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ffrench-Constant RH. Transposable elements and xenobiotic resistance. FRONTIERS IN INSECT SCIENCE 2023; 3:1178212. [PMID: 38469483 PMCID: PMC10926513 DOI: 10.3389/finsc.2023.1178212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/24/2023] [Indexed: 03/13/2024]
Abstract
Transposable elements or TEs are well known drivers of adaptive change in plants and animals but their role in insecticide resistance remains poorly documented. This review examines the potential role of transposons in resistance and identifies key areas where our understanding remains unclear. Despite well-known model systems such as upregulation of Drosophila Cyp6g1, many putative examples lack functional validation. The potential types of transposon-associated changes that could lead to resistance are reviewed, including changes in up-regulation, message stability, loss of function and alternative splicing. Where potential mechanisms appear absent from the resistance literature examples are drawn from other areas of biology. Finally, ways are suggested in which transgenic expression could be used to validate the biological significance of TE insertion. In the absence of such functional expression studies many examples of the association of TEs and resistance genes therefore remain as correlations.
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2
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New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork. Genes (Basel) 2022; 13:genes13040614. [PMID: 35456420 PMCID: PMC9024903 DOI: 10.3390/genes13040614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/18/2022] Open
Abstract
Gene-by-environment interactions are important for all facets of biology, especially behaviour. Families of isogenic strains of mice, such as the BXD strains, are excellently placed to study these interactions, as the same genome can be tested in multiple environments. BXD strains are recombinant inbred mouse strains derived from crossing two inbred strains—C57BL/6J and DBA/2J mice. Many reproducible genometypes can be leveraged, and old data can be reanalysed with new tools to produce novel insights. We obtained drug and behavioural phenotypes from Philip et al. Genes, Brain and Behaviour 2010, and reanalysed their data with new genotypes from sequencing, as well as new models (Genome-wide Efficient Mixed Model Association (GEMMA) and R/qtl2). We discovered QTLs on chromosomes 3, 5, 9, 11, and 14, not found in the original study. We reduced the candidate genes based on their ability to alter gene expression or protein function. Candidate genes included Slitrk6 and Cdk14. Slitrk6, in a Chromosome14 QTL for locomotion, was found to be part of a co-expression network involved in voluntary movement and associated with neuropsychiatric phenotypes. Cdk14, one of only three genes in a Chromosome5 QTL, is associated with handling induced convulsions after ethanol treatment, that is regulated by the anticonvulsant drug valproic acid. By using families of isogenic strains, we can reanalyse data to discover novel candidate genes involved in response to drugs of abuse.
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3
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Ashbrook DG, Arends D, Prins P, Mulligan MK, Roy S, Williams EG, Lutz CM, Valenzuela A, Bohl CJ, Ingels JF, McCarty MS, Centeno AG, Hager R, Auwerx J, Lu L, Williams RW. A platform for experimental precision medicine: The extended BXD mouse family. Cell Syst 2021; 12:235-247.e9. [PMID: 33472028 PMCID: PMC7979527 DOI: 10.1016/j.cels.2020.12.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/29/2020] [Accepted: 12/21/2020] [Indexed: 12/17/2022]
Abstract
The challenge of precision medicine is to model complex interactions among DNA variants, phenotypes, development, environments, and treatments. We address this challenge by expanding the BXD family of mice to 140 fully isogenic strains, creating a uniquely powerful model for precision medicine. This family segregates for 6 million common DNA variants-a level that exceeds many human populations. Because each member can be replicated, heritable traits can be mapped with high power and precision. Current BXD phenomes are unsurpassed in coverage and include much omics data and thousands of quantitative traits. BXDs can be extended by a single-generation cross to as many as 19,460 isogenic F1 progeny, and this extended BXD family is an effective platform for testing causal modeling and for predictive validation. BXDs are a unique core resource for the field of experimental precision medicine.
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Affiliation(s)
- David G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Danny Arends
- Lebenswissenschaftliche Fakultät, Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Megan K Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan G Williams
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Cathleen M Lutz
- Mouse Repository and the Rare and Orphan Disease Center, the Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Alicia Valenzuela
- Mouse Repository and the Rare and Orphan Disease Center, the Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Casey J Bohl
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jesse F Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Melinda S McCarty
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Arthur G Centeno
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Reinmar Hager
- Division of Evolution & Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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4
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Anderson KR, Harris JA, Ng L, Prins P, Memar S, Ljungquist B, Fürth D, Williams RW, Ascoli GA, Dumitriu D. Highlights from the Era of Open Source Web-Based Tools. J Neurosci 2021; 41:927-936. [PMID: 33472826 PMCID: PMC7880282 DOI: 10.1523/jneurosci.1657-20.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/22/2020] [Accepted: 11/29/2020] [Indexed: 12/20/2022] Open
Abstract
High digital connectivity and a focus on reproducibility are contributing to an open science revolution in neuroscience. Repositories and platforms have emerged across the whole spectrum of subdisciplines, paving the way for a paradigm shift in the way we share, analyze, and reuse vast amounts of data collected across many laboratories. Here, we describe how open access web-based tools are changing the landscape and culture of neuroscience, highlighting six free resources that span subdisciplines from behavior to whole-brain mapping, circuits, neurons, and gene variants.
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Affiliation(s)
- Kristin R Anderson
- Departments of Pediatrics and Psychiatry, Columbia University, New York, New York 10032
- Division of Developmental Psychobiology, New York State Psychiatric Institute, New York, New York 10032
- The Sackler Institute for Developmental Psychobiology, Columbia University, New York, New York 10032
- Columbia Population Research Center, Columbia University, New York, New York 10027
- Zuckerman Institute, Columbia University, New York, New York 10027
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, Washington 98109
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington 98109
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Sara Memar
- Robarts Research Institute, BrainsCAN, Schulich School of Medicine & Dentistry, Western University, London, Ontario N6A 3K7, Canada
| | - Bengt Ljungquist
- Center for Neural Informatics, Structures, and Plasticity, Krasnow Institute for Advanced Study; and Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, Virginia 22030
| | - Daniel Fürth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures, and Plasticity, Krasnow Institute for Advanced Study; and Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, Virginia 22030
| | - Dani Dumitriu
- Departments of Pediatrics and Psychiatry, Columbia University, New York, New York 10032
- Division of Developmental Psychobiology, New York State Psychiatric Institute, New York, New York 10032
- The Sackler Institute for Developmental Psychobiology, Columbia University, New York, New York 10032
- Columbia Population Research Center, Columbia University, New York, New York 10027
- Zuckerman Institute, Columbia University, New York, New York 10027
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5
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Jones BC, Miller DB, Lu L, Zhao W, Ashbrook DG, Xu F, Mulligan MK, Williams RW, Zhuang D, Torres-Rojas C, O’Callaghan JP. Modeling the Genetic Basis of Individual Differences in Susceptibility to Gulf War Illness. Brain Sci 2020; 10:brainsci10030143. [PMID: 32131477 PMCID: PMC7139661 DOI: 10.3390/brainsci10030143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 01/22/2023] Open
Abstract
Between 25% and 30% of the nearly one million military personnel who participated in the 1991 Persian Gulf War became ill with chronic symptoms ranging from gastrointestinal to nervous system dysfunction. This disorder is now referred to as Gulf War Illness (GWI) and the underlying pathophysiology has been linked to exposure-based neuroinflammation caused by organophosphorous (OP) compounds coupled with high circulating glucocorticoids. In a mouse model of GWI we developed, corticosterone was shown to act synergistically with an OP (diisopropylflurophosphate) to dramatically increase proinflammatory cytokine gene expression in the brain. Because not all Gulf War participants became sick, the question arises as to whether differential genetic constitution might underlie individual differences in susceptibility. To address this question of genetic liability, we tested the impact of OP and glucocorticoid exposure in a genetic reference population of 30 inbred mouse strains. We also studied both sexes. The results showed wide differences among strains and overall that females were less sensitive to the combined treatment than males. Furthermore, we identified one OP-glucocorticoid locus and nominated a candidate gene-Spon1-that may underlie the marked differences in response.
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Affiliation(s)
- Byron C. Jones
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
- Correspondence: (B.C.J.); (J.P.O.); Tel.: +901-448-2814 (B.C.J.); +304-285-6079 (J.P.O.)
| | - Diane B. Miller
- Molecular Neurotoxicology Laboratory, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA;
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
| | - Wenyuan Zhao
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
| | - Daming Zhuang
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
| | - Carolina Torres-Rojas
- Department of Genetics, Genomics and Informatics, Department of Pharmacology, University of Tennessee Health Science Center, 71 South Manassas Street, Memphis, TN 38163, USA; (L.L.); (W.Z.); (D.G.A.); (F.X.); (M.K.M.); (R.W.W.); (D.Z.); (C.T.-R.)
| | - James P. O’Callaghan
- Molecular Neurotoxicology Laboratory, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA;
- Correspondence: (B.C.J.); (J.P.O.); Tel.: +901-448-2814 (B.C.J.); +304-285-6079 (J.P.O.)
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6
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Parks C, Giorgianni F, Jones BC, Beranova-Giorgianni S, Moore Ii BM, Mulligan MK. Comparison and Functional Genetic Analysis of Striatal Protein Expression Among Diverse Inbred Mouse Strains. Front Mol Neurosci 2019; 12:128. [PMID: 31178692 PMCID: PMC6543464 DOI: 10.3389/fnmol.2019.00128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/01/2019] [Indexed: 11/19/2022] Open
Abstract
C57BL/6J (B6) and DBA/2J (D2) inbred mouse strains are highly variable genetically and differ in a large number of behavioral traits related to striatal function, including depression, anxiety, stress response, and response to drugs of abuse. The genetic basis of these phenotypic differences are, however, unknown. Here, we present a comparison of the striatal proteome between B6 and D2 and relate differences at the protein level to strain differences at the mRNA level. We also leverage a recombinant inbred BXD population derived from B6 and D2 strains to investigate the role of genetic variation on the regulation of mRNA and protein levels. Finally, we test the hypothesis that differential protein expression contributes to differential behavioral responses between the B6 and D2 strain. We detected the expression of over 2,500 proteins in membrane-enriched protein fractions from B6 and D2 striatum. Of these, 160 proteins demonstrated significant differential expression between B6 and D2 strains at a 10% false discovery level, including COMT, GABRA2, and cannabinoid receptor 1 (CNR1)—key proteins involved in synaptic transmission and behavioral response. Similar to previous reports, there was little overlap between protein and transcript levels (25%). However, the overlap was greater (51%) for proteins demonstrating genetic regulation of cognate gene expression. We also found that striatal proteins with significantly higher or lower relative expression in B6 and D2 were enriched for dopaminergic and glutamatergic synapses and processes involved in synaptic plasticity [e.g., long-term potentiation (LTP) and long-term depression (LTD)]. Finally, we validated higher expression of CNR1 in B6 striatum and demonstrated greater sensitivity of this strain to the locomotor inhibiting effects of the CNR1 agonist, Δ9-tetrahydrocannabinol (THC). Our study is the first comparison of differences in striatal proteins between the B6 and D2 strains and suggests that alterations in the striatal proteome may underlie strain differences in related behaviors, such as drug response. Furthermore, we propose that genetic variants that impact transcript levels are more likely to also exhibit differential expression at the protein level.
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Affiliation(s)
- Cory Parks
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN, United States
| | - Francesco Giorgianni
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center (UTHSC), Memphis, TN, United States
| | - Byron C Jones
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN, United States
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center (UTHSC), Memphis, TN, United States
| | - Bob M Moore Ii
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center (UTHSC), Memphis, TN, United States
| | - Megan K Mulligan
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, TN, United States
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7
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Gagnier L, Belancio VP, Mager DL. Mouse germ line mutations due to retrotransposon insertions. Mob DNA 2019; 10:15. [PMID: 31011371 PMCID: PMC6466679 DOI: 10.1186/s13100-019-0157-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/01/2019] [Indexed: 12/24/2022] Open
Abstract
Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.
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Affiliation(s)
- Liane Gagnier
- 1Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| | - Victoria P Belancio
- 2Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - Dixie L Mager
- 1Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
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8
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Mulligan MK, Abreo T, Neuner SM, Parks C, Watkins CE, Houseal MT, Shapaker TM, Hook M, Tan H, Wang X, Ingels J, Peng J, Lu L, Kaczorowski CC, Bryant CD, Homanics GE, Williams RW. Identification of a Functional Non-coding Variant in the GABA A Receptor α2 Subunit of the C57BL/6J Mouse Reference Genome: Major Implications for Neuroscience Research. Front Genet 2019; 10:188. [PMID: 30984232 PMCID: PMC6449455 DOI: 10.3389/fgene.2019.00188] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
GABA type-A (GABA-A) receptors containing the α2 subunit (GABRA2) are expressed in most brain regions and are critical in modulating inhibitory synaptic function. Genetic variation at the GABRA2 locus has been implicated in epilepsy, affective and psychiatric disorders, alcoholism and drug abuse. Gabra2 expression varies as a function of genotype and is modulated by sequence variants in several brain structures and populations, including F2 crosses originating from C57BL/6J (B6J) and the BXD recombinant inbred family derived from B6J and DBA/2J. Here we demonstrate a global reduction of GABRA2 brain protein and mRNA in the B6J strain relative to other inbred strains, and identify and validate the causal mutation in B6J. The mutation is a single base pair deletion located in an intron adjacent to a splice acceptor site that only occurs in the B6J reference genome. The deletion became fixed in B6J between 1976 and 1991 and is now pervasive in many engineered lines, BXD strains generated after 1991, the Collaborative Cross, and the majority of consomic lines. Repair of the deletion using CRISPR-Cas9-mediated gene editing on a B6J genetic background completely restored brain levels of GABRA2 protein and mRNA. Comparison of transcript expression in hippocampus, cortex, and striatum between B6J and repaired genotypes revealed alterations in GABA-A receptor subunit expression, especially in striatum. These results suggest that naturally occurring variation in GABRA2 levels between B6J and other substrains or inbred strains may also explain strain differences in anxiety-like or alcohol and drug response traits related to striatal function. Characterization of the B6J private mutation in the Gabra2 gene is of critical importance to molecular genetic studies in neurobiological research because this strain is widely used to generate genetically engineered mice and murine genetic populations, and is the most widely utilized strain for evaluation of anxiety-like, depression-like, pain, epilepsy, and drug response traits that may be partly modulated by GABRA2 function.
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Affiliation(s)
- Megan K Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Timothy Abreo
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Sarah M Neuner
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States.,The Jackson Laboratory, Bar Harbor, ME, United States
| | - Cory Parks
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Christine E Watkins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - M Trevor Houseal
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Thomas M Shapaker
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Michael Hook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Haiyan Tan
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Xusheng Wang
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Jesse Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | | | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, United States
| | - Gregg E Homanics
- Departments of Anesthesiology and Perioperative Medicine, Neurobiology, and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
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9
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Harrison BJ, Park JW, Gomes C, Petruska JC, Sapio MR, Iadarola MJ, Chariker JH, Rouchka EC. Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs. Front Genet 2019; 10:182. [PMID: 30915105 PMCID: PMC6422928 DOI: 10.3389/fgene.2019.00182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 01/08/2023] Open
Abstract
The length of untranslated regions at the 3' end of transcripts (3'UTRs) is regulated by alternate polyadenylation (APA). 3'UTRs contain regions that harbor binding motifs for regulatory molecules. However, the mechanisms that coordinate the 3'UTR length of specific groups of transcripts are not well-understood. We therefore developed a method, CSI-UTR, that models 3'UTR structure as tandem segments between functional alternative-polyadenylation sites (termed cleavage site intervals-CSIs). This approach facilitated (1) profiling of 3'UTR isoform expression changes and (2) statistical enrichment of putative regulatory motifs. CSI-UTR analysis is UTR-annotation independent and can interrogate legacy data generated from standard RNA-Seq libraries. CSI-UTR identified a set of CSIs in human and rodent transcriptomes. Analysis of RNA-Seq datasets from neural tissue identified differential expression events within 3'UTRs not detected by standard gene-based differential expression analyses. Further, in many instances 3'UTR and CDS from the same gene were regulated differently. This modulation of motifs for RNA-interacting molecules with potential condition-dependent and tissue-specific RNA binding partners near the polyA signal and CSI junction may play a mechanistic role in the specificity of alternative polyadenylation. Source code, CSI BED files and example datasets are available at: https://github.com/UofLBioinformatics/CSI-UTR.
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Affiliation(s)
- Benjamin J Harrison
- Department of Biomedical Sciences, Center for Excellence in the Neurosciences, College of Osteopathic Medicine, University of New England, Biddeford, ME, United States.,Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States
| | - Juw Won Park
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States.,Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, United States
| | - Cynthia Gomes
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States
| | - Jeffrey C Petruska
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, United States.,Department of Neurological Surgery, University of Louisville, Louisville, KY, United States
| | - Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Julia H Chariker
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States.,Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, United States
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10
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Ashbrook DG, Mulligan MK, Williams RW. Post-genomic behavioral genetics: From revolution to routine. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12441. [PMID: 29193773 PMCID: PMC5876106 DOI: 10.1111/gbb.12441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/02/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022]
Abstract
What was once expensive and revolutionary-full-genome sequence-is now affordable and routine. Costs will continue to drop, opening up new frontiers in behavioral genetics. This shift in costs from the genome to the phenome is most notable in large clinical studies of behavior and associated diseases in cohorts that exceed hundreds of thousands of subjects. Examples include the Women's Health Initiative (www.whi.org), the Million Veterans Program (www. RESEARCH va.gov/MVP), the 100 000 Genomes Project (genomicsengland.co.uk) and commercial efforts such as those by deCode (www.decode.com) and 23andme (www.23andme.com). The same transition is happening in experimental neuro- and behavioral genetics, and sample sizes of many hundreds of cases are becoming routine (www.genenetwork.org, www.mousephenotyping.org). There are two major consequences of this new affordability of massive omics datasets: (1) it is now far more practical to explore genetic modulation of behavioral differences and the key role of gene-by-environment interactions. Researchers are already doing the hard part-the quantitative analysis of behavior. Adding the omics component can provide powerful links to molecules, cells, circuits and even better treatment. (2) There is an acute need to highlight and train behavioral scientists in how best to exploit new omics approaches. This review addresses this second issue and highlights several new trends and opportunities that will be of interest to experts in animal and human behaviors.
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Affiliation(s)
- D G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, College of Medicine, Memphis, Tennessee
| | - M K Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, College of Medicine, Memphis, Tennessee
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, College of Medicine, Memphis, Tennessee
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Parker CC, Dickson PE, Philip VM, Thomas M, Chesler EJ. Systems Genetic Analysis in GeneNetwork.org. CURRENT PROTOCOLS IN NEUROSCIENCE 2017; 79:8.39.1-8.39.20. [PMID: 28398643 PMCID: PMC5548442 DOI: 10.1002/cpns.23] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies (GWAS) have emerged as a powerful tool to identify alleles and molecular pathways that influence susceptibility to psychiatric disorders and other diseases. Forward genetics using mouse mapping populations allows for a complementary approach that provides rigorous genetic and environmental control. In this unit, we describe techniques and tools that reduce the technical burden traditionally associated with genetic mapping in mice and enhance their translational utility to human psychiatric disorders. We provide guidance on choosing the appropriate mapping population, discuss the importance of phenotype, and offer detailed instructions on using the Web-based resource GeneNetwork to aid neuroscientists in better understanding the mechanisms through which genes influence behavior. We believe that the continued development of mouse mapping populations, genetic tools, bioinformatics resources, and statistical methodologies should remain a parallel strategy by which to investigate the genetic and environmental underpinnings of psychiatric disorders and other diseases in humans. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Clarissa C Parker
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont
| | - Price E Dickson
- Center for Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine
| | - Vivek M Philip
- Center for Computational Sciences, The Jackson Laboratory, Bar Harbor, Maine
| | - Mary Thomas
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont
| | - Elissa J Chesler
- Center for Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine
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12
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Malan-Müller S, Hemmings S. The Big Role of Small RNAs in Anxiety and Stress-Related Disorders. ANXIETY 2017; 103:85-129. [DOI: 10.1016/bs.vh.2016.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and Diversity Outcross to relatively simple crosses such as sets of consomic strains and reduced complexity crosses. This protocol is intended to help investigators make more informed decisions about choices of resources given different types of questions. We consider factors such as costs, availability, and ease of breeding for common scenarios. In general, we recommend using complementary resources and minimizing depth of resampling of any given genome or strain.
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Affiliation(s)
- Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, 77 S. Manassas Street, Memphis, TN, 38163, USA.
| | - Evan G Williams
- Department of Biology, Institute for Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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14
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Abstract
The goal of systems genetics is to understand the impact of genetic variation across all levels of biological organization, from mRNAs, proteins, and metabolites, to higher-order physiological and behavioral traits. This approach requires the accumulation and integration of many types of data, and also requires the use of many types of statistical tools to extract relevant patterns of covariation and causal relations as a function of genetics, environment, stage, and treatment. In this protocol we explain how to use the GeneNetwork web service, a powerful and free online resource for systems genetics. We provide workflows and methods to navigate massive multiscalar data sets and we explain how to use an extensive systems genetics toolkit for analysis and synthesis. Finally, we provide two detailed case studies that take advantage of human and mouse cohorts to evaluate linkage between gene variants, addiction, and aging.
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Abstract
A functional allele of the mouse catechol-O-methyltransferase (Comt) gene is defined by the insertion of a B2 short interspersed repeat element in its 3'-untranslated region (UTR). This allele has been associated with a number of phenotypes, such as pain and anxiety. In comparison with mice carrying the ancestral allele (Comt+), Comt B2i mice show higher Comt mRNA and enzymatic activity levels. Here, we investigated the molecular genetic mechanisms underlying this allelic specific regulation of Comt expression. Insertion of the B2 element introduces an early polyadenylation signal generating a shorter Comt transcript, in addition to the longer ancestral mRNA. Comparative analysis and in silico prediction of Comt mRNA potential targets within the transcript 3' to the B2 element was performed and allowed choosing microRNA (miRNA) candidates for experimental screening: mmu-miR-3470a, mmu-miR-3470b, and mmu-miR-667. Cell transfection with each miRNA downregulated the expression of the ancestral transcript and COMT enzymatic activity. Our in vivo experiments showed that mmu-miR-667-3p is strongly correlated with decreasing amounts of Comt mRNA in the brain, and lentiviral injections of mmu-miR-3470a, mmu-miR-3470b, and mmu-miR-667 increase hypersensitivity in the mouse formalin model, consistent with reduced COMT activity. In summary, our data demonstrate that the Comt+ transcript contains regulatory miRNA signals in its 3'-untranslated region leading to mRNA degradation; these signals, however, are absent in the shorter transcript, resulting in higher mRNA expression and activity levels.
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Oster M, Muráni E, Ponsuksili S, D'Eath R, Turner S, Evans G, Thölking L, Kurt E, Klont R, Foury A, Mormède P, Wimmers K. Hepatic expression patterns in psychosocially high-stressed pigs suggest mechanisms following allostatic principles. Physiol Behav 2014; 128:159-65. [DOI: 10.1016/j.physbeh.2014.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/30/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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Toth LA, Trammell RA, Williams RW. Mapping complex traits using families of recombinant inbred strains: an overview and example of mapping susceptibility to Candida albicans induced illness phenotypes. Pathog Dis 2014; 71:234-48. [PMID: 24535895 DOI: 10.1111/2049-632x.12160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/06/2014] [Accepted: 02/06/2014] [Indexed: 12/20/2022] Open
Abstract
This overview and data-based example indicate how large families of recombinant inbred (RI) strains can be used to identify genetic loci and genes that underlie complex phenotypic differences among inbred mice. The RI approach requires no a priori expectations or assumptions about mechanisms that influence the phenotype, other than that variability is partly heritable. RI strains, which are produced by inbreeding the F2 progeny of two parental strains for at least 20 generations, have two major advantages. First, numerous subjects with identical genotypes can be analyzed to determine the average phenotype associated with that genotype, and second, it becomes practical to systematically accumulate large genome and phenome data sets for entire RI families, including sequence data, transcriptomes for many organs, and cell types and extensive data on gene-by-pathogen interactions. This enables the construction of far more sophisticated models of disease cause and progression. To illustrate the use of the systems genetics approach to infectious disease, we designed a simple study using three complementary families of RI strains (CXB, BXD, and AXB/BXA) that are differentially susceptible to intravenous challenge with the yeast Candida albicans.
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Affiliation(s)
- Linda A Toth
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
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19
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Functionally enigmatic genes: a case study of the brain ignorome. PLoS One 2014; 9:e88889. [PMID: 24523945 PMCID: PMC3921226 DOI: 10.1371/journal.pone.0088889] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 01/14/2014] [Indexed: 12/26/2022] Open
Abstract
What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.
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Abstract
Transcriptome studies have revealed a surprisingly high level of variation among individuals in expression of key genes in the CNS under both normal and experimental conditions. Ten-fold variation is common, yet the specific causes and consequences of this variation are largely unknown. By combining classic gene mapping methods-family linkage studies and genomewide association-with high-throughput genomics, it is now possible to define quantitative trait loci (QTLs), single-gene variants, and even single SNPs and indels that control gene expression in different brain regions and cells. This review considers some of the major technical and conceptual challenges in analyzing variation in expression in the CNS with a focus on mRNAs, rather than noncoding RNAs or proteins. At one level of analysis, this work has been highly successful, and we finally have techniques that can be used to track down small numbers of loci that control expression in the CNS. But at a higher level of analysis, we still do not understand the genetic architecture of gene expression in brain, the consequences of expression QTLs on protein levels or on cell function, or the combined impact of expression differences on behavior and disease risk. These important gaps are likely to be bridged over the next several decades using (1) much larger sample sizes, (2) more powerful RNA sequencing and proteomic methods, and (3) novel statistical and computational models to predict genome-to-phenome relations.
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Affiliation(s)
- Ashutosh K Pandey
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
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Chesler EJ. Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research. Mamm Genome 2013; 25:3-11. [PMID: 24272351 PMCID: PMC3916706 DOI: 10.1007/s00335-013-9492-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/08/2013] [Indexed: 11/28/2022]
Abstract
The historical origins of classical laboratory mouse strains have led to a relatively limited range of genetic and phenotypic variation, particularly for the study of behavior. Many recent efforts have resulted in improved diversity and precision of mouse genetic resources for behavioral research, including the Collaborative Cross and Diversity Outcross population. These two populations, derived from an eight way cross of common and wild-derived strains, have high precision and allelic diversity. Behavioral variation in the population is expanded, both qualitatively and quantitatively. Variation that had once been canalized among the various inbred lines has been made amenable to genetic dissection. The genetic attributes of these complementary populations, along with advances in genetic and genomic technologies, makes a systems genetic analyses of behavior more readily tractable, enabling discovery of a greater range of neurobiological phenomena underlying behavioral variation.
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Affiliation(s)
- Elissa J Chesler
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA,
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22
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Juárez P, Valdovinos MG, May ME, Lloyd BP, Couppis MH, Kennedy CH. Serotonin2A/C receptors mediate the aggressive phenotype of TLX gene knockout mice. Behav Brain Res 2013; 256:354-61. [DOI: 10.1016/j.bbr.2013.07.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 07/23/2013] [Accepted: 07/25/2013] [Indexed: 01/31/2023]
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23
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Belfer I, Segall SK, Lariviere WR, Smith SB, Dai F, Slade GD, Rashid NU, Mogil JS, Campbell CM, Edwards RR, Liu Q, Bair E, Maixner W, Diatchenko L. Pain modality- and sex-specific effects of COMT genetic functional variants. Pain 2013; 154:1368-76. [PMID: 23701723 PMCID: PMC3700530 DOI: 10.1016/j.pain.2013.04.028] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/29/2013] [Accepted: 04/11/2013] [Indexed: 12/11/2022]
Abstract
The enzyme catechol-O-methyltransferase (COMT) metabolizes catecholamine neurotransmitters involved in a number of physiological functions, including pain perception. Both human and mouse COMT genes possess functional polymorphisms contributing to interindividual variability in pain phenotypes such as sensitivity to noxious stimuli, severity of clinical pain, and response to pain treatment. In this study, we found that the effects of Comt functional variation in mice are modality specific. Spontaneous inflammatory nociception and thermal nociception behaviors were correlated the most with the presence of the B2 SINE transposon insertion residing in the 3'UTR mRNA region. Similarly, in humans, COMT functional haplotypes were associated with thermal pain perception and with capsaicin-induced pain. Furthermore, COMT genetic variations contributed to pain behaviors in mice and pain ratings in humans in a sex-specific manner. The ancestral Comt variant, without a B2 SINE insertion, was more strongly associated with sensitivity to capsaicin in female vs male mice. In humans, the haplotype coding for low COMT activity increased capsaicin-induced pain perception in women, but not men. These findings reemphasize the fundamental contribution of COMT to pain processes, and provide a fine-grained resolution of this contribution at the genetic level that can be used to guide future studies in the area of pain genetics.
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Affiliation(s)
- Inna Belfer
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA, USA.
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24
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Akagi K, Li J, Symer DE. How do mammalian transposons induce genetic variation? A conceptual framework: the age, structure, allele frequency, and genome context of transposable elements may define their wide-ranging biological impacts. Bioessays 2013; 35:397-407. [PMID: 23319453 DOI: 10.1002/bies.201200133] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this essay, we discuss new insights into the wide-ranging impacts of mammalian transposable elements (TE) on gene expression and function. Nearly half of each mammalian genome is comprised of these mobile, repetitive elements. While most TEs are ancient relics, certain classes can move from one chromosomal location to another even now. Indeed, striking recent data show that extensive transposition occurs not only in the germline over evolutionary time, but also in developing somatic tissues and particular human cancers. While occasional germline TE insertions may contribute to genetic variation, many other, similar TEs appear to have little or no impact on neighboring genes. However, the effects of somatic insertions on gene expression and function remain almost completely unknown. We present a conceptual framework to understand how the ages, allele frequencies, molecular structures, and especially the genomic context of mammalian TEs each can influence their various possible functional consequences.
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Affiliation(s)
- Keiko Akagi
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
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25
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Swerdlow NR, Shilling PD, Breier M, Trim RS, Light GA, Saint Marie R. Fronto-temporal-mesolimbic gene expression and heritable differences in amphetamine-disrupted sensorimotor gating in rats. Psychopharmacology (Berl) 2012; 224:349-62. [PMID: 22700037 PMCID: PMC5215002 DOI: 10.1007/s00213-012-2758-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/25/2012] [Indexed: 10/28/2022]
Abstract
RATIONALE Differences in sensitivity to the prepulse inhibition (PPI)-disruptive effects of D2-family agonists in Sprague-Dawley (SD) vs. Long Evans (LE) rats are heritable, reflect differential activation of DA signaling in the nucleus accumbens (NAC), and are associated with differences in expression of specific NAC genes. These differences may inform us about the biology of PPI deficits in disorders such as schizophrenia. OBJECTIVES After confirming these strain-based PPI differences, we measured expression of four genes in NAC and other regions that regulate PPI: medial prefrontal cortex and ventral hippocampus (VH). METHODS Startle and PPI were assessed in SD and LE rats administered D-amphetamine (0 vs. 4.5 mg/kg, sc). Two weeks later, brain tissue was processed for comt, nrg1, grid2, and csnk1e expression; blood comt expression was also tested. RESULTS Data confirmed expected PPI phenotypes. Gene expression levels differed across strains, sexes, and brain regions, with LE > SD expression in most genes and regions, and female > male expression for all NAC genes. Within any brain region, expression of the four genes was highly inter-correlated; across regions, correlations were less robust, reflecting distinct strain- or sex-based subgroups. PPI amphetamine sensitivity at 120 ms correlated significantly with NAC nrg1 expression, while amphetamine sensitivity for 30 ms PPI and startle magnitude correlated significantly with VH nrg1 and blood comt expression. CONCLUSIONS Rat strains differing in a schizophrenia-linked phenotype also differ in expression levels of genes associated both with that phenotype, and with schizophrenia, within brain regions associated with that phenotype and schizophrenia.
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Affiliation(s)
- Neal R. Swerdlow
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093-0804, USA
| | - Paul D. Shilling
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093-0804, USA
| | - Michelle Breier
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093-0804, USA
| | - Ryan S. Trim
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093-0804, USA
| | - Gregory A. Light
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093-0804, USA,VA San Diego Healthcare System, San Diego, CA, USA,VISN 22, Mental Illness Research, Education and Clinical Center (MIRECC), San Diego, CA, USA
| | - Richard Saint Marie
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093-0804, USA
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26
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Segall SK, Maixner W, Belfer I, Wiltshire T, Seltzer Z, Diatchenko L. Janus molecule I: dichotomous effects of COMT in neuropathic vs nociceptive pain modalities. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2012; 11:222-35. [PMID: 22483297 DOI: 10.2174/187152712800672490] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 10/27/2011] [Accepted: 10/28/2012] [Indexed: 01/02/2023]
Abstract
The enzyme catechol-O-methyltransferase (COMT) has been shown to play a critical role in pain perception by regulating levels of epinephrine (Epi) and norepinephrine (NE). Although the key contribution of catecholamines to the perception of pain has been recognized for a long time, there is a clear dichotomy of observations. More than a century of research has demonstrated that increasing adrenergic transmission in the spinal cord decreases pain sensitivity in animals. Equally abundant evidence demonstrates the opposite effect of adrenergic signaling in the peripheral nervous system, where adrenergic signaling increases pain sensitivity. Viewing pain processing within spinal and peripheral compartments and determining the directionality of adrenergic signaling helps clarify the seemingly contradictory findings of the pain modulatory properties of adrenergic receptor agonists and antagonists presented in other reviews. Available evidence suggests that adrenergic signaling contributes to pain phenotypes through α(1/2) and β(2/3) receptors. While stimulation of α(2) adrenergic receptors seems to uniformly produce analgesia, stimulation of α(1) or β receptors produces either analgesic or hyperalgesic effects. Establishing the directionality of adrenergic receptor modulation of pain processing, and related COMT activity in different pain models are needed to bring meaning to recent human molecular genetic findings. This will enable the translation of current findings into meaningful clinical applications such as diagnostic markers and novel therapeutic targets for complex human pain conditions.
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Affiliation(s)
- S K Segall
- Center for Neurosensory Disorders, University of North Carolina, Chapel Hill, USA.
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27
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Oliver KR, Greene WK. Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis. Ecol Evol 2012; 2:2912-33. [PMID: 23170223 PMCID: PMC3501640 DOI: 10.1002/ece3.400] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 09/11/2012] [Accepted: 09/17/2012] [Indexed: 12/17/2022] Open
Abstract
In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. “Adaptive potential” and “evolutionary potential” are proposed as the extremes of a continuum of “intra-genomic potential” due to TE-Thrust. Specific data is given, indicating “adaptive potential” being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of “evolutionary potential” is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.
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Affiliation(s)
- Keith R Oliver
- School of Biological Science and Biotechnology, Faculty of Science and Engineering, Murdoch University Perth, W.A., 6150, Australia
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28
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Palmer AA, de Wit H. Translational genetic approaches to substance use disorders: bridging the gap between mice and humans. Hum Genet 2012; 131:931-9. [PMID: 22170288 PMCID: PMC3352994 DOI: 10.1007/s00439-011-1123-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 11/27/2011] [Indexed: 10/14/2022]
Abstract
While substance abuse disorders only occur in humans, mice and other model organisms can make valuable contributions to genetic studies of these disorders. In this review, we consider a few specific examples of how model organisms have been used in conjunction with studies in humans to study the role of genetic factors in substance use disorders. In some examples genes that were first discovered in mice were subsequently studied in humans. In other examples genes or specific polymorphisms in genes were first studied in humans and then modeled in mice. Using anatomically and temporally specific genetic, pharmacological and other environmental manipulations in conjunction with histological analyses, mechanistic insights that would be difficult to obtain in humans have been obtained in mice. We hope these examples illustrate how novel biological insights about the effect of genes on substance use disorders can be obtained when mouse and human genetic studies are successfully integrated.
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Affiliation(s)
- Abraham A Palmer
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
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29
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Boughter JD, Mulligan MK, St John SJ, Tokita K, Lu L, Heck DH, Williams RW. Genetic control of a central pattern generator: rhythmic oromotor movement in mice is controlled by a major locus near Atp1a2. PLoS One 2012; 7:e38169. [PMID: 22675444 PMCID: PMC3364982 DOI: 10.1371/journal.pone.0038169] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/04/2012] [Indexed: 12/21/2022] Open
Abstract
Fluid licking in mice is a rhythmic behavior that is controlled by a central pattern generator (CPG) located in a complex of brainstem nuclei. C57BL/6J (B6) and DBA/2J (D2) strains differ significantly in water-restricted licking, with a highly heritable difference in rates (h(2)≥0.62) and a corresponding 20% difference in interlick interval (mean ± SEM = 116.3±1 vs 95.4±1.1 ms). We systematically quantified motor output in these strains, their F(1) hybrids, and a set of 64 BXD progeny strains. The mean primary interlick interval (MPI) varied continuously among progeny strains. We detected a significant quantitative trait locus (QTL) for a CPG controlling lick rate on Chr 1 (Lick1), and a suggestive locus on Chr 10 (Lick10). Linkage was verified by testing of B6.D2-1D congenic stock in which a segment of Chr 1 of the D2 strain was introgressed onto the B6 parent. The Lick1 interval on distal Chr 1 contains several strong candidate genes. One of these is a sodium/potassium pump subunit (Atp1a2) with widespread expression in astrocytes, as well as in a restricted population of neurons. Both this subunit and the entire Na(+)/K(+)-ATPase molecule have been implicated in rhythmogenesis for respiration and locomotion. Sequence variants in or near Apt1a2 strongly modulate expression of the cognate mRNA in multiple brain regions. This gene region has recently been sequenced exhaustively and we have cataloged over 300 non-coding and synonymous mutations segregating among BXD strains, one or more of which is likely to contribute to differences in central pattern generator tempo.
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Affiliation(s)
- John D Boughter
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America.
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Li J, Akagi K, Hu Y, Trivett AL, Hlynialuk CJ, Swing DA, Volfovsky N, Morgan TC, Golubeva Y, Stephens RM, Smith DE, Symer DE. Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance. Genome Res 2012; 22:870-84. [PMID: 22367191 PMCID: PMC3337433 DOI: 10.1101/gr.130740.111] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 02/09/2012] [Indexed: 01/15/2023]
Abstract
Endogenous retrotransposons have caused extensive genomic variation within mammalian species, but the functional implications of such mobilization are mostly unknown. We mapped thousands of endogenous retrovirus (ERV) germline integrants in highly divergent, previously unsequenced mouse lineages, facilitating a comparison of gene expression in the presence or absence of local insertions. Polymorphic ERVs occur relatively infrequently in gene introns and are particularly depleted from genes involved in embryogenesis or that are highly expressed in embryonic stem cells. Their genomic distribution implies ongoing negative selection due to deleterious effects on gene expression and function. A polymorphic, intronic ERV at Slc15a2 triggers up to 49-fold increases in premature transcriptional termination and up to 39-fold reductions in full-length transcripts in adult mouse tissues, thereby disrupting protein expression and functional activity. Prematurely truncated transcripts also occur at Polr1a, Spon1, and up to ∼5% of other genes when intronic ERV polymorphisms are present. Analysis of expression quantitative trait loci (eQTLs) in recombinant BxD mouse strains demonstrated very strong genetic associations between the polymorphic ERV in cis and disrupted transcript levels. Premature polyadenylation is triggered at genomic distances up to >12.5 kb upstream of the ERV, both in cis and between alleles. The parent of origin of the ERV is associated with variable expression of nonterminated transcripts and differential DNA methylation at its 5'-long terminal repeat. This study defines an unexpectedly strong functional impact of ERVs in disrupting gene transcription at a distance and demonstrates that ongoing retrotransposition can contribute significantly to natural phenotypic diversity.
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Affiliation(s)
- Jingfeng Li
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Keiko Akagi
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Yongjun Hu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Christopher J.W. Hlynialuk
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Deborah A. Swing
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Natalia Volfovsky
- Advanced Biomedical Computing Center, Information Systems Program and
| | - Tamara C. Morgan
- Histotechnology Laboratory, SAIC-Frederick, Inc., National Cancer Institute, Frederick, Maryland 21702, USA
| | - Yelena Golubeva
- Histotechnology Laboratory, SAIC-Frederick, Inc., National Cancer Institute, Frederick, Maryland 21702, USA
| | | | - David E. Smith
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - David E. Symer
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
- Department of Internal Medicine and Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
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Mulligan MK, Wang X, Adler AL, Mozhui K, Lu L, Williams RW. Complex control of GABA(A) receptor subunit mRNA expression: variation, covariation, and genetic regulation. PLoS One 2012; 7:e34586. [PMID: 22506031 PMCID: PMC3323555 DOI: 10.1371/journal.pone.0034586] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/06/2012] [Indexed: 12/13/2022] Open
Abstract
GABA type-A receptors are essential for fast inhibitory neurotransmission and are critical in brain function. Surprisingly, expression of receptor subunits is highly variable among individuals, but the cause and impact of this fluctuation remains unknown. We have studied sources of variation for all 19 receptor subunits using massive expression data sets collected across multiple brain regions and platforms in mice and humans. Expression of Gabra1, Gabra2, Gabrb2, Gabrb3, and Gabrg2 is highly variable and heritable among the large cohort of BXD strains derived from crosses of fully sequenced parents—C57BL/6J and DBA/2J. Genetic control of these subunits is complex and highly dependent on tissue and mRNA region. Remarkably, this high variation is generally not linked to phenotypic differences. The single exception is Gabrb3, a locus that is linked to anxiety. We identified upstream genetic loci that influence subunit expression, including three unlinked regions of chromosome 5 that modulate the expression of nine subunits in hippocampus, and that are also associated with multiple phenotypes. Candidate genes within these loci include, Naaa, Nos1, and Zkscan1. We confirmed a high level of coexpression for subunits comprising the major channel—Gabra1, Gabrb2, and Gabrg2—and identified conserved members of this expression network in mice and humans. Gucy1a3, Gucy1b3, and Lis1 are novel and conserved associates of multiple subunits that are involved in inhibitory signaling. Finally, proximal and distal regions of the 3′ UTRs of single subunits have remarkably independent expression patterns in both species. However, corresponding regions of different subunits often show congruent genetic control and coexpression (proximal-to-proximal or distal-to-distal), even in the absence of sequence homology. Our findings identify novel sources of variation that modulate subunit expression and highlight the extraordinary capacity of biological networks to buffer 4–100 fold differences in mRNA levels.
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Affiliation(s)
- Megan K Mulligan
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America.
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Advances in biotechnology and linking outputs to variation in complex traits: Plant and Animal Genome meeting January 2012. Funct Integr Genomics 2012; 12:1-9. [DOI: 10.1007/s10142-012-0270-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 12/22/2022]
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Williams RW, Mulligan MK. Genetic and molecular network analysis of behavior. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2012. [PMID: 23195314 DOI: 10.1016/b978-0-12-398323-7.00006-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This chapter provides an introduction into the genetic control and analysis of behavioral variation using powerful online resources. We introduce you to the new field of systems genetics using "case studies" drawn from the world of behavioral genetics that exploit populations of genetically diverse lines of mice. These lines differ very widely in patterns of gene and protein expression in the brain and in patterns of behavior. In this chapter, we address the following set of related questions: (1) Can we combine massive genomic data sets with large aggregates of precise quantitative data on behavior? (2) Can we map causal relations between gene variants and behavioral differences? (3) Can we simultaneously use these highly coherent data sets to understand more about the underlying molecular and cellular basis of behavior?
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Affiliation(s)
- Robert W Williams
- Department of Anatomy and Neurobiology, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
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Wang X, Mozhui K, Li Z, Mulligan MK, Ingels JF, Zhou X, Hori RT, Chen H, Cook MN, Williams RW, Lu L. A promoter polymorphism in the Per3 gene is associated with alcohol and stress response. Transl Psychiatry 2012; 2:e73. [PMID: 22832735 PMCID: PMC3309544 DOI: 10.1038/tp.2011.71] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The period homolog genes Per1, Per2 and Per3 are important components of the circadian clock system. In addition to their role in maintaining circadian rhythm, these genes have been linked to mood disorders, stress response and vulnerability to addiction and alcoholism. In this study, we combined high-resolution sequence analysis and quantitative trait locus (QTL) mapping of gene expression and behavioral traits to identify Per3 as a compelling candidate for the interaction between circadian rhythm, alcohol and stress response. In the BXD family of mouse strains, sequence variants in Per3 have marked effects on steady-state mRNA and protein levels. As a result, the transcript maps as a cis-acting expression QTL (eQTL). We found that an insertion/deletion (indel) variant in a putative stress response element in the promoter region of Per3 causes local control of transcript abundance. This indel results in differences in protein binding affinities between the two alleles through the Nrf2 transcriptional activator. Variation in Per3 is also associated with downstream differences in the expression of genes involved in circadian rhythm, alcohol, stress response and schizophrenia. We found that the Per3 locus is linked to stress/anxiety traits, and that the basal expression of Per3 is also correlated with several anxiety and addiction-related phenotypes. Treatment with alcohol results in increased expression of Per3 in the hippocampus, and this effect interacts with acute restraint stress. Our data provide strong evidence that variation in the Per3 transcript is causally associated with and also responsive to stress and alcohol.
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Affiliation(s)
- X Wang
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Mozhui
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Z Li
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - M K Mulligan
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - J F Ingels
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - X Zhou
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - R T Hori
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - H Chen
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - M N Cook
- Department of Psychology, University of Memphis, Memphis, TN, USA
| | - R W Williams
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - L Lu
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA,Jiangsu Ley Laboratory of Neuroregeneration, Nantong University, Nantong, China,Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, TN 38163, USA. E-mail:
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Alberts R, Chen H, Pommerenke C, Smit AB, Spijker S, Williams RW, Geffers R, Bruder D, Schughart K. Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease. BMC Genomics 2011; 12:610. [PMID: 22182475 PMCID: PMC3277499 DOI: 10.1186/1471-2164-12-610] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/19/2011] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Regulatory T cells (Tregs) play an essential role in the control of the immune response. Treg cells represent important targets for therapeutic interventions of the immune system. Therefore, it will be very important to understand in more detail which genes are specifically activated in Treg cells versus T helper (Th) cells, and which gene regulatory circuits may be involved in specifying and maintaining Treg cell homeostasis. RESULTS We isolated Treg and Th cells from a genetically diverse family of 31 BXD type recombinant inbred strains and the fully inbred parental strains of this family--C57BL/6J and DBA/2J. Subsequently genome-wide gene expression studies were performed from the isolated Treg and Th cells. A comparative analysis of the transcriptomes of these cell populations allowed us to identify many novel differentially expressed genes. Analysis of cis- and trans-expression Quantitative Trait Loci (eQTLs) highlighted common and unique regulatory mechanisms that are active in the two cell types. Trans-eQTL regions were found for the Treg functional genes Nrp1, Stat3 and Ikzf4. Analyses of the respective QTL intervals suggested several candidate genes that may be involved in regulating these genes in Treg cells. Similarly, possible candidate genes were found which may regulate the expression of F2rl1, Ctla4, Klrb1f. In addition, we identified a focused group of candidate genes that may be important for the maintenance of self-tolerance and the prevention of allergy. CONCLUSIONS Variation of expression across the strains allowed us to find many novel gene-interaction networks in both T cell subsets. In addition, these two data sets enabled us to identify many differentially expressed genes and to nominate candidate genes that may have important functions for the maintenance of self-tolerance and the prevention of allergy.
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Affiliation(s)
- Rudi Alberts
- Department of Infection Genetics, University of Veterinary Medicine Hannover, Braunschweig, Germany
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Stress-related methylation of the catechol-O-methyltransferase Val 158 allele predicts human prefrontal cognition and activity. J Neurosci 2011; 31:6692-8. [PMID: 21543598 DOI: 10.1523/jneurosci.6631-10.2011] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
DNA methylation at CpG dinucleotides is associated with gene silencing, stress, and memory. The catechol-O-methyltransferase (COMT) Val(158) allele in rs4680 is associated with differential enzyme activity, stress responsivity, and prefrontal activity during working memory (WM), and it creates a CpG dinucleotide. We report that methylation of the Val(158) allele measured from peripheral blood mononuclear cells (PBMCs) of Val/Val humans is associated negatively with lifetime stress and positively with WM performance; it interacts with stress to modulate prefrontal activity during WM, such that greater stress and lower methylation are related to reduced cortical efficiency; and it is inversely related to mRNA expression and protein levels, potentially explaining the in vivo effects. Finally, methylation of COMT in prefrontal cortex and that in PBMCs of rats are correlated. The relationship of methylation of the COMT Val(158) allele with stress, gene expression, WM performance, and related brain activity suggests that stress-related methylation is associated with silencing of the gene, which partially compensates the physiological role of the high-activity Val allele in prefrontal cognition and activity. Moreover, these results demonstrate how stress-related DNA methylation of specific functional alleles impacts directly on human brain physiology beyond sequence variation.
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O'Tuathaigh CMP, Desbonnet L, Moran PM, Waddington JL. Susceptibility genes for schizophrenia: mutant models, endophenotypes and psychobiology. Curr Top Behav Neurosci 2011; 12:209-50. [PMID: 22367925 DOI: 10.1007/7854_2011_194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Schizophrenia is characterised by a multifactorial aetiology that involves genetic liability interacting with epigenetic and environmental factors to increase risk for developing the disorder. A consensus view is that the genetic component involves several common risk alleles of small effect and/or rare but penetrant copy number variations. Furthermore, there is increasing evidence for broader, overlapping genetic-phenotypic relationships in psychosis; for example, the same susceptibility genes also confer risk for bipolar disorder. Phenotypic characterisation of genetic models of candidate risk genes and/or putative pathophysiological processes implicated in schizophrenia, as well as examination of epidemiologically relevant gene × environment interactions in these models, can illuminate molecular and pathobiological mechanisms involved in schizophrenia. The present chapter outlines both the evidence from phenotypic studies in mutant mouse models related to schizophrenia and recently described mutant models addressing such gene × environment interactions. Emphasis is placed on evaluating the extent to which mutant phenotypes recapitulate the totality of the disease phenotype or model selective endophenotypes. We also discuss new developments and trends in relation to the functional genomics of psychosis which might help to inform on the construct validity of mutant models of schizophrenia and highlight methodological challenges in phenotypic evaluation that relate to such models.
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Affiliation(s)
- Colm M P O'Tuathaigh
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland,
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38
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Palmer AA, Dulawa SC. Murine Warriors or Worriers: The Saga of Comt1, B2 SINE Elements, and the Future of Translational Genetics. Front Neurosci 2010; 4:177. [PMID: 20976038 PMCID: PMC2958038 DOI: 10.3389/fnins.2010.00177] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 09/21/2010] [Indexed: 01/21/2023] Open
Affiliation(s)
- Abraham A Palmer
- Department of Human Genetics, University of Chicago Chicago, IL, USA
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