STRs in parallel, and provides the accurate genotyping of microsatellites. STR-Seq employs in vitro CRISPR-Cas9-targeted fragmentation to produce specific DNA molecules covering the complete microsatellite sequence. Amplification-free library preparation provides single molecule sequences without unique molecular barcodes. STR-selective primers enable massively parallel, targeted sequencing of large STR sets. Overall, STR-Seq has higher throughput, improved accuracy and provides a greater number of informative haplotypes compared with other microsatellite analysis approaches. With these new features, STR-Seq can identify a 0.1% minor genome fraction in a DNA mixture composed of different, unrelated samples.
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Affiliation(s)
- GiWon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, California 94305, USA
| | - Susan M Grimes
- Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, California 94304, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, California 94305, USA
| | - Billy T Lau
- Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, California 94304, USA
| | - Li C Xia
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, California 94305, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, California 94305, USA.,Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, California 94304, USA
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64
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Chen HY, Ma SL, Huang W, Ji L, Leung VHK, Jiang H, Yao X, Tang NLS. The mechanism of transactivation regulation due to polymorphic short tandem repeats (STRs) using IGF1 promoter as a model. Sci Rep 2016; 6:38225. [PMID: 27910883 PMCID: PMC5133613 DOI: 10.1038/srep38225] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/07/2016] [Indexed: 11/09/2022] Open
Abstract
Functional short tandem repeats (STR) are polymorphic in the population, and the number of repeats regulates the expression of nearby genes (known as expression STR, eSTR). STR in IGF1 promoter has been extensively studied for its association with IGF1 concentration in blood and various clinical traits and represents an important eSTR. We previously used an in-vitro luciferase reporter model to examine the interaction between STRs and SNPs in IGF1 promoter. Here, we further explored the mechanism how the number of repeats of the STR regulates gene transcription. An inverse correlation between the number of repeats and the extent of transactivation was found in a haplotype consisting of three promoter SNPs (C-STR-T-T). We showed that these adjacent SNPs located outside the STR were required for the STR to function as eSTR. The C allele of rs35767 provides a binding site for CCAAT/enhancer-binding-protein δ (C/EBPD), which is essential for the gradational transactivation property of eSTR and FOXA3 may also be involved. Therefore, we propose a mechanism in which the gradational transactivation by the eSTR is caused by the interaction of one or more transcriptional complexes located outside the STR, rather than by direct binding to a repeat motif of the STR.
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Affiliation(s)
- Holly Y Chen
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Suk Ling Ma
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wei Huang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of Pharmaceutics, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lindan Ji
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, China
| | - Vincent H K Leung
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Honglin Jiang
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Xiaoqiang Yao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Nelson L S Tang
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Laboratory of Genetics of Disease Susceptibility, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Functional Genomics and Biostatistical Computing laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
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65
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Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights. PLoS One 2016; 11:e0166854. [PMID: 27893794 PMCID: PMC5125637 DOI: 10.1371/journal.pone.0166854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 11/05/2016] [Indexed: 12/15/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSR) are abundant, highly diverse stretches of short DNA repeats present in all genomes. Tandem mono/tri/hexanucleotide repeats in the coding regions contribute to single amino acids repeats (SAARs) in the proteome. While SSRs in the coding region always result in amino acid repeats, a majority of SAARs arise due to a combination of various codons representing the same amino acid and not as a consequence of SSR events. Certain amino acids are abundant in repeat regions indicating a positive selection pressure behind the accumulation of SAARs. By analysing 22 proteomes including the human proteome, we explored the functional and structural relationship of amino acid repeats in an evolutionary context. Only ~15% of repeats are present in any known functional domain, while ~74% of repeats are present in the disordered regions, suggesting that SAARs add to the functionality of proteins by providing flexibility, stability and act as linker elements between domains. Comparison of SAAR containing proteins across species reveals that while shorter repeats are conserved among orthologs, proteins with longer repeats, >15 amino acids, are unique to the respective organism. Lysine repeats are well conserved among orthologs with respect to their length and number of occurrences in a protein. Other amino acids such as glutamic acid, proline, serine and alanine repeats are generally conserved among the orthologs with varying repeat lengths. These findings suggest that SAARs have accumulated in the proteome under positive selection pressure and that they provide flexibility for optimal folding of functional/structural domains of proteins. The insights gained from our observations can help in effective designing and engineering of proteins with novel features.
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66
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Variability in a Short Tandem Repeat Mediates Complex Epistatic Interactions in Arabidopsis thaliana. Genetics 2016; 205:455-464. [PMID: 27866166 DOI: 10.1534/genetics.116.193359] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/27/2016] [Indexed: 01/15/2023] Open
Abstract
Short tandem repeats (STRs) are hypervariable genetic elements that occur frequently in coding regions. Their high mutation rate readily generates genetic variation, contributing to adaptive evolution and human diseases. We previously reported that natural ELF3 polyglutamine variants cause reciprocal genetic incompatibilities in two divergent Arabidopsis thaliana backgrounds. Here, we dissect the genetic architecture of this incompatibility, revealing as many as four loci putatively interacting with ELF3 We were able to specifically identify one such ELF3-interacting gene, LSH9 We further used a yeast two-hybrid strategy to identify proteins whose physical interactions with ELF3 were affected by polyglutamine tract length. We found two proteins for which this was the case, ELF4 and AtGLDP1. Using these two approaches, we identify specific genetic interactions and physical mechanisms by which the ELF3 polyglutamine tract may mediate the observed genetic incompatibilities. Our work elucidates how STR variation, which is generally underascertained in population-scale sequencing, can contribute to phenotypic variation. Furthermore, our results support our proposal that highly variable STR loci can contribute to the epistatic component of heritability.
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Abstract
Genes encode components of coevolved and interconnected networks. The effect of genotype on phenotype therefore depends on genotypic context through gene interactions known as epistasis. Epistasis is important in predicting phenotype from genotype for an individual. It is also examined in population studies to identify genetic risk factors in complex traits and to predict evolution under selection. Paradoxically, the effects of genotypic context in individuals and populations are distinct and sometimes contradictory. We argue that predicting genotype from phenotype for individuals based on population studies is difficult and, especially in human genetics, likely to result in underestimating the effects of genotypic context.
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Affiliation(s)
- Timothy B Sackton
- Informatics Group, 38 Oxford Street, Harvard University, Cambridge, MA 02138, USA
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA.
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A novel polymorphic repeat in the upstream regulatory region of the estrogen-induced gene EIG121 is not associated with the risk of developing breast or endometrial cancer. BMC Res Notes 2016; 9:287. [PMID: 27230222 PMCID: PMC4882813 DOI: 10.1186/s13104-016-2086-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/11/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The estrogen-induced gene 121 (EIG121) has been associated with breast and endometrial cancers, but its mechanism of action remains unknown. In a genome-wide search for tandem repeats, we found that EIG121 contains a short tandem repeat (STR) in its upstream regulatory region which has the potential to alter gene expression. The presence of this STR has not previously been analysed in relation to breast or endometrial cancer risk. RESULTS In this study, the lengths of this STR were determined by PCR, fragment analysis and sequencing using DNA from 223 breast cancer patients, 204 endometrial cancer patients and 220 healthy controls to determine if they were associated with the risk of developing breast or endometrial cancer. We found this repeat to be highly variable with the number of copies of the AG motif ranging from 27 to 72 and having a bimodal distribution. No statistically significant association was identified between the length of this STR and the risk of developing breast or endometrial cancer or age at diagnosis. CONCLUSIONS The STR in the upstream regulatory region of EIG121 is highly polymorphic, but is not associated with the risk of developing breast or endometrial cancer in the cohorts analysed here. While this polymorphic STR in the regulatory region of EIG121 appears to have no impact on the risk of developing breast or endometrial cancer, its association with disease recurrence or overall survival remains to be determined.
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Bolton KA, Avery-Kiejda KA, Holliday EG, Attia J, Bowden NA, Scott RJ. A polymorphic repeat in the IGF1 promoter influences the risk of endometrial cancer. Endocr Connect 2016; 5:115-22. [PMID: 27090263 PMCID: PMC5002956 DOI: 10.1530/ec-16-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/18/2016] [Indexed: 01/22/2023]
Abstract
Due to the lack of high-throughput genetic assays for tandem repeats, there is a paucity of knowledge about the role they may play in disease. A polymorphic CA repeat in the promoter region of the insulin-like growth factor 1 gene (IGF1 has been studied extensively over the past 10 years for association with the risk of developing breast cancer, among other cancers, with variable results. The aim of this study was to determine if this CA repeat is associated with the risk of developing breast cancer and endometrial cancer. Using a case-control design, we analysed the length of this CA repeat in a series of breast cancer and endometrial cancer cases and compared this with a control population. Our results showed an association when both alleles were considered in breast and endometrial cancers (P=0.029 and 0.011, respectively), but this did not pass our corrected threshold for significance due to multiple testing. When the allele lengths were analysed categorically against the most common allele length of 19 CA repeats, an association was observed with the risk of endometrial cancer due to a reduction in the number of long alleles (P=0.013). This was confirmed in an analysis of the long alleles separately for endometrial cancer risk (P=0.0012). Our study found no association between the length of this polymorphic CA repeat and breast cancer risk. The significant association observed between the CA repeat length and the risk of developing endometrial cancer has not been previously reported.
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Affiliation(s)
- Katherine A Bolton
- Centre for BioinformaticsBiomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia Priority Research Centre for CancerSchool of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - Kelly A Avery-Kiejda
- Centre for BioinformaticsBiomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia Priority Research Centre for CancerSchool of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - Elizabeth G Holliday
- Centre for Clinical Epidemiology and BiostatisticsSchool of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia Clinical Research DesignIT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - John Attia
- Centre for Clinical Epidemiology and BiostatisticsSchool of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia Clinical Research DesignIT and Statistical Support Unit, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Nikola A Bowden
- Centre for BioinformaticsBiomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia Priority Research Centre for CancerSchool of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - Rodney J Scott
- Centre for BioinformaticsBiomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales, Australia Priority Research Centre for CancerSchool of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia Molecular MedicinePathology North, John Hunter Hospital, Newcastle, New South Wales, Australia Discipline of Medical GeneticsSchool of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, University Drive, Newcastle, New South Wales, Australia
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Wilkins JF, McHale PT, Gervin J, Lander AD. Survival of the Curviest: Noise-Driven Selection for Synergistic Epistasis. PLoS Genet 2016; 12:e1006003. [PMID: 27123867 PMCID: PMC4849581 DOI: 10.1371/journal.pgen.1006003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 04/01/2016] [Indexed: 11/20/2022] Open
Abstract
A major goal of human genetics is to elucidate the genetic architecture of human disease, with the goal of fueling improvements in diagnosis and the understanding of disease pathogenesis. The degree to which epistasis, or non-additive effects of risk alleles at different loci, accounts for common disease traits is hotly debated, in part because the conditions under which epistasis evolves are not well understood. Using both theory and evolutionary simulation, we show that the occurrence of common diseases (i.e. unfit phenotypes with frequencies on the order of 1%) can, under the right circumstances, be expected to be driven primarily by synergistic epistatic interactions. Conditions that are necessary, collectively, for this outcome include a strongly non-linear phenotypic landscape, strong (but not too strong) selection against the disease phenotype, and "noise" in the genotype-phenotype map that is both environmental (extrinsic, time-correlated) and developmental (intrinsic, uncorrelated) and, in both cases, neither too little nor too great. These results suggest ways in which geneticists might identify, a priori, those disease traits for which an "epistatic explanation" should be sought, and in the process better focus ongoing searches for risk alleles.
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Affiliation(s)
- Jon F. Wilkins
- Ronin Institute, Montclair, New Jersey, United States of America
| | - Peter T. McHale
- Center for Complex Biological Systems & Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, United States of America
| | - Joshua Gervin
- Center for Complex Biological Systems & Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, United States of America
| | - Arthur D. Lander
- Center for Complex Biological Systems & Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, United States of America
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71
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Burrows EL, Hannan AJ. Cognitive endophenotypes, gene-environment interactions and experience-dependent plasticity in animal models of schizophrenia. Biol Psychol 2015; 116:82-9. [PMID: 26687973 DOI: 10.1016/j.biopsycho.2015.11.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 11/26/2015] [Accepted: 11/30/2015] [Indexed: 12/22/2022]
Abstract
Schizophrenia is a devastating brain disorder caused by a complex and heterogeneous combination of genetic and environmental factors. In order to develop effective new strategies to prevent and treat schizophrenia, valid animal models are required which accurately model the disorder, and ideally provide construct, face and predictive validity. The cognitive deficits in schizophrenia represent some of the most debilitating symptoms and are also currently the most poorly treated. Therefore it is crucial that animal models are able to capture the cognitive dysfunction that characterizes schizophrenia, as well as the negative and psychotic symptoms. The genomes of mice have, prior to the recent gene-editing revolution, proven the most easily manipulable of mammalian laboratory species, and hence most genetic targeting has been performed using mouse models. Importantly, when key environmental factors of relevance to schizophrenia are experimentally manipulated, dramatic changes in the phenotypes of these animal models are often observed. We will review recent studies in rodent models which provide insight into gene-environment interactions in schizophrenia. We will focus specifically on environmental factors which modulate levels of experience-dependent plasticity, including environmental enrichment, cognitive stimulation, physical activity and stress. The insights provided by this research will not only help refine the establishment of optimally valid animal models which facilitate development of novel therapeutics, but will also provide insight into the pathogenesis of schizophrenia, thus identifying molecular and cellular targets for future preclinical and clinical investigations.
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Affiliation(s)
- Emma L Burrows
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia; Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC 3010, Australia.
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72
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Stewart AM, Nguyen M, Song C, Kalueff AV. Understanding the genetic architectonics of complex CNS traits: Lost by the association, but found in the interaction? J Psychopharmacol 2015; 29:872-7. [PMID: 26156859 DOI: 10.1177/0269881115593904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recent evidence supports the value of endophenotypes and genome-wide association studies in psychiatric genetics, and their importance for dissecting the neural pathways and molecular mechanisms of complex neuropsychiatric disorders. Continuing this important discussion, here we outline three new mechanisms by which novel classes of genes may facilitate CNS pathogenesis without directly worsening its individual 'established' endophenotypes. These putative genetic mechanisms can apply to other human disorders in general, and may also be used for designing novel effective CNS drug treatments.
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Affiliation(s)
| | - Michael Nguyen
- ZENEREI Institute, Slidell, LA, USA Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Cai Song
- Research Institute for Marine Drugs and Nutrition, College for Food Science and Technology, Guangdong Ocean University, Zhanjiang, China Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada
| | - Allan V Kalueff
- ZENEREI Institute, Slidell, LA, USA Research Institute for Marine Drugs and Nutrition, College for Food Science and Technology, Guangdong Ocean University, Zhanjiang, China Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
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73
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Etokebe GE, Zienolddiny S, Kupanovac Z, Enersen M, Balen S, Flego V, Bulat-Kardum L, Radojčić-Badovinac A, Skaug V, Bakke P, Haugen A, Dembic Z. Association of the FAM46A gene VNTRs and BAG6 rs3117582 SNP with non small cell lung cancer (NSCLC) in Croatian and Norwegian populations. PLoS One 2015; 10:e0122651. [PMID: 25884493 PMCID: PMC4401550 DOI: 10.1371/journal.pone.0122651] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 02/11/2015] [Indexed: 12/25/2022] Open
Abstract
We analyzed for associations between a variable number of tandem repeat (VNTR) polymorphism in the Family with sequence similarity 46, member A (FAM46A) gene and a single nucleotide polymorphism (rs3117582) in the BCL2-Associated Athanogene 6 (BAG6) with non small cell lung cancer in Croatian and Norwegian subjects. A total of 503 (262 Croatian and 241Norwegian) non small cell lung cancer patients and 897 controls (568 Croatian and 329 Norwegian) were analyzed. We found that the frequency of allele b (three VNTR repeats) of FAM46A gene was significantly increased in the patients compared to the healthy controls in the Croatian and the combined Croatian and Norwegian subjects. Genotype frequencies of cd (four and five VNTR repeats) and cc (four VNTR repeats homozygote) of the FAM46A gene were significantly decreased in the patients compared to the healthy controls in the Croatian and Norwegian subjects, respectively. Logistic regression analyses revealed FAM46A genotype cc to be an independent predictive factor for non small cell lung cancer risk in the Norwegian subjects after adjustment for age, gender and smoking status. This is the first study to suggest an association between the FAM46A gene VNTR polymorphisms and non small cell lung cancer. We found also that BAG6 rs3117582 SNP was associated with non small cell lung cancer in the Norwegian subjects and the combined Croatian-Norwegian subjects corroborating the earlier finding that BAG6 rs3117582 SNP was associated with lung cancer in Europeans. Logistic regression analyses revealed that genotypes and alleles of BAG6 were independent predictive factor for non small cell lung cancer risk in the Norwegian and combined Croatian-Norwegian subjects, after adjustment for age and gender.
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Affiliation(s)
- Godfrey Essien Etokebe
- Institute for Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- * E-mail:
| | - Shanbeh Zienolddiny
- Department of Chemical and Biological Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Zeljko Kupanovac
- Institute for Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Section of Pulmology, Department of Internal Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | - Morten Enersen
- Institute for Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Sanja Balen
- Institute for Transfusion Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | - Veljko Flego
- Section of Pulmology, Department of Internal Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | - Ljiljana Bulat-Kardum
- Section of Pulmology, Department of Internal Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | | | - Vidar Skaug
- Department of Chemical and Biological Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Per Bakke
- Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Aage Haugen
- Department of Chemical and Biological Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Zlatko Dembic
- Institute for Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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Alisoltani A, Fallahi H, Shiran B, Alisoltani A, Ebrahimie E. RNA-Seq SSRs and small RNA-Seq SSRs: New approaches in cancer biomarker discovery. Gene 2015; 560:34-43. [DOI: 10.1016/j.gene.2015.01.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/02/2014] [Accepted: 01/13/2015] [Indexed: 11/24/2022]
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Anisimova M, Pečerska J, Schaper E. Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Front Bioeng Biotechnol 2015; 3:31. [PMID: 25853125 PMCID: PMC4362331 DOI: 10.3389/fbioe.2015.00031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/26/2015] [Indexed: 11/13/2022] Open
Abstract
Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions and can be associated with virulence, resistance, and infectious/neurodegenerative diseases. Genome-scale systematic studies of TRs have the potential to unveil core mechanisms governing TR evolution and TR roles in shaping genomes. However, TR-related studies are often non-trivial due to heterogeneous and sometimes fast evolving TR regions. In this review, we discuss these intricacies and their consequences. We present our recent contributions to computational and statistical approaches for TR significance testing, sequence profile-based TR annotation, TR-aware sequence alignment, phylogenetic analyses of TR unit number and order, and TR benchmarks. Importantly, all these methods explicitly rely on the evolutionary definition of a tandem repeat as a sequence of adjacent repeat units stemming from a common ancestor. The discussed work has a focus on protein TRs, yet is generally applicable to nucleic acid TRs, sharing similar features.
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Affiliation(s)
- Maria Anisimova
- Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW) , Wädenswil , Switzerland
| | - Julija Pečerska
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland ; Department of Computer Science, ETH Zürich , Zürich , Switzerland
| | - Elke Schaper
- Department of Computer Science, ETH Zürich , Zürich , Switzerland ; Vital-IT Competency Center, Swiss Institute for Bioinformatics , Lausanne , Switzerland
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76
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Etokebe GE, Jotanovic Z, Mihelic R, Mulac-Jericevic B, Nikolic T, Balen S, Sestan B, Dembic Z. Susceptibility to large-joint osteoarthritis (hip and knee) is associated with BAG6 rs3117582 SNP and the VNTR polymorphism in the second exon of the FAM46A gene on chromosome 6. J Orthop Res 2015; 33:56-62. [PMID: 25231575 DOI: 10.1002/jor.22738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/25/2014] [Indexed: 02/04/2023]
Abstract
Family with sequence similarity 46, member A (FAM46A) gene VNTR and BCL2-Associated Athanogene 6 (BAG6) gene rs3117582 polymorphisms were genotyped in a case-control study with 474 large-joint (hip and knee) osteoarthritis (OA) patients and 568 controls in Croatian population by candidate-gene approach for association with OA. We found that BAG6 rs3117582 SNP genotypes were associated with protection (major allele homozygote) and susceptibility (major-minor allele heterozygote) to OA. BAG6 rs3117582 major allele (A) was associated with reduced risk to OA while the minor allele (C) was associated with increased risk to OA. We identified 6 alleles harboring 2 to 7 repeats making 20 genotypes for FAM46A. A rare FAM46A VNTR genotype comprising VNTR alleles with four and seven repeats (c/f) was associated with increased OA risk in both genders. The genotype with four and six repeats (c/e) was also associated with increased risk to OA in males. A polymorphic FAM46A allele with six repeats (e) was associated with reduced risk to OA in females. Our results suggest association between the FAM46A gene, BAG6 gene and OA in Croatian population, respectively. This is the first study to show associations between these genetic loci and OA.
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Affiliation(s)
- Godfrey E Etokebe
- Department of Oral Biology, Molecular Genetics Laboratory, University of Oslo, Oslo, 0316, Norway
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Zavodna M, Bagshaw A, Brauning R, Gemmell NJ. The accuracy, feasibility and challenges of sequencing short tandem repeats using next-generation sequencing platforms. PLoS One 2014; 9:e113862. [PMID: 25436869 PMCID: PMC4250034 DOI: 10.1371/journal.pone.0113862] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 10/31/2014] [Indexed: 12/15/2022] Open
Abstract
To date we have little knowledge of how accurate next-generation sequencing (NGS) technologies are in sequencing repetitive sequences beyond known limitations to accurately sequence homopolymers. Only a handful of previous reports have evaluated the potential of NGS for sequencing short tandem repeats (microsatellites) and no empirical study has compared and evaluated the performance of more than one NGS platform with the same dataset. Here we examined yeast microsatellite variants from both long-read (454-sequencing) and short-read (Illumina) NGS platforms and compared these to data derived through Sanger sequencing. In addition, we investigated any locus-specific biases and differences that might have resulted from variability in microsatellite repeat number, repeat motif or type of mutation. Out of 112 insertion/deletion variants identified among 45 microsatellite amplicons in our study, we found 87.5% agreement between the 454-platform and Sanger sequencing in frequency of variant detection after Benjamini-Hochberg correction for multiple tests. For a subset of 21 microsatellite amplicons derived from Illumina sequencing, the results of short-read platform were highly consistent with the other two platforms, with 100% agreement with 454-sequencing and 93.6% agreement with the Sanger method after Benjamini-Hochberg correction. We found that the microsatellite attributes copy number, repeat motif and type of mutation did not have a significant effect on differences seen between the sequencing platforms. We show that both long-read and short-read NGS platforms can be used to sequence short tandem repeats accurately, which makes it feasible to consider the use of these platforms in high-throughput genotyping. It appears the major requirement for achieving both high accuracy and rare variant detection in microsatellite genotyping is sufficient read depth coverage. This might be a challenge because each platform generates a consistent pattern of non-uniform sequence coverage, which, as our study suggests, may affect some types of tandem repeats more than others.
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Affiliation(s)
- Monika Zavodna
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- * E-mail:
| | - Andrew Bagshaw
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Rudiger Brauning
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Neil J. Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand
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78
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Rusinova GG, Glazkova IV, Azizova TV, Osovets SV, Vyazovskaya NS. Analysis of genome instability in offspring of Mayak workers’ families: Minisatellite CEB. RUSS J GENET+ 2014. [DOI: 10.1134/s102279541411012x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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79
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Wray NR, Lee SH, Mehta D, Vinkhuyzen AAE, Dudbridge F, Middeldorp CM. Research review: Polygenic methods and their application to psychiatric traits. J Child Psychol Psychiatry 2014; 55:1068-87. [PMID: 25132410 DOI: 10.1111/jcpp.12295] [Citation(s) in RCA: 456] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND Despite evidence from twin and family studies for an important contribution of genetic factors to both childhood and adult onset psychiatric disorders, identifying robustly associated specific DNA variants has proved challenging. In the pregenomics era the genetic architecture (number, frequency and effect size of risk variants) of complex genetic disorders was unknown. Empirical evidence for the genetic architecture of psychiatric disorders is emerging from the genetic studies of the last 5 years. METHODS AND SCOPE We review the methods investigating the polygenic nature of complex disorders. We provide mini-guides to genomic profile (or polygenic) risk scoring and to estimation of variance (or heritability) from common SNPs; a glossary of key terms is also provided. We review results of applications of the methods to psychiatric disorders and related traits and consider how these methods inform on missing heritability, hidden heritability and still-missing heritability. FINDINGS Genome-wide genotyping and sequencing studies are providing evidence that psychiatric disorders are truly polygenic, that is they have a genetic architecture of many genetic variants, including risk variants that are both common and rare in the population. Sample sizes published to date are mostly underpowered to detect effect sizes of the magnitude presented by nature, and these effect sizes may be constrained by the biological validity of the diagnostic constructs. CONCLUSIONS Increasing the sample size for genome wide association studies of psychiatric disorders will lead to the identification of more associated genetic variants, as already found for schizophrenia. These loci provide the starting point of functional analyses that might eventually lead to new prevention and treatment options and to improved biological validity of diagnostic constructs. Polygenic analyses will contribute further to our understanding of complex genetic traits as sample sizes increase and as sample resources become richer in phenotypic descriptors, both in terms of clinical symptoms and of nongenetic risk factors.
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Affiliation(s)
- Naomi R Wray
- Queensland Brain Institute, The University of Queensland, St Lucia, Qld, Australia
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80
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Genetic Basis of Complex Genetic Disease: The Contribution of Disease Heterogeneity to Missing Heritability. CURR EPIDEMIOL REP 2014. [DOI: 10.1007/s40471-014-0023-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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81
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Press MO, Carlson KD, Queitsch C. The overdue promise of short tandem repeat variation for heritability. Trends Genet 2014; 30:504-12. [PMID: 25182195 DOI: 10.1016/j.tig.2014.07.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 12/11/2022]
Abstract
Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. We review here the promise of STRs in contributing to complex trait heritability and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single-nucleotide variants to have epistatic interactions, reiterate the need for targeted assays to genotype STRs accurately, and call for more appropriate statistical methods in detecting STR-phenotype associations. Lastly, we suggest that somatic STR variation within individuals may serve as a read-out of disease susceptibility, and is thus potentially a valuable covariate for future association studies.
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Affiliation(s)
- Maximilian O Press
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Keisha D Carlson
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
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82
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Abstract
It is widely appreciated that short tandem repeat (STR) variation underlies substantial phenotypic variation in organisms. Some propose that the high mutation rates of STRs in functional genomic regions facilitate evolutionary adaptation. Despite their high mutation rate, some STRs show little to no variation in populations. One such STR occurs in the Arabidopsis thaliana gene PFT1 (MED25), where it encodes an interrupted polyglutamine tract. Although the PFT1 STR is large (∼270 bp), and thus expected to be extremely variable, it shows only minuscule variation across A. thaliana strains. We hypothesized that the PFT1 STR is under selective constraint, due to previously undescribed roles in PFT1 function. We investigated this hypothesis using plants expressing transgenic PFT1 constructs with either an endogenous STR or synthetic STRs of varying length. Transgenic plants carrying the endogenous PFT1 STR generally performed best in complementing a pft1 null mutant across adult PFT1-dependent traits. In stark contrast, transgenic plants carrying a PFT1 transgene lacking the STR phenocopied a pft1 loss-of-function mutant for flowering time phenotypes and were generally hypomorphic for other traits, establishing the functional importance of this domain. Transgenic plants carrying various synthetic constructs occupied the phenotypic space between wild-type and pft1 loss-of-function mutants. By varying PFT1 STR length, we discovered that PFT1 can act as either an activator or repressor of flowering in a photoperiod-dependent manner. We conclude that the PFT1 STR is constrained to its approximate wild-type length by its various functional requirements. Our study implies that there is strong selection on STRs not only to generate allelic diversity, but also to maintain certain lengths pursuant to optimal molecular function.
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83
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Paraboschi EM, Rimoldi V, Solda G, Tabaglio T, Dall'Osso C, Saba E, Vigliano M, Salviati A, Leone M, Benedetti MD, Fornasari D, Saarela J, De Jager PL, Patsopoulos NA, D'Alfonso S, Gemmati D, Duga S, Asselta R. Functional variations modulating PRKCA expression and alternative splicing predispose to multiple sclerosis. Hum Mol Genet 2014; 23:6746-61. [DOI: 10.1093/hmg/ddu392] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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84
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Lamina C, Haun M, Coassin S, Kloss-Brandstätter A, Gieger C, Peters A, Grallert H, Strauch K, Meitinger T, Kedenko L, Paulweber B, Kronenberg F. A systematic evaluation of short tandem repeats in lipid candidate genes: riding on the SNP-wave. PLoS One 2014; 9:e102113. [PMID: 25050552 PMCID: PMC4106801 DOI: 10.1371/journal.pone.0102113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/14/2014] [Indexed: 01/09/2023] Open
Abstract
Structural genetic variants as short tandem repeats (STRs) are not targeted in SNP-based association studies and thus, their possible association signals are missed. We systematically searched for STRs in gene regions known to contribute to total cholesterol, HDL cholesterol, LDL cholesterol and triglyceride levels in two independent studies (KORA F4, n = 2553 and SAPHIR, n = 1648), resulting in 16 STRs that were finally evaluated. In a combined dataset of both studies, the sum of STR alleles was regressed on each phenotype, adjusted for age and sex. The association analyses were repeated for SNPs in a 200 kb region surrounding the respective STRs in the KORA F4 Study. Three STRs were significantly associated with total cholesterol (within LDLR, the APOA1/C3/A4/A5/BUD13 gene region and ABCG5/8), five with HDL cholesterol (3 within CETP, one in LPL and one inAPOA1/C3/A4/A5/BUD13), three with LDL cholesterol (LDLR, ABCG5/8 and CETP) and two with triglycerides (APOA1/C3/A4/A5/BUD13 and LPL). None of the investigated STRs, however, showed a significant association after adjusting for the lead or adjacent SNPs within that gene region. The evaluated STRs were found to be well tagged by the lead SNP within the respective gene regions. Therefore, the STRs reflect the association signals based on surrounding SNPs. In conclusion, none of the STRs contributed additionally to the SNP-based association signals identified in GWAS on lipid traits.
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Affiliation(s)
- Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Margot Haun
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Stefan Coassin
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Anita Kloss-Brandstätter
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald Grallert
- Department of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, TechnischeUniversitätMünchen, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Lyudmyla Kedenko
- First Department of Internal Medicine, Paracelsus Private Medical University Salzburg, Salzburg, Austria
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Private Medical University Salzburg, Salzburg, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
- * E-mail:
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85
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Ananda G, Hile SE, Breski A, Wang Y, Kelkar Y, Makova KD, Eckert KA. Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes. PLoS Genet 2014; 10:e1004498. [PMID: 25033203 PMCID: PMC4102424 DOI: 10.1371/journal.pgen.1004498] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 05/28/2014] [Indexed: 01/01/2023] Open
Abstract
Interruptions of microsatellite sequences impact genome evolution and can alter disease manifestation. However, human polymorphism levels at interrupted microsatellites (iMSs) are not known at a genome-wide scale, and the pathways for gaining interruptions are poorly understood. Using the 1000 Genomes Phase-1 variant call set, we interrogated mono-, di-, tri-, and tetranucleotide repeats up to 10 units in length. We detected ∼26,000–40,000 iMSs within each of four human population groups (African, European, East Asian, and American). We identified population-specific iMSs within exonic regions, and discovered that known disease-associated iMSs contain alleles present at differing frequencies among the populations. By analyzing longer microsatellites in primate genomes, we demonstrate that single interruptions result in a genome-wide average two- to six-fold reduction in microsatellite mutability, as compared with perfect microsatellites. Centrally located interruptions lowered mutability dramatically, by two to three orders of magnitude. Using a biochemical approach, we tested directly whether the mutability of a specific iMS is lower because of decreased DNA polymerase strand slippage errors. Modeling the adenomatous polyposis coli tumor suppressor gene sequence, we observed that a single base substitution interruption reduced strand slippage error rates five- to 50-fold, relative to a perfect repeat, during synthesis by DNA polymerases α, β, or η. Computationally, we demonstrate that iMSs arise primarily by base substitution mutations within individual human genomes. Our biochemical survey of human DNA polymerase α, β, δ, κ, and η error rates within certain microsatellites suggests that interruptions are created most frequently by low fidelity polymerases. Our combined computational and biochemical results demonstrate that iMSs are abundant in human genomes and are sources of population-specific genetic variation that may affect genome stability. The genome-wide identification of iMSs in human populations presented here has important implications for current models describing the impact of microsatellite polymorphisms on gene expression. Microsatellites are short tandem repeat DNA sequences located throughout the human genome that display a high degree of inter-individual variation. This characteristic makes microsatellites an attractive tool for population genetics and forensics research. Some microsatellites affect gene expression, and mutations within such microsatellites can cause disease. Interruption mutations disrupt the perfect repeated array and are frequently associated with altered disease risk, but they have not been thoroughly studied in human genomes. We identified interrupted mono-, di-, tri- and tetranucleotide MSs (iMS) within individual genomes from African, European, Asian and American population groups. We show that many iMSs, including some within disease-associated genes, are unique to a single population group. By measuring the conservation of microsatellites between human and chimpanzee genomes, we demonstrate that interruptions decrease the probability of microsatellite mutations throughout the genome. We demonstrate that iMSs arise in the human genome by single base changes within the DNA, and provide biochemical data suggesting that these stabilizing changes may be created by error-prone DNA polymerases. Our genome-wide study supports the model in which iMSs act to stabilize individual genomes, and suggests that population-specific differences in microsatellite architecture may be an avenue by which genetic ancestry impacts individual disease risk.
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Affiliation(s)
- Guruprasad Ananda
- Department of Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Suzanne E. Hile
- Department of Pathology, Gittlen Cancer Research Foundation, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Amanda Breski
- Department of Pathology, Gittlen Cancer Research Foundation, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Yanli Wang
- Department of Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Yogeshwar Kelkar
- Department of Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Kateryna D. Makova
- Department of Biology, Penn State University, University Park, Pennsylvania, United States of America
- Center for Medical Genomics, Penn State University, University Park, Pennsylvania, United States of America
- * E-mail: (KDM); (KAE)
| | - Kristin A. Eckert
- Department of Pathology, Gittlen Cancer Research Foundation, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
- Center for Medical Genomics, Penn State University, University Park, Pennsylvania, United States of America
- * E-mail: (KDM); (KAE)
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86
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Qin L, Ma Y, Liang P, Tan Z, Li S. Differential distributions of mononucleotide repeat sequences in 256 viral genomes and its potential implications. Gene 2014; 544:159-64. [PMID: 24786215 DOI: 10.1016/j.gene.2014.04.063] [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: 02/27/2014] [Revised: 04/14/2014] [Accepted: 04/26/2014] [Indexed: 11/18/2022]
Abstract
Mononucleotide repeats (MNRs) have been systematically investigated in the genomes of eukaryotic and prokaryotic organisms. However, detailed information on the distribution of MNRs in viral genomes is limited. In this study, we examined the distributions of MNRs in 256 fully sequenced virus genomes which showed extensive variations across viral genomes, and is significantly influenced by both genome size and CG content. Furthermore, the ratio of the observed to the expected number of MNRs (O/E ratio) appears to be influenced by both the host range and genome type of a particular virus. Additionally, the densities and frequencies of MNRs in genic regions are lower than in non-coding regions, suggesting that selective pressure acts on viral genomes. We also discuss the potential functional roles that these MNR loci could play in virus genomes. To our knowledge, this is the first analysis focusing on MNRs in viruses, and our study could have potential implications for a deeper understanding of virus genome stability and the co-evolution that occurs between a virus and its host.
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Affiliation(s)
- Lü Qin
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Biology, State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Yuxin Ma
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pengbo Liang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Zhongyang Tan
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Biology, State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China.
| | - Shifang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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87
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McOmish CE, Burrows EL, Hannan AJ. Identifying novel interventional strategies for psychiatric disorders: integrating genomics, 'enviromics' and gene-environment interactions in valid preclinical models. Br J Pharmacol 2014; 171:4719-28. [PMID: 24846457 DOI: 10.1111/bph.12783] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/25/2014] [Accepted: 05/01/2014] [Indexed: 01/13/2023] Open
Abstract
Psychiatric disorders affect a substantial proportion of the population worldwide. This high prevalence, combined with the chronicity of the disorders and the major social and economic impacts, creates a significant burden. As a result, an important priority is the development of novel and effective interventional strategies for reducing incidence rates and improving outcomes. This review explores the progress that has been made to date in establishing valid animal models of psychiatric disorders, while beginning to unravel the complex factors that may be contributing to the limitations of current methodological approaches. We propose some approaches for optimizing the validity of animal models and developing effective interventions. We use schizophrenia and autism spectrum disorders as examples of disorders for which development of valid preclinical models, and fully effective therapeutics, have proven particularly challenging. However, the conclusions have relevance to various other psychiatric conditions, including depression, anxiety and bipolar disorders. We address the key aspects of construct, face and predictive validity in animal models, incorporating genetic and environmental factors. Our understanding of psychiatric disorders is accelerating exponentially, revealing extraordinary levels of genetic complexity, heterogeneity and pleiotropy. The environmental factors contributing to individual, and multiple, disorders also exhibit breathtaking complexity, requiring systematic analysis to experimentally explore the environmental mediators and modulators which constitute the 'envirome' of each psychiatric disorder. Ultimately, genetic and environmental factors need to be integrated via animal models incorporating the spatiotemporal complexity of gene-environment interactions and experience-dependent plasticity, thus better recapitulating the dynamic nature of brain development, function and dysfunction.
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Affiliation(s)
- Caitlin E McOmish
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, Vic., Australia; The Sackler Institute for Developmental Psychobiology and Department of Psychiatry, Columbia University, New York, NY, USA
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88
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Etokebe GE, Bulat-Kardum L, Munthe LA, Balen S, Dembic Z. Association of variable number of tandem repeats in the coding region of the FAM46A gene, FAM46A rs11040 SNP and BAG6 rs3117582 SNP with susceptibility to tuberculosis. PLoS One 2014; 9:e91385. [PMID: 24625963 PMCID: PMC3953334 DOI: 10.1371/journal.pone.0091385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 02/10/2014] [Indexed: 12/20/2022] Open
Abstract
We analyzed for association between the Family with sequence similarity 46, member A (FAM46A) gene (located on chromosome 6q14.1), BCL2-Associated Athanogene 6 (BAG6) gene (located on chromosome 6p21.3) and tuberculosis in Croatian Caucasian. We genotyped the FAM46A rs11040 SNP, FAM46A VNTR and BAG6 rs3117582 polymorphisms in a case-control study with 257 tuberculosis patients and 493 healthy individuals in a Croatian Caucasian population. We found that genotype FAM46A 3/3 (three VNTR repeats homozygote) was associated with susceptibility to tuberculosis (p<0.0015, Pcorr.<0.029, Odds ratio = 2.42, 95% Confidence Interval = 1.34–4.3). This association suggests that the protein domain encoded by the VNTR might be important for the function of the FAM46A protein, which, in turn, could be relevant in developing tuberculosis. In addition, we found that FAM46A rs11040 SNP:FAM46A VNTR:BAG6 haplotype 132 (G-3-C) is associated with susceptibility to tuberculosis (p<0.012, pcorr.<0.024, Odds ratio 3.45, 95% Confidence Interval = 1.26–9.74). This may suggests that the interaction between the FAM46A and BAG6 proteins may be involved in tuberculosis etiology. We found also that infection of human macrophages with heat-killed M. tuberculosis (H37Rv) led to over-expression of FAM46A (VNTR 3/4) transcript. This is the first study to show associations between the FAM46A gene VNTR polymorphisms, FAM46A rs11040 SNP:FAM46A VNTR:BAG6 haplotypes and any disease.
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Affiliation(s)
- Godfrey Essien Etokebe
- Molecular Genetics Laboratory Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- * E-mail:
| | - Ljiljana Bulat-Kardum
- Section of Pulmology, Department of Internal Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | | | - Sanja Balen
- Clinical Institute for Transfusion Medicine, Universal Hospital Center Rijeka, School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Zlatko Dembic
- Molecular Genetics Laboratory Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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89
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Fenoglio C. Genetics and Epigenetics: Basic Concepts. NEURODEGENER DIS 2014. [DOI: 10.1007/978-1-4471-6380-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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90
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Xu X, Tao Y, Fu X, Yu T, Li Y, Chen K, Ding X, Ruan K, Jing N, Hu R. ZIP-seq: genome-wide mapping of trinucleotide repeats at single-base resolution. J Mol Cell Biol 2013; 6:93-6. [PMID: 24334259 DOI: 10.1093/jmcb/mjt048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Xingxing Xu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China
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91
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Bolton KA, Ross JP, Grice DM, Bowden NA, Holliday EG, Avery-Kiejda KA, Scott RJ. STaRRRT: a table of short tandem repeats in regulatory regions of the human genome. BMC Genomics 2013; 14:795. [PMID: 24228761 PMCID: PMC3840602 DOI: 10.1186/1471-2164-14-795] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 11/05/2013] [Indexed: 11/22/2022] Open
Abstract
Background Tandem repeats (TRs) are unstable regions commonly found within genomes that have consequences for evolution and disease. In humans, polymorphic TRs are known to cause neurodegenerative and neuromuscular disorders as well as being associated with complex diseases such as diabetes and cancer. If present in upstream regulatory regions, TRs can modify chromatin structure and affect transcription; resulting in altered gene expression and protein abundance. The most common TRs are short tandem repeats (STRs), or microsatellites. Promoter located STRs are considerably more polymorphic than coding region STRs. As such, they may be a common driver of phenotypic variation. To study STRs located in regulatory regions, we have performed genome-wide analysis to identify all STRs present in a region that is 2 kilobases upstream and 1 kilobase downstream of the transcription start sites of genes. Results The Short Tandem Repeats in Regulatory Regions Table, STaRRRT, contains the results of the genome-wide analysis, outlining the characteristics of 5,264 STRs present in the upstream regulatory region of 4,441 human genes. Gene set enrichment analysis has revealed significant enrichment for STRs in cellular, transcriptional and neurological system gene promoters and genes important in ion and calcium homeostasis. The set of enriched terms has broad similarity to that seen in coding regions, suggesting that regulatory region STRs are subject to similar evolutionary pressures as STRs in coding regions and may, like coding region STRs, have an important role in controlling gene expression. Conclusions STaRRRT is a readily-searchable resource for investigating potentially polymorphic STRs that could influence the expression of any gene of interest. The processes and genes enriched for regulatory region STRs provide potential novel targets for diagnosing and treating disease, and support a role for these STRs in the evolution of the human genome.
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Affiliation(s)
| | | | | | | | | | | | - Rodney J Scott
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, NSW, Australia.
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Burrows EL, Hannan AJ. Decanalization mediating gene-environment interactions in schizophrenia and other psychiatric disorders with neurodevelopmental etiology. Front Behav Neurosci 2013; 7:157. [PMID: 24312026 PMCID: PMC3826253 DOI: 10.3389/fnbeh.2013.00157] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/21/2013] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emma L. Burrows
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, ParkvilleVIC, Australia
| | - Anthony J. Hannan
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, ParkvilleVIC, Australia
- Department of Anatomy and Neuroscience, The University of Melbourne, ParkvilleVIC, Australia
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Hannan AJ. Nature, nurture and neurobiology: Gene–environment interactions in neuropsychiatric disorders. Neurobiol Dis 2013; 57:1-4. [DOI: 10.1016/j.nbd.2013.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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95
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Dickey AM, Hall PM, Shatters RG, Mckenzie CL. Evolution and homoplasy at the Bem6 microsatellite locus in three sweetpotato whitefly (Bemisia tabaci) cryptic species. BMC Res Notes 2013; 6:249. [PMID: 23819589 PMCID: PMC3716913 DOI: 10.1186/1756-0500-6-249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/26/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The evolution of individual microsatellite loci is often complex and homoplasy is common but often goes undetected. Sequencing alleles at a microsatellite locus can provide a more complete picture of the common evolutionary mechanisms occurring at that locus and can reveal cases of homoplasy. Within species homoplasy can lead to an underestimate of differentiation among populations and among species homoplasy can produce a misleading interpretation regarding shared alleles and hybridization. This is especially problematic with cryptic species. RESULTS By sequencing alleles from three cryptic species of the sweetpotato whitefly (Bemisia tabaci), designated MEAM1, MED, and NW, the evolution of the putatively dinucleotide Bem6 (CA₈)imp microsatellite locus is inferred as one of primarily stepwise mutation occurring at four distinct heptaucleotide tandem repeats. In two of the species this pattern yields a compound tandem repeat. Homoplasy was detected both among species and within species. CONCLUSIONS In the absence of sequencing, size homoplasious alleles at the Bem6 locus lead to an overestimate of alleles shared and hybridization among cryptic species of Bemisia tabaci. Furthermore, the compound heptanucleotide motif structure of a putative dinucleotide microsatellite has implications for the nomenclature of heptanucleotide tandem repeats with step-wise evolution.
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Affiliation(s)
- Aaron M Dickey
- USDA-ARS, U.S. Horticultural Research Laboratory, 2001 South Rock Rd, Fort Pierce, FL 34945, USA
- Current address: Mid-Florida Research & Education Center, University of Florida, 2725 Binion Rd, Apopka, FL 32703, USA
| | - Paula M Hall
- Mid-Florida Research & Education Center, University of Florida, 2725 Binion Rd, Apopka, FL 32703, USA
| | - Robert G Shatters
- USDA-ARS, U.S. Horticultural Research Laboratory, 2001 South Rock Rd, Fort Pierce, FL 34945, USA
| | - Cindy L Mckenzie
- USDA-ARS, U.S. Horticultural Research Laboratory, 2001 South Rock Rd, Fort Pierce, FL 34945, USA
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96
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Brookes K. The VNTR in complex disorders: The forgotten polymorphisms? A functional way forward? Genomics 2013; 101:273-81. [DOI: 10.1016/j.ygeno.2013.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 12/16/2022]
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97
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Sawaya S, Bagshaw A, Buschiazzo E, Kumar P, Chowdhury S, Black MA, Gemmell N. Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements. PLoS One 2013; 8:e54710. [PMID: 23405090 PMCID: PMC3566118 DOI: 10.1371/journal.pone.0054710] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/18/2012] [Indexed: 12/13/2022] Open
Abstract
Tandem repeats are genomic elements that are prone to changes in repeat number and are thus often polymorphic. These sequences are found at a high density at the start of human genes, in the gene’s promoter. Increasing empirical evidence suggests that length variation in these tandem repeats can affect gene regulation. One class of tandem repeats, known as microsatellites, rapidly alter in repeat number. Some of the genetic variation induced by microsatellites is known to result in phenotypic variation. Recently, our group developed a novel method for measuring the evolutionary conservation of microsatellites, and with it we discovered that human microsatellites near transcription start sites are often highly conserved. In this study, we examined the properties of microsatellites found in promoters. We found a high density of microsatellites at the start of genes. We showed that microsatellites are statistically associated with promoters using a wavelet analysis, which allowed us to test for associations on multiple scales and to control for other promoter related elements. Because promoter microsatellites tend to be G/C rich, we hypothesized that G/C rich regulatory elements may drive the association between microsatellites and promoters. Our results indicate that CpG islands, G-quadruplexes (G4) and untranslated regulatory regions have highly significant associations with microsatellites, but controlling for these elements in the analysis does not remove the association between microsatellites and promoters. Due to their intrinsic lability and their overlap with predicted functional elements, these results suggest that many promoter microsatellites have the potential to affect human phenotypes by generating mutations in regulatory elements, which may ultimately result in disease. We discuss the potential functions of human promoter microsatellites in this context.
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Affiliation(s)
- Sterling Sawaya
- Centre for Reproduction and Genomics, Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
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98
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Burrows EL, Hannan AJ. Characterizing social behavior in genetically targeted mouse models of brain disorders. Methods Mol Biol 2013; 1017:95-104. [PMID: 23719910 DOI: 10.1007/978-1-62703-438-8_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fragile X syndrome, the leading inherited cause of mental retardation and autism spectrum disorders worldwide, is caused by a tandem repeat expansion in the FMR1 (fragile X mental retardation 1) gene. It presents with a distinct behavioral phenotype which overlaps significantly with that of autism. Emerging evidence suggests that tandem repeat polymorphisms (TRPs) might also play a key role in modulating disease susceptibility for a range of common polygenic disorders, including the broader autism spectrum of disorders (ASD) and other forms of psychiatric illness such as schizophrenia, depression, and bipolar disorder [1]. In order to understand how TRPs and associated gene mutations mediate pathogenesis, various mouse models have been generated. A crucial step in such functional genomics is high-quality behavioral and cognitive phenotyping. This chapter presents a basic behavioral battery for standardized tests for assaying social phenotypes in mouse models of brain disorders, with a focus on aggression.
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Affiliation(s)
- Emma L Burrows
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC, Australia
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99
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The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite. Genome Biol 2012; 13:R70. [PMID: 22906166 PMCID: PMC3491370 DOI: 10.1186/gb-2012-13-8-r70] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 08/20/2012] [Indexed: 12/20/2022] Open
Abstract
Background The X-linked macrosatellite DXZ4 is a large homogenous tandem repeat that in females adopts an alternative chromatin organization on the primate X chromosome in response to X-chromosome inactivation. It is packaged into heterochromatin on the active X chromosome but into euchromatin and bound by the epigenetic organizer protein CTCF on the inactive X chromosome. Because its DNA sequence diverges rapidly beyond the New World monkeys, the existence of DXZ4 outside the primate lineage is unknown. Results Here we extend our comparative genome analysis and report the identification and characterization of the mouse homolog of the macrosatellite. Furthermore, we provide evidence of DXZ4 in a conserved location downstream of the PLS3 gene in a diverse group of mammals, and reveal that DNA sequence conservation is restricted to the CTCF binding motif, supporting a central role for this protein at this locus. However, many features that characterize primate DXZ4 differ in mouse, including the overall size of the array, the mode of transcription, the chromatin organization and conservation between adjacent repeat units of DNA sequence and length. Ctcf binds Dxz4 but is not exclusive to the inactive X chromosome, as evidenced by association in some males and equal binding to both X chromosomes in trophoblast stem cells. Conclusions Characterization of Dxz4 reveals substantial differences in the organization of DNA sequence, chromatin packaging, and the mode of transcription, so the potential roles performed by this sequence in mouse have probably diverged from those on the primate X chromosome.
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100
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Horakova AH, Moseley SC, McLaughlin CR, Tremblay DC, Chadwick BP. The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome. Hum Mol Genet 2012; 21:4367-77. [PMID: 22791747 DOI: 10.1093/hmg/dds270] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The human X-linked macrosatellite DXZ4 is a large tandem repeat located at Xq23 that is packaged into heterochromatin on the male X chromosome and female active X chromosome and, in response to X chromosome, inactivation is organized into euchromatin bound by the insulator protein CCCTC-binding factor (CTCF) on the inactive X chromosome (Xi). The purpose served by this unusual epigenetic regulation is unclear, but suggests a Xi-specific gain of function for DXZ4. Other less extensive bands of euchromatin can be observed on the Xi, but the identity of the underlying DNA sequences is unknown. Here, we report the identification of two novel human X-linked tandem repeats, located 58 Mb proximal and 16 Mb distal to the macrosatellite DXZ4. Both tandem repeats are entirely contained within the transcriptional unit of novel spliced transcripts. Like DXZ4, the tandem repeats are packaged into Xi-specific CTCF-bound euchromatin. These sequences undergo frequent CTCF-dependent interactions with DXZ4 on the Xi, implicating DXZ4 as an epigenetically regulated Xi-specific structural element and providing the first putative functional attribute of a macrosatellite in the human genome.
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Affiliation(s)
- Andrea H Horakova
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
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