1
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Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 2023; 381:eadd1250. [PMID: 37733848 DOI: 10.1126/science.add1250] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.
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Affiliation(s)
- Connor A Horton
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amr M Alexandari
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael G B Hayes
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Nilay Shah
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
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2
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Kucharski M, Wirjanata G, Nayak S, Boentoro J, Dziekan JM, Assisi C, van der Pluijm RW, Miotto O, Mok S, Dondorp AM, Bozdech Z. Short tandem repeat polymorphism in the promoter region of cyclophilin 19B drives its transcriptional upregulation and contributes to drug resistance in the malaria parasite Plasmodium falciparum. PLoS Pathog 2023; 19:e1011118. [PMID: 36696458 PMCID: PMC9901795 DOI: 10.1371/journal.ppat.1011118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 02/06/2023] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Resistance of the human malaria parasites, Plasmodium falciparum, to artemisinins is now fully established in Southeast Asia and is gradually emerging in Sub-Saharan Africa. Although nonsynonymous SNPs in the pfk13 Kelch-repeat propeller (KREP) domain are clearly associated with artemisinin resistance, their functional relevance requires cooperation with other genetic factors/alterations of the P. falciparum genome, collectively referred to as genetic background. Here we provide experimental evidence that P. falciparum cyclophilin 19B (PfCYP19B) may represent one putative factor in this genetic background, contributing to artemisinin resistance via its increased expression. We show that overexpression of PfCYP19B in vitro drives limited but significant resistance to not only artemisinin but also piperaquine, an important partner drug in artemisinin-based combination therapies. We showed that PfCYP19B acts as a negative regulator of the integrated stress response (ISR) pathway by modulating levels of phosphorylated eIF2α (eIF2α-P). Curiously, artemisinin and piperaquine affect eIF2α-P in an inverse direction that in both cases can be modulated by PfCYP19B towards resistance. Here we also provide evidence that the upregulation of PfCYP19B in the drug-resistant parasites appears to be maintained by a short tandem repeat (SRT) sequence polymorphism in the gene's promoter region. These results support a model that artemisinin (and other drugs) resistance mechanisms are complex genetic traits being contributed to by altered expression of multiple genes driven by genetic polymorphism at their promoter regions.
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Affiliation(s)
- Michal Kucharski
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sourav Nayak
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Josephine Boentoro
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Christina Assisi
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Rob W. van der Pluijm
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Olivo Miotto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sachel Mok
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Arjen M. Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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3
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Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Han J, Munro JE, Kocoski A, Barry AE, Bahlo M. Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PLoS Genet 2022; 18:e1009604. [PMID: 35007277 PMCID: PMC8782505 DOI: 10.1371/journal.pgen.1009604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).
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Affiliation(s)
- Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Anthony Kocoski
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail:
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5
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Xiao X, Zhang CY, Zhang Z, Hu Z, Li M, Li T. Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution. Mol Psychiatry 2022; 27:466-475. [PMID: 34650204 DOI: 10.1038/s41380-021-01329-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 01/28/2023]
Abstract
Genome-wide association studies (GWASs) have revealed substantial genetic components comprised of single nucleotide polymorphisms (SNPs) in the heritable risk of psychiatric disorders. However, genetic risk factors not covered by GWAS also play pivotal roles in these illnesses. Tandem repeats, which are likely functional but frequently overlooked by GWAS, may account for an important proportion in the "missing heritability" of psychiatric disorders. Despite difficulties in characterizing and quantifying tandem repeats in the genome, studies have been carried out in an attempt to describe impact of tandem repeats on gene regulation and human phenotypes. In this review, we have introduced recent research progress regarding the genomic distribution and regulatory mechanisms of tandem repeats. We have also summarized the current knowledge of the genetic architecture and biological underpinnings of psychiatric disorders brought by studies of tandem repeats. These findings suggest that tandem repeats, in candidate psychiatric risk genes or in different levels of linkage disequilibrium (LD) with psychiatric GWAS SNPs and haplotypes, may modulate biological phenotypes related to psychiatric disorders (e.g., cognitive function and brain physiology) through regulating alternative splicing, promoter activity, enhancer activity and so on. In addition, many tandem repeats undergo tight natural selection in the human lineage, and likely exert crucial roles in human brain evolution. Taken together, the putative roles of tandem repeats in the pathogenesis of psychiatric disorders is strongly implicated, and using examples from previous literatures, we wish to call for further attention to tandem repeats in the post-GWAS era of psychiatric disorders.
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Affiliation(s)
- Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chu-Yi Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhonghua Hu
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Eye Center of Xiangya Hospital and Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, Hunan, China. .,National Clinical Research Center on Mental Disorders, Changsha, Hunan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Tao Li
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China.
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6
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Gharesouran J, Hosseinzadeh H, Ghafouri-Fard S, Taheri M, Rezazadeh M. STRs: Ancient Architectures of the Genome beyond the Sequence. J Mol Neurosci 2021; 71:2441-2455. [PMID: 34056692 DOI: 10.1007/s12031-021-01850-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/22/2021] [Indexed: 01/24/2023]
Abstract
Short tandem repeats (STRs) are commonly defined as short runs of repetitive nucleotides, consisting of tandemly repeating 2-6- bp motif units, which are ubiquitously distributed throughout genomes. Functional STRs are polymorphic in the population, and their variations influence gene expression, which subsequently may result in pathogenic phenotypes. To understand STR phenotypic effects and their functional roles, we describe four different mutational mechanisms including the unequal crossing-over model, gene conversion, retrotransposition mechanism and replication slippage. Due to the multi-allelic nature, small length, abundance, high variability, codominant inheritance, nearly neutral evolution, extensive genome coverage and simple assaying of STRs, these markers are widely used in various types of biological research, including population genetics studies, genome mapping, molecular epidemiology, paternity analysis and gene flow studies. In this review, we focus on the current knowledge regarding STR genomic distribution, function, mutation and applications.
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Affiliation(s)
- Jalal Gharesouran
- Molecular Genetics Division, GMG center, Tabriz, Iran.,Division of Medical Genetics, Tabriz Childrens Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Hosseinzadeh
- Molecular Genetics Division, GMG center, Tabriz, Iran.,Division of Medical Genetics, Tabriz Childrens Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Division of Medical Genetics, Tabriz Childrens Hospital, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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7
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Rivero-Hinojosa S, Kinney N, Garner HR, Rood BR. Germline microsatellite genotypes differentiate children with medulloblastoma. Neuro Oncol 2020; 22:152-162. [PMID: 31562520 PMCID: PMC6954392 DOI: 10.1093/neuonc/noz179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The germline genetic events underpinning medulloblastoma (MB) initiation, and therefore the ability to determine who is at risk, are still unknown for the majority of cases. Microsatellites are short repeated sequences that make up ~3% of the genome. Repeat lengths vary among individuals and are often nonrandomly associated with disease, including several cancers such as breast, glioma, lung, and ovarian. Due to their effects on gene function, they have been called the "tuning knobs of the genome." METHODS We have developed a novel approach for identifying a microsatellite-based signature to differentiate MB patients from controls using germline DNA. RESULTS Analyzing germline whole exome sequencing data from a training set of 120 MB subjects and 425 controls, we identified 139 individual microsatellite loci whose genotypes differ significantly between the groups. Using a genetic algorithm, we identified a subset of 43 microsatellites that distinguish MB subjects from controls with a sensitivity and specificity of 92% and 88%, respectively. This microsatellite signature was validated in an independent dataset consisting of 102 subjects and 428 controls, with comparable sensitivity and specificity of 95% and 90%, respectively. Analysis of the allele genotypes of those 139 informative loci demonstrates that their association with MB is a consequence of individual microsatellites' genotypes rather than their hypermutability. Finally, an analysis of the genes harboring these microsatellite loci reveals cellular functions important for tumorigenesis. CONCLUSION This study demonstrates that MB-specific germline microsatellite variations mark those at risk for MB development and suggests mechanisms of predisposition.
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Affiliation(s)
- Samuel Rivero-Hinojosa
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center (CNMC), Washington, DC
| | - Nicholas Kinney
- Center for Bioinformatics and Genetics, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
- Gibbs Cancer Center and Research Institute, Spartanburg, South Carolina
| | - Harold R Garner
- Center for Bioinformatics and Genetics, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
- Gibbs Cancer Center and Research Institute, Spartanburg, South Carolina
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center (CNMC), Washington, DC
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Kinney N, Kang L, Eckstrand L, Pulenthiran A, Samuel P, Anandakrishnan R, Varghese RT, Michalak P, Garner HR. Abundance of ethnically biased microsatellites in human gene regions. PLoS One 2019; 14:e0225216. [PMID: 31830051 PMCID: PMC6907796 DOI: 10.1371/journal.pone.0225216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022] Open
Abstract
Microsatellites-a type of short tandem repeat (STR)-have been used for decades as putatively neutral markers to study the genetic structure of diverse human populations. However, recent studies have demonstrated that some microsatellites contribute to gene expression, cis heritability, and phenotype. As a corollary, some microsatellites may contribute to differential gene expression and RNA/protein structure stability in distinct human populations. To test this hypothesis, we investigate genotype frequencies, functional relevance, and adaptive potential of microsatellites in five super-populations (ethnicities) drawn from the 1000 Genomes Project. We discover 3,984 ethnically-biased microsatellite loci (EBML); for each EBML at least one ethnicity has genotype frequencies statistically different from the remaining four. South Asian, East Asian, European, and American EBML show significant overlap; on the contrary, the set of African EBML is mostly unique. We cross-reference the 3,984 EBML with 2,060 previously identified expression STRs (eSTRs); repeats known to affect gene expression (64 total) are over-represented. The most significant pathway enrichments are those associated with the matrisome: a broad collection of genes encoding the extracellular matrix and its associated proteins. At least 14 of the EBML have established links to human disease. Analysis of the 3,984 EBML with respect to known selective sweep regions in the genome shows that allelic variation in some of them is likely associated with adaptive evolution.
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Affiliation(s)
- Nick Kinney
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, SC, United States of America
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, SC, United States of America
| | - Laurel Eckstrand
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, United States of America
| | - Arichanah Pulenthiran
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
| | - Peter Samuel
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
| | - Ramu Anandakrishnan
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
| | - Robin T. Varghese
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
| | - P. Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, United States of America
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Harold R. Garner
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, SC, United States of America
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9
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Li D, Zhang H, Peng S, Pan S, Tan Z. Conserved microsatellites may contribute to stem-loop structures in 5', 3' terminals of Ebolavirus genomes. Biochem Biophys Res Commun 2019; 514:726-733. [PMID: 31078274 PMCID: PMC7092875 DOI: 10.1016/j.bbrc.2019.04.192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/25/2019] [Accepted: 04/28/2019] [Indexed: 12/12/2022]
Abstract
Microsatellites (SSRs) are ubiquitous in coding and non-coding regions of the Ebolavirus genomes. We synthetically analyzed the microsatellites in whole-genome and terminal regions of 219 Ebolavirus genomes from five species. The Ebolavirus sequences were observed with small intraspecies variations and large interspecific variations, especially in the terminal non-coding regions. Only five conserved microsatellites were detected in the complete genomes, and four of them which well base-paired to help forming conserved stem-loop structures mainly appeared in the terminal non-coding regions. These results suggest that the conserved microsatellites may be evolutionary selected to form conserved secondary structures in 5′, 3′ terminals of Ebolavirus genomes. It may help to understand the biological significance of microsatellites in Ebolavirus and also other virus genomes. Conserved microsatellites mainly occurred in 5′, 3′ terminal non-coding regions. Conserved microsatellites may contribute to conserved stem-loop structures. Conserved microsatellites might be preserved under greater evolutionary pressure.
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Affiliation(s)
- Douyue Li
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Hongxi Zhang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Shan Peng
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Saichao Pan
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Zhongyang Tan
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China.
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10
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Kinney N, Titus-Glover K, Wren JD, Varghese RT, Michalak P, Liao H, Anandakrishnan R, Pulenthiran A, Kang L, Garner HR. CAGm: a repository of germline microsatellite variations in the 1000 genomes project. Nucleic Acids Res 2019; 47:D39-D45. [PMID: 30329086 PMCID: PMC6323891 DOI: 10.1093/nar/gky969] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022] Open
Abstract
The human genome harbors an abundance of repetitive DNA; however, its function continues to be debated. Microsatellites-a class of short tandem repeat-are established as an important source of genetic variation. Array length variants are common among microsatellites and affect gene expression; but, efforts to understand the role and diversity of microsatellite variation has been hampered by several challenges. Without adequate depth, both long-read and short-read sequencing may not detect the variants present in a sample; additionally, large sample sizes are needed to reveal the degree of population-level polymorphism. To address these challenges we present the Comparative Analysis of Germline Microsatellites (CAGm): a database of germline microsatellites from 2529 individuals in the 1000 genomes project. A key novelty of CAGm is the ability to aggregate microsatellite variation by population, ethnicity (super population) and gender. The database provides advanced searching for microsatellites embedded in genes and functional elements. All data can be downloaded as Microsoft Excel spreadsheets. Two use-case scenarios are presented to demonstrate its utility: a mononucleotide (A) microsatellite at the BAT-26 locus and a dinucleotide (CA) microsatellite in the coding region of FGFRL1. CAGm is freely available at http://www.cagmdb.org/.
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Affiliation(s)
- Nicholas Kinney
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060, USA
| | - Kyle Titus-Glover
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Research Program, Division of Genomics and Data Sciences Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Robin T Varghese
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060, USA
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060, USA
- One Health Research Center, Virginia-Maryland College of Veterinary Medicine, 1410 Prices Fork Rd, Blacksburg, VA 24060, USA
- Institute of Evolution,University of Haifa, Abba Khoushy Ave 199, Haifa, 3498838, Israel
| | - Han Liao
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Ramu Anandakrishnan
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060, USA
| | - Arichanah Pulenthiran
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060, USA
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060, USA
| | - Harold R Garner
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060, USA
- Gibbs Cancer Center & Research Institute, 101 E Wood St., Spartanburg, SC 29303, USA
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Corney BPA, Widnall CL, Rees DJ, Davies JS, Crunelli V, Carter DA. Regulatory Architecture of the Neuronal Cacng2/Tarpγ2 Gene Promoter: Multiple Repressive Domains, a Polymorphic Regulatory Short Tandem Repeat, and Bidirectional Organization with Co-regulated lncRNAs. J Mol Neurosci 2018; 67:282-294. [PMID: 30478755 PMCID: PMC6373327 DOI: 10.1007/s12031-018-1208-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/08/2018] [Indexed: 12/14/2022]
Abstract
CACNG2 (TARPγ2, Stargazin) is a multi-functional regulator of excitatory neurotransmission and has been implicated in the pathological processes of several brain diseases. Cacng2 function is dependent upon expression level, but currently, little is known about the molecular mechanisms that control expression of this gene. To address this deficit and investigate disease-related gene variants, we have cloned and characterized the rat Cacng2 promoter and have defined three major features: (i) multiple repressive domains that include an array of RE-1 silencing transcription factor (REST) elements, and a calcium regulatory element-binding factor (CaRF) element, (ii) a (poly-GA) short tandem repeat (STR), and (iii) bidirectional organization with expressed lncRNAs. Functional activity of the promoter was demonstrated in transfected neuronal cell lines (HT22 and PC12), but although selective removal of REST and CaRF domains was shown to enhance promoter-driven transcription, the enhanced Cacng2 promoter constructs were still about fivefold weaker than a comparable rat Synapsin-1 promoter sequence. Direct evidence of REST activity at the Cacng2 promoter was obtained through co-transfection with an established dominant-negative REST (DNR) construct. Investigation of the GA-repeat STR revealed polymorphism across both animal strains and species, and size variation was also observed in absence epilepsy disease model cohorts (Genetic Absence Epilepsy Rats, Strasbourg [GAERS] and non-epileptic control [NEC] rats). These data provide evidence of a genotype (STR)-phenotype correlation that may be unique with respect to proximal gene regulatory sequence in the demonstrated absence of other promoter, or 3' UTR variants in GAERS rats. However, although transcriptional regulatory activity of the STR was demonstrated in further transfection studies, we did not find a GAERS vs. NEC difference, indicating that this specific STR length variation may only be relevant in the context of other (Cacna1h and Kcnk9) gene variants in this disease model. Additional studies revealed further (bidirectional) complexity at the Cacng2 promoter, and we identified novel, co-regulated, antisense rat lncRNAs that are paired with Cacng2 mRNA. These studies have provided novel insights into the organization of a synaptic protein gene promoter, describing multiple repressive and modulatory domains that can mediate diverse regulatory inputs.
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Affiliation(s)
- B P A Corney
- School of Biosciences, Cardiff University, CF103AX, Cardiff, UK
| | - C L Widnall
- School of Biosciences, Cardiff University, CF103AX, Cardiff, UK
| | - D J Rees
- Molecular Neurobiology, Institute of Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - J S Davies
- Molecular Neurobiology, Institute of Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - V Crunelli
- School of Biosciences, Cardiff University, CF103AX, Cardiff, UK
| | - D A Carter
- School of Biosciences, Cardiff University, CF103AX, Cardiff, UK.
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12
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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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13
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Dahlhaus R. Of Men and Mice: Modeling the Fragile X Syndrome. Front Mol Neurosci 2018; 11:41. [PMID: 29599705 PMCID: PMC5862809 DOI: 10.3389/fnmol.2018.00041] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022] Open
Abstract
The Fragile X Syndrome (FXS) is one of the most common forms of inherited intellectual disability in all human societies. Caused by the transcriptional silencing of a single gene, the fragile x mental retardation gene FMR1, FXS is characterized by a variety of symptoms, which range from mental disabilities to autism and epilepsy. More than 20 years ago, a first animal model was described, the Fmr1 knock-out mouse. Several other models have been developed since then, including conditional knock-out mice, knock-out rats, a zebrafish and a drosophila model. Using these model systems, various targets for potential pharmaceutical treatments have been identified and many treatments have been shown to be efficient in preclinical studies. However, all attempts to turn these findings into a therapy for patients have failed thus far. In this review, I will discuss underlying difficulties and address potential alternatives for our future research.
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Affiliation(s)
- Regina Dahlhaus
- Institute for Biochemistry, Emil-Fischer Centre, University of Erlangen-Nürnberg, Erlangen, Germany
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14
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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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15
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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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16
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Kinney N, Varghese RT, Anandakrishnan R, Garner HR“S. ZDHHC3 as a Risk and Mortality Marker for Breast Cancer in African American Women. Cancer Inform 2017; 16:1176935117746644. [PMID: 29276372 PMCID: PMC5734450 DOI: 10.1177/1176935117746644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/26/2017] [Indexed: 11/16/2022] Open
Abstract
African American woman are 43% more likely to die from breast cancer than white women and have increased the risk of tumor recurrence despite lower incidence. We investigate variations in microsatellite genomic regions-a type of repetitive DNA-and possible links to the breast cancer mortality gap. We screen 33 854 microsatellites in germline DNA of African American women with and without breast cancer: 4 are statistically significant. These are located in the 3' UTR (untranslated region) of gene ZDHHC3, an intron of transcribed pseudogene INTS4L1, an intron of ribosomal gene RNA5-8S5, and an intergenic region of chromosome 16. The marker in ZDHHC3 is interesting for 3 reasons: (a) the ZDHHC3 gene is located in region 3p21 which has already been linked to early invasive breast cancer, (b) the Kaplan-Meier estimator demonstrates that ZDHHC3 alterations are associated with poor breast cancer survival in all racial/ethnic groups combined, and (c) data from cBioPortal suggest that ZDHHC3 messenger RNA expression is significantly lower in African Americans compared with whites. These independent lines of evidence make ZDHHC3 a candidate for further investigation.
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Affiliation(s)
- Nick Kinney
- Center for Bioinformatics and Genetics & Primary Care Research Network, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Robin T Varghese
- Center for Bioinformatics and Genetics & Primary Care Research Network, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Ramu Anandakrishnan
- Center for Bioinformatics and Genetics & Primary Care Research Network, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Harold R “Skip” Garner
- Center for Bioinformatics and Genetics & Primary Care Research Network, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Gibbs Cancer Center & Research Institute, Spartanburg, SC, USA
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17
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Bagshaw AT. Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes. Genome Biol Evol 2017; 9:2428-2443. [PMID: 28957459 PMCID: PMC5622345 DOI: 10.1093/gbe/evx164] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2017] [Indexed: 02/06/2023] Open
Abstract
Microsatellite repeat DNA is best known for its length mutability, which is implicated in several neurological diseases and cancers, and often exploited as a genetic marker. Less well-known is the body of work exploring the widespread and surprisingly diverse functional roles of microsatellites. Recently, emerging evidence includes the finding that normal microsatellite polymorphism contributes substantially to the heritability of human gene expression on a genome-wide scale, calling attention to the task of elucidating the mechanisms involved. At present, these are underexplored, but several themes have emerged. I review evidence demonstrating roles for microsatellites in modulation of transcription factor binding, spacing between promoter elements, enhancers, cytosine methylation, alternative splicing, mRNA stability, selection of transcription start and termination sites, unusual structural conformations, nucleosome positioning and modification, higher order chromatin structure, noncoding RNA, and meiotic recombination hot spots.
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18
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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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19
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Bagshaw ATM, Horwood LJ, Fergusson DM, Gemmell NJ, Kennedy MA. Microsatellite polymorphisms associated with human behavioural and psychological phenotypes including a gene-environment interaction. BMC MEDICAL GENETICS 2017; 18:12. [PMID: 28158988 PMCID: PMC5291968 DOI: 10.1186/s12881-017-0374-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/25/2017] [Indexed: 02/05/2023]
Abstract
Background The genetic and environmental influences on human personality and behaviour are a complex matter of ongoing debate. Accumulating evidence indicates that short tandem repeats (STRs) in regulatory regions are good candidates to explain heritability not accessed by genome-wide association studies. Methods We tested for associations between the genotypes of four selected repeats and 18 traits relating to personality, behaviour, cognitive ability and mental health in a well-studied longitudinal birth cohort (n = 458-589) using one way analysis of variance. The repeats were a highly conserved poly-AC microsatellite in the upstream promoter region of the T-box brain 1 (TBR1) gene and three previously studied STRs in the activating enhancer-binding protein 2-beta (AP2-β) and androgen receptor (AR) genes. Where significance was found we used multiple regression to assess the influence of confounding factors. Results Carriers of the shorter, most common, allele of the AR gene’s GGN microsatellite polymorphism had fewer anxiety-related symptoms, which was consistent with previous studies, but in our study this was not significant following Bonferroni correction. No associations with two repeats in the AP2-β gene withstood this correction. A novel finding was that carriers of the minor allele of the TBR1 AC microsatellite were at higher risk of conduct problems in childhood at age 7-9 (p = 0.0007, which did pass Bonferroni correction). Including maternal smoking during pregnancy (MSDP) in models controlling for potentially confounding influences showed that an interaction between TBR1 genotype and MSDP was a significant predictor of conduct problems in childhood and adolescence (p < 0.001), and of self-reported criminal behaviour up to age 25 years (p ≤ 0.02). This interaction remained significant after controlling for possible confounders including maternal age at birth, socio-economic status and education, and offspring birth weight. Conclusions The potential functional importance of the TBR1 gene’s promoter microsatellite deserves further investigation. Our results suggest that it participates in a gene-environment interaction with MDSP and antisocial behaviour. However, previous evidence that mothers who smoke during pregnancy carry genes for antisocial behaviour suggests that epistasis may influence the interaction. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0374-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew T M Bagshaw
- Department of Pathology, University of Otago, Christchurch, PO Box 4345, Christchurch, New Zealand.
| | - L John Horwood
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - David M Fergusson
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Gravida - National Centre for Growth and Development, University of Otago, Dunedin, New Zealand
| | - Martin A Kennedy
- Department of Pathology, University of Otago, Christchurch, PO Box 4345, Christchurch, New Zealand
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20
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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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21
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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: 16] [Impact Index Per Article: 2.0] [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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22
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George B, George B, awasthi M, Singh RN. Genome wide survey and analysis of microsatellites in Tombusviridae family. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0295-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Abstract
MOTIVATION Resolving tandemly repeated genomic sequences is a necessary step in improving our understanding of the human genome. Short tandem repeats (TRs), or microsatellites, are often used as molecular markers in genetics, and clinically, variation in microsatellites can lead to genetic disorders like Huntington's diseases. Accurately resolving repeats, and in particular TRs, remains a challenging task in genome alignment, assembly and variation calling. Though tools have been developed for detecting microsatellites in short-read sequencing data, these are limited in the size and types of events they can resolve. Single-molecule sequencing technologies may potentially resolve a broader spectrum of TRs given their increased length, but require new approaches given their significantly higher raw error profiles. However, due to inherent error profiles of the single-molecule technologies, these reads presents a unique challenge in terms of accurately identifying and estimating the TRs. RESULTS Here we present PacmonSTR, a reference-based probabilistic approach, to identify the TR region and estimate the number of these TR elements in long DNA reads. We present a multistep approach that requires as input, a reference region and the reference TR element. Initially, the TR region is identified from the long DNA reads via a 3-stage modified Smith-Waterman approach and then, expected number of TR elements is calculated using a pair-Hidden Markov Models-based method. Finally, TR-based genotype selection (or clustering: homozygous/heterozygous) is performed with Gaussian mixture models, using the Akaike information criteria, and coverage expectations.
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Affiliation(s)
- Ajay Ummat
- Department of Genetics and Genomic Science and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ali Bashir
- Department of Genetics and Genomic Science and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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24
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George B, Gnanasekaran P, Jain SK, Chakraborty S. Genome wide survey and analysis of small repetitive sequences in caulimoviruses. INFECTION GENETICS AND EVOLUTION 2014; 27:15-24. [PMID: 24999243 DOI: 10.1016/j.meegid.2014.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 06/01/2014] [Accepted: 06/22/2014] [Indexed: 12/19/2022]
Abstract
Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life including viruses. Members of the Caulimoviridae family severely affect growth of vegetable and fruit plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 44 species of Caulimoviridae. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, mono- and dinucleotide repeats were found to be highly predominant and are overrepresented in genome of majority of caulimoviruses. AT/TA and GAA/AAG/AGA was the most abundant di- and trinucleotide repeat motif, respectively. Repeats larger than trinucleotide were rarely found in these genomes. Comparative study of occurrence, abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were least abundant in genomes of caulimoviruses. Polymorphic repeats even though rare were observed in the large intergenic region of the genome, indicating strand slippage and/or unequal recombination processes do occur in caulimoviruses. To our knowledge, this is the first analysis of microsatellites occurring in any dsDNA viral genome. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.
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Affiliation(s)
- Biju George
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Prabu Gnanasekaran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - S K Jain
- Department of Biotechnology, Jamia Hamdard University, New Delhi, Delhi 110062, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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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: 108] [Impact Index Per Article: 9.8] [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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