351
|
Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nat Genet 2017; 49:387-394. [PMID: 28135246 PMCID: PMC5359078 DOI: 10.1038/ng.3778] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/29/2016] [Indexed: 12/14/2022]
Abstract
After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males ZZ, but in mammals females are XX and males XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly-expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction related genes on sex chromosomes may be specific to the male germ line.
Collapse
|
352
|
Meiotic Consequences of Genetic Divergence Across the Murine Pseudoautosomal Region. Genetics 2017; 205:1089-1100. [PMID: 28100589 PMCID: PMC5340325 DOI: 10.1534/genetics.116.189092] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023] Open
Abstract
The production of haploid gametes during meiosis is dependent on the homology-driven processes of pairing, synapsis, and recombination. On the mammalian heterogametic sex chromosomes, these key meiotic activities are confined to the pseudoautosomal region (PAR), a short region of near-perfect sequence homology between the X and Y chromosomes. Despite its established importance for meiosis, the PAR is rapidly evolving, raising the question of how proper X/Y segregation is buffered against the accumulation of homology-disrupting mutations. Here, I investigate the interplay of PAR evolution and function in two interfertile house mouse subspecies characterized by structurally divergent PARs, Mus musculus domesticus and M. m. castaneus. Using cytogenetic methods to visualize the sex chromosomes at meiosis, I show that intersubspecific F1 hybrids harbor an increased frequency of pachytene spermatocytes with unsynapsed sex chromosomes. This high rate of asynapsis is due, in part, to the premature release of synaptic associations prior to completion of prophase I. Further, I show that when sex chromosomes do synapse in intersubspecific hybrids, recombination is reduced across the paired region. Together, these meiotic defects afflict ∼50% of spermatocytes from F1 hybrids and lead to increased apoptosis in meiotically dividing cells. Despite flagrant disruption of the meiotic program, a subset of spermatocytes complete meiosis and intersubspecific F1 males remain fertile. These findings cast light on the meiotic constraints that shape sex chromosome evolution and offer initial clues to resolve the paradox raised by the rapid evolution of this functionally significant locus.
Collapse
|
353
|
Nelson LH, Lenz KM. The immune system as a novel regulator of sex differences in brain and behavioral development. J Neurosci Res 2017; 95:447-461. [PMID: 27870450 PMCID: PMC8008603 DOI: 10.1002/jnr.23821] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 01/02/2023]
Abstract
Sexual differentiation of the brain occurs early in life as a result of sex-typical hormone action and sex chromosome effects. Immunocompetent cells are being recognized as underappreciated regulators of sex differences in brain and behavioral development, including microglia, astrocytes, and possibly other less well studied cell types, including T cells and mast cells. Immunocompetent cells in the brain are responsive to steroid hormones, but their role in sex-specific brain development is an emerging field of interest. This Review presents a summary of what is currently known about sex differences in the number, morphology, and signaling profile of immune cells in the developing brain and their role in the early-life programming of sex differences in brain and behavior. We review what is currently known about sex differences in the response to early-life perturbations, including stress, inflammation, diet, and environmental pollutants. We also discuss how and why understanding sex differences in the developing neuroimmune environment may provide insight into understanding the etiology of several neurodevelopmental disorders. This Review also highlights what remains to be discovered in this emerging field of developmental neuroimmunology and underscores the importance of filling in these knowledge gaps. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Lars H Nelson
- Program in Neuroscience, The Ohio State University, Columbus, Ohio
- Group in Behavioral Neuroendocrinology, The Ohio State University, Columbus, Ohio
| | - Kathryn M Lenz
- Group in Behavioral Neuroendocrinology, The Ohio State University, Columbus, Ohio
- Department of Psychology, The Ohio State University, Columbus, Ohio
- Department of Neuroscience, The Ohio State University, Columbus, Ohio
| |
Collapse
|
354
|
de Souza Santos R, Frank AP, Nelson MD, Garcia MM, Palmer BF, Clegg DJ. Sex, Gender, and Transgender: Metabolic Impact of Cross Hormone Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1043:611-627. [PMID: 29224113 DOI: 10.1007/978-3-319-70178-3_27] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Most preclinical and clinical, animal, and human research has been biased with respect to sex and even more so with respect to gender. In fact, little is known about the impact of sex and even less about the influence of gender on overall metabolic processes. The National Institutes of Health has recognized this gap in scientific knowledge and now mandates that studies be conducted in both sexes and to include gender as variables influencing physiological processes such as metabolism. It is therefore critical to understand and appreciate how to incorporate sex and gender in preclinical and clinical research in order to enhance our understanding of the mechanisms by which metabolic processes differ by sex and gender. In this chapter, we define sex and gender and discuss when sex and gender are not aligned, such as that which occurs in transgender individuals, and how this impacts metabolic processes. We discuss the importance of understanding the influence and interactions between sex hormones and sex chromosomes rather than focusing on their relative contributions to metabolism in isolation. This knowledge will optimize therapies specific for individuals which need to encompass sex and gender.
Collapse
Affiliation(s)
- Roberta de Souza Santos
- Biomedical Research Department, Diabetes and Obesity Research Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Aaron P Frank
- Biomedical Research Department, Diabetes and Obesity Research Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael Douglas Nelson
- Applied Physiology and Advanced Imaging Lab, University of Texas, Arlington, TX, USA.,Kinesiology, University of Texas, Arlington, TX, USA.,Bioengineering, University of Texas, Arlington, TX, USA.,Cedars-Sinai Medical Center, University of Texas, Arlington, TX, USA
| | - Maurice M Garcia
- Division of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Cedars-Sinai Medical Center Transgender Surgery and Health Program, Los Angeles, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Biff F Palmer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Deborah J Clegg
- Biomedical Research Department, Diabetes and Obesity Research Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| |
Collapse
|
355
|
Ma W, Gabriel TS, Martis MM, Gursinsky T, Schubert V, Vrána J, Doležel J, Grundlach H, Altschmied L, Scholz U, Himmelbach A, Behrens SE, Banaei-Moghaddam AM, Houben A. Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog. THE NEW PHYTOLOGIST 2017; 213:916-928. [PMID: 27468091 DOI: 10.1111/nph.14110] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/18/2016] [Indexed: 05/21/2023]
Abstract
B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.
Collapse
Affiliation(s)
- Wei Ma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Tobias Sebastian Gabriel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Mihaela Maria Martis
- Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- National Bioinformatics Infrastructure Sweden, Department of Clinical and Experimental Medicine, Linköping University, SE-558185, Linköping, Sweden
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Faculty of Life Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Jan Vrána
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Heidrun Grundlach
- Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Faculty of Life Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Ali Mohammad Banaei-Moghaddam
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, PO Box 13145-1384, Tehran, Iran
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| |
Collapse
|
356
|
Burgoyne PS, Arnold AP. A primer on the use of mouse models for identifying direct sex chromosome effects that cause sex differences in non-gonadal tissues. Biol Sex Differ 2016; 7:68. [PMID: 27999654 PMCID: PMC5154145 DOI: 10.1186/s13293-016-0115-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/08/2016] [Indexed: 12/15/2022] Open
Abstract
In animals with heteromorphic sex chromosomes, all sex differences originate from the sex chromosomes, which are the only factors that are consistently different in male and female zygotes. In mammals, the imbalance in Y gene expression, specifically the presence vs. absence of Sry, initiates the differentiation of testes in males, setting up lifelong sex differences in the level of gonadal hormones, which in turn cause many sex differences in the phenotype of non-gonadal tissues. The inherent imbalance in the expression of X and Y genes, or in the epigenetic impact of X and Y chromosomes, also has the potential to contribute directly to the sexual differentiation of non-gonadal cells. Here, we review the research strategies to identify the X and Y genes or chromosomal regions that cause direct, sexually differentiating effects on non-gonadal cells. Some mouse models are useful for separating the effects of sex chromosomes from those of gonadal hormones. Once direct “sex chromosome effects” are detected in these models, further studies are required to narrow down the list of candidate X and/or Y genes and then to identify the sexually differentiating genes themselves. Logical approaches to the search for these genes are reviewed here.
Collapse
Affiliation(s)
- Paul S Burgoyne
- Stem Cell Biology and Developmental Genetics, Mill Hill Laboratory, Francis Crick Institute, The Ridgeway, London, NW7 1AA UK
| | - Arthur P Arnold
- Department of Integrative Biology and Physiology, and Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, 610 Charles Young Drive South, Los Angeles, CA 90095-7239 USA
| |
Collapse
|
357
|
Abstract
The association between chromosomal abnormalities and reduced fertility in domestic animals is well recorded and has been studied for decades. Chromosome aberrations directly affect meiosis, gametogenesis, and the viability of zygotes and embryos. In some instances, balanced structural rearrangements can be transmitted, causing fertility problems in subsequent generations. Here, we aim to give a comprehensive overview of the current status and future prospects of clinical cytogenetics of animal reproduction by focusing on the advances in molecular cytogenetics during the genomics era. We describe how advancing knowledge about animal genomes has improved our understanding of connections between gross structural or molecular chromosome variations and reproductive disorders. Further, we expand on a key area of reproduction genetics: cytogenetics of animal gametes and embryos. Finally, we describe how traditional cytogenetics is interfacing with advanced genomics approaches, such as array technologies and next-generation sequencing, and speculate about the future prospects.
Collapse
Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458;
| | | |
Collapse
|
358
|
Bearoff F, Del Rio R, Case LK, Dragon JA, Nguyen-Vu T, Lin CY, Blankenhorn EP, Teuscher C, Krementsov DN. Natural genetic variation profoundly regulates gene expression in immune cells and dictates susceptibility to CNS autoimmunity. Genes Immun 2016; 17:386-395. [PMID: 27653816 PMCID: PMC5133152 DOI: 10.1038/gene.2016.37] [Citation(s) in RCA: 11] [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: 06/28/2016] [Revised: 08/15/2016] [Accepted: 08/18/2016] [Indexed: 02/08/2023]
Abstract
Regulation of gene expression in immune cells is known to be under genetic control, and likely contributes to susceptibility to autoimmune diseases such as multiple sclerosis (MS). How this occurs in concert across multiple immune cell types is poorly understood. Using a mouse model that harnesses the genetic diversity of wild-derived mice, more accurately reflecting genetically diverse human populations, we provide an extensive characterization of the genetic regulation of gene expression in five different naive immune cell types relevant to MS. The immune cell transcriptome is shown to be under profound genetic control, exhibiting diverse patterns: global, cell-specific and sex-specific. Bioinformatic analysis of the genetically controlled transcript networks reveals reduced cell type specificity and inflammatory activity in wild-derived PWD/PhJ mice, compared with the conventional laboratory strain C57BL/6J. Additionally, candidate MS-GWAS (genome-wide association study candidate genes for MS susceptibility) genes were significantly enriched among transcripts overrepresented in C57BL/6J cells compared with PWD. These expression level differences correlate with robust differences in susceptibility to experimental autoimmune encephalomyelitis, the principal model of MS, and skewing of the encephalitogenic T-cell responses. Taken together, our results provide functional insights into the genetic regulation of the immune transcriptome, and shed light on how this in turn contributes to susceptibility to autoimmune disease.
Collapse
Affiliation(s)
- F Bearoff
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - R Del Rio
- Department of Medicine, University of Vermont, Burlington, VT, USA
| | - L K Case
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - J A Dragon
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - T Nguyen-Vu
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - C-Y Lin
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - E P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - C Teuscher
- Department of Medicine, University of Vermont, Burlington, VT, USA
- Department of Pathology, University of Vermont, Burlington, VT, USA
| | - D N Krementsov
- Department of Medicine, University of Vermont, Burlington, VT, USA
| |
Collapse
|
359
|
Prakash SK, Bondy CA, Maslen CL, Silberbach M, Lin AE, Perrone L, Limongelli G, Michelena HI, Bossone E, Citro R, Lemaire SA, Body SC, Milewicz DM. Autosomal and X chromosome structural variants are associated with congenital heart defects in Turner syndrome: The NHLBI GenTAC registry. Am J Med Genet A 2016; 170:3157-3164. [PMID: 27604636 PMCID: PMC5115959 DOI: 10.1002/ajmg.a.37953] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 08/11/2016] [Indexed: 12/14/2022]
Abstract
Turner Syndrome (TS) is a developmental disorder caused by partial or complete loss of one sex chromosome. Bicuspid aortic valve and other left-sided congenital heart lesions (LSL), including thoracic aortic aneurysms and acute aortic dissections, are 30-50 times more frequent in TS than in the general population. In 454 TS subjects, we found that LSL are significantly associated with reduced dosage of Xp genes and increased dosage of Xq genes. We also showed that genome-wide copy number variation is increased in TS and identify a common copy number variant (CNV) in chromosome 12p13.31 that is associated with LSL with an odds ratio of 3.7. This CNV contains three protein-coding genes (SLC2A3, SLC2A14, and NANOGP1) and was previously implicated in congenital heart defects in the 22q11 deletion syndrome. In addition, we identified a subset of rare and recurrent CNVs that are also enriched in non-syndromic BAV cases. These observations support our hypothesis that X chromosome and autosomal variants affecting cardiac developmental genes may interact to cause the increased prevalence of LSL in TS. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Siddharth K Prakash
- Division of Medical Genetics, Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Carolyn A Bondy
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Cheryl L Maslen
- Departments of Molecular and Medical Genetics and Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - Michael Silberbach
- Departments of Molecular and Medical Genetics and Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - Angela E Lin
- Department of Medical Genetics, MassGeneral Hospital for Children, Boston, Massachusetts
| | - Laura Perrone
- Department of Pediatrics "F. Fede", Seconda Università degli Studi di Napoli, Naples, Italy
| | - Giuseppe Limongelli
- Department of Pediatrics "F. Fede", Seconda Università degli Studi di Napoli, Naples, Italy
| | | | - Eduardo Bossone
- Department of Cardiology and Cardiac Surgery, University Hospital "Scuola Medica Salernitana", Salerno, Italy
| | - Rodolfo Citro
- Department of Cardiology and Cardiac Surgery, University Hospital "Scuola Medica Salernitana", Salerno, Italy
| | - Scott A Lemaire
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - Simon C Body
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dianna M Milewicz
- Division of Medical Genetics, Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| |
Collapse
|
360
|
Praktiknjo SD, Picard S, Deschepper CF. Comparisons of chromosome Y-substituted mouse strains reveal that the male-specific chromosome modulates the effects of androgens on cardiac functions. Biol Sex Differ 2016; 7:61. [PMID: 27980711 PMCID: PMC5143463 DOI: 10.1186/s13293-016-0116-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/09/2016] [Indexed: 01/06/2023] Open
Abstract
Background The C57BL/6J.YA/J mouse strain is a chromosome-substituted line where the original male-specific portion of chromosome Y (MSY) from C57BL/6J mice was substituted for that from A/J mice. In hearts from male C57BL/6J.YA/J and C57BL/6J mice, orchidectomy (ORX) affected in a strictly strain-specific fashion the expression a subset of genes showing enrichment for functional categories, including that of circadian rhythms and cardiac contractility. We further tested whether: (1) there were strain-specific differences in cardiac circadian rhythms; (2) strain-dependent differences in the effects of ORX on contractility genes translated into differences in cardiac functions; and (3) differential contractility responses occurred preferentially at times when circadian rhythms also showed strain-specific differences. Methods In hearts from the two above strains, we (1) profiled the expression levels of 15 circadian genes at 4-h intervals across a 24 h period; (2) tested the effects of either ORX or androgen replacement on expression of cardiac contractility genes, and that of ORX on myocardial functional reserve; and (3) verified whether the effects of MSY variants on cardiac contractility-related responses showed synchronicity with differences in circadian rhythms. Results Among the 15 tested circadian genes, a subset of them were affected by strain (and thus the genetic origin of MSY), which interacted with the amplitude of their peak of maximal expression at 2:00 PM. At that same time-point, ORX decreased (and androgen supplementation increased) the expression of three contractility-related genes, and decreased myocardial relaxation reserve in C57BL/6J.YA/J, but not in C57BL/6J mice. These effects were not detected at 10:00 AM, i.e., at another time-point when circadian genes showed no strain-specific differences. Conclusions The results indicate that in mice, androgens have activational effects on cardiac circadian rhythms, contractile gene expression, and myocardial functional reserve. All effects occurred preferentially at the same time of the day, but varied as a function of the genetic origin of MSY. Androgens may therefore be necessary but not sufficient to impart male-specific characteristics to some particular cardiac functions, with genetic material from MSY being one other necessary factor to fully define their range of actions. Electronic supplementary material The online version of this article (doi:10.1186/s13293-016-0116-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samantha D Praktiknjo
- Institut de recherches cliniques de Montréal (IRCM) and Dept of Medicine, Cardiovascular Biology Research Unit, Université de Montréal, 100 Pine Ave West, Montreal, QC H2W 1R7 Canada ; Present address: Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, D-13125 Berlin, Germany
| | - Sylvie Picard
- Institut de recherches cliniques de Montréal (IRCM) and Dept of Medicine, Cardiovascular Biology Research Unit, Université de Montréal, 100 Pine Ave West, Montreal, QC H2W 1R7 Canada
| | - Christian F Deschepper
- Institut de recherches cliniques de Montréal (IRCM) and Dept of Medicine, Cardiovascular Biology Research Unit, Université de Montréal, 100 Pine Ave West, Montreal, QC H2W 1R7 Canada
| |
Collapse
|
361
|
Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Dunning Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JMC, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. The genome of Onchocerca volvulus, agent of river blindness. Nat Microbiol 2016; 2:16216. [PMID: 27869790 PMCID: PMC5310847 DOI: 10.1038/nmicrobiol.2016.216] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/26/2016] [Indexed: 01/08/2023]
Abstract
Human onchocerciasis is a serious neglected tropical disease caused by the filarial nematode Onchocerca volvulus that can lead to blindness and chronic disability. Control of the disease relies largely on mass administration of a single drug, and the development of new drugs and vaccines depends on a better knowledge of parasite biology. Here, we describe the chromosomes of O. volvulus and its Wolbachia endosymbiont. We provide the highest-quality sequence assembly for any parasitic nematode to date, giving a glimpse into the evolution of filarial parasite chromosomes and proteomes. This resource was used to investigate gene families with key functions that could be potentially exploited as targets for future drugs. Using metabolic reconstruction of the nematode and its endosymbiont, we identified enzymes that are likely to be essential for O. volvulus viability. In addition, we have generated a list of proteins that could be targeted by Federal-Drug-Agency-approved but repurposed drugs, providing starting points for anti-onchocerciasis drug development.
Collapse
Affiliation(s)
- James A. Cotton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Alexandra Grote
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - Bhavana Harsha
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Alan Tracey
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Robin Beech
- Institute of Parasitology, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Stephen R. Doyle
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Matthew Dunn
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Taisei Kikuchi
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Olivia Lambert
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Amruta Mhashilkar
- Global Health Infectious Disease Research Program, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida 33612, USA
| | - Prudence Mutowo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Nirvana Nursimulu
- Department of Computer Science, University of Toronto, Toronto M5S 3G4, Canada
- Division of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Jose M. C. Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Matthew B. Rogers
- Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224, USA
| | - Eleanor Stanley
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Lakshmipuram S. Swapna
- Division of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Isheng J. Tsai
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Thomas R. Unnasch
- Global Health Infectious Disease Research Program, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida 33612, USA
| | - Denis Voronin
- New York Blood Center, New York, New York 10065, USA
| | - John Parkinson
- Department of Computer Science, University of Toronto, Toronto M5S 3G4, Canada
- Division of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
- Departments of Biochemistry and Molecular Genetics, University of Toronto, M5S 1A8, Canada
| | - Thomas B. Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
- College of Global Public Health, New York University, New York, New York 10003, USA
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | | |
Collapse
|
362
|
Dunford A, Weinstock DM, Savova V, Schumacher SE, Cleary JP, Yoda A, Sullivan TJ, Hess JM, Gimelbrant AA, Beroukhim R, Lawrence MS, Getz G, Lane AA. Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias. Nat Genet 2016; 49:10-16. [PMID: 27869828 PMCID: PMC5206905 DOI: 10.1038/ng.3726] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/24/2016] [Indexed: 12/14/2022]
Abstract
There is a striking and unexplained male predominance across many cancer types. A subset of X-chromosome genes can escape X-inactivation, which would protect females from complete functional loss by a single mutation. To identify putative 'escape from X-inactivation tumor-suppressor' (EXITS) genes, we examined somatic alterations from >4,100 cancers across 21 tumor types for sex bias. Six of 783 non-pseudoautosomal region (PAR) X-chromosome genes (ATRX, CNKSR2, DDX3X, KDM5C, KDM6A, and MAGEC3) harbored loss-of-function mutations more frequently in males (based on a false discovery rate < 0.1), in comparison to zero of 18,055 autosomal and PAR genes (Fisher's exact P < 0.0001). Male-biased mutations in genes that escape X-inactivation were observed in combined analysis across many cancers and in several individual tumor types, suggesting a generalized phenomenon. We conclude that biallelic expression of EXITS genes in females explains a portion of the reduced cancer incidence in females as compared to males across a variety of tumor types.
Collapse
Affiliation(s)
- Andrew Dunford
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - David M Weinstock
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Virginia Savova
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven E Schumacher
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - John P Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Akinori Yoda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Julian M Hess
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Alexander A Gimelbrant
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michael S Lawrence
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Pathology and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew A Lane
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
363
|
Gobinath AR, Choleris E, Galea LA. Sex, hormones, and genotype interact to influence psychiatric disease, treatment, and behavioral research. J Neurosci Res 2016; 95:50-64. [DOI: 10.1002/jnr.23872] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Aarthi R. Gobinath
- Centre for Brain Health, Program in Neuroscience; University of British Columbia; Vancouver British Columbia V6T1Z3 Canada
| | - Elena Choleris
- Department of Psychology; University of Guelph; Guelph Ontario N1G 2W1 Canada
| | - Liisa A.M. Galea
- Centre for Brain Health, Program in Neuroscience; University of British Columbia; Vancouver British Columbia V6T1Z3 Canada
- Department of Psychology; University of British Columbia; Vancouver British Columbia V6T1Z3 Canada
| |
Collapse
|
364
|
Zemp N, Tavares R, Muyle A, Charlesworth D, Marais GAB, Widmer A. Evolution of sex-biased gene expression in a dioecious plant. NATURE PLANTS 2016; 2:16168. [PMID: 27808231 DOI: 10.1038/nplants.2016.168] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/29/2016] [Indexed: 05/25/2023]
Abstract
Separate sexes and sex-biased gene expression have repeatedly evolved in animals and plants, but the underlying changes in gene expression remain unknown. Here, we studied a pair of plant species, one in which separate sexes and sex chromosomes evolved recently and one which maintained hermaphrodite flowers resembling the ancestral state, to reconstruct expression changes associated with the evolution of dioecy. We found that sex-biased gene expression has evolved in autosomal and sex-linked genes in the dioecious species. Most expression changes relative to hermaphrodite flowers occurred in females rather than males, with higher and lower expression in females leading to female-biased and male-biased expression, respectively. Expression changes were more common in genes located on the sex chromosomes than the autosomes and led to feminization of the X chromosome and masculinization of the Y chromosome. Our results support a scenario in which sex-biased gene expression evolved during the evolution of dioecy to resolve intralocus sexual conflicts over the allocation of resources.
Collapse
Affiliation(s)
- Niklaus Zemp
- ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Raquel Tavares
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Aline Muyle
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Deborah Charlesworth
- University of Edinburgh, Institute of Evolutionary Biology, Edinburgh EH9 3JT, UK
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Alex Widmer
- ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092 Zürich, Switzerland
| |
Collapse
|
365
|
Abstract
X-chromosome inactivation, which was discovered by Mary Lyon in 1961 results in random silencing of one X chromosome in female mammals. This review is dedicated to Mary Lyon, who passed away last year. She predicted many of the features of X inactivation, for e.g., the existence of an X inactivation center, the role of L1 elements in spreading of silencing and the existence of genes that escape X inactivation. Starting from her published work here we summarize advances in the field.
Collapse
|
366
|
Moretti C, Vaiman D, Tores F, Cocquet J. Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells. Epigenetics Chromatin 2016; 9:47. [PMID: 27795737 PMCID: PMC5081929 DOI: 10.1186/s13072-016-0099-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During meiosis, the X and Y chromosomes are transcriptionally silenced. The persistence of repressive chromatin marks on the sex chromatin after meiosis initially led to the assumption that XY gene silencing persists to some extent in spermatids. Considering the many reports of XY-linked genes expressed and needed in the post-meiotic phase of mouse spermatogenesis, it is still unclear whether or not the mouse sex chromatin is a repressive or permissive environment, after meiosis. RESULTS To determine the transcriptional and chromatin state of the sex chromosomes after meiosis, we re-analyzed ten ChIP-Seq datasets performed on mouse round spermatids and four RNA-seq datasets from male germ cells purified at different stages of spermatogenesis. For this, we used the last version of the genome (mm10/GRCm38) and included reads that map to several genomic locations in order to properly interpret the high proportion of sex chromosome-encoded multicopy genes. Our study shows that coverage of active epigenetic marks H3K4me3 and Kcr is similar on the sex chromosomes and on autosomes. The post-meiotic sex chromatin nevertheless differs from autosomal chromatin in its enrichment in H3K9me3 and its depletion in H3K27me3 and H4 acetylation. We also identified a posttranslational modification, H3K27ac, which specifically accumulates on the Y chromosome. In parallel, we found that the X and Y chromosomes are enriched in genes expressed post-meiotically and display a higher proportion of spermatid-specific genes compared to autosomes. Finally, we observed that portions of chromosome 14 and of the sex chromosomes share specific features, such as enrichment in H3K9me3 and the presence of multicopy genes that are specifically expressed in round spermatids, suggesting that parts of chromosome 14 are under the same evolutionary constraints than the sex chromosomes. CONCLUSIONS Based on our expression and epigenomic studies, we conclude that, after meiosis, the mouse sex chromosomes are no longer silenced but are nevertheless regulated differently than autosomes and accumulate different chromatin marks. We propose that post-meiotic selective constraints are at the basis of the enrichment of spermatid-specific genes and of the peculiar chromatin composition of the sex chromosomes and of parts of chromosome 14.
Collapse
Affiliation(s)
- Charlotte Moretti
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Daniel Vaiman
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Frederic Tores
- INSERM U1163, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Julie Cocquet
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
367
|
Howe CG, Liu X, Hall MN, Ilievski V, Caudill MA, Malysheva O, Lomax-Luu AM, Parvez F, Siddique AB, Shahriar H, Uddin MN, Islam T, Graziano JH, Costa M, Gamble MV. Sex-Specific Associations between One-Carbon Metabolism Indices and Posttranslational Histone Modifications in Arsenic-Exposed Bangladeshi Adults. Cancer Epidemiol Biomarkers Prev 2016; 26:261-269. [PMID: 27765800 DOI: 10.1158/1055-9965.epi-16-0202] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 09/09/2016] [Accepted: 10/10/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Posttranslational histone modifications (PTHMs) are altered by arsenic, an environmental carcinogen. PTHMs are also influenced by nutritional methyl donors involved in one-carbon metabolism (OCM), which may protect against epigenetic dysregulation. METHODS We measured global levels of three PTHMs, which are dysregulated in cancers (H3K36me2, H3K36me3, H3K79me2), in peripheral blood mononuclear cells (PBMC) from 324 participants enrolled in the Folic Acid and Creatine Trial, a randomized trial in arsenic-exposed Bangladeshi adults. Sex-specific associations between several blood OCM indices (folate, vitamin B12, choline, betaine, homocysteine) and PTHMs were examined at baseline using regression models, adjusted for multiple tests by controlling for the false discovery rate (PFDR). We also evaluated the effects of folic acid supplementation (400 μg/d for 12 weeks), compared with placebo, on PTHMs. RESULTS Associations between choline and H3K36me2 and between vitamin B12 and H3K79me2 differed significantly by sex (Pdiff < 0.01 and <0.05, respectively). Among men, plasma choline was positively associated with H3K36me2 (PFDR < 0.05), and among women, plasma vitamin B12 was positively associated with H3K79me2 (PFDR < 0.01). Folic acid supplementation did not alter any of the PTHMs examined (PFDR = 0.80). CONCLUSIONS OCM indices may influence PTHMs in a sex-dependent manner, and folic acid supplementation, at this dose and duration, does not alter PTHMs in PBMCs. IMPACT This is the first study to examine the influences of OCM indices on PTHMs in a population that may have increased susceptibility to cancer development due to widespread exposure to arsenic-contaminated drinking water and a high prevalence of hyperhomocysteinemia. Cancer Epidemiol Biomarkers Prev; 26(2); 261-9. ©2016 AACR.
Collapse
Affiliation(s)
- Caitlin G Howe
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Xinhua Liu
- Department of Biostatistics, Mailman School of Public Health, New York
| | - Megan N Hall
- Department of Epidemiology, Mailman School of Public Health, New York
| | - Vesna Ilievski
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | - Olga Malysheva
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | - Angela M Lomax-Luu
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Abu B Siddique
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Hasan Shahriar
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Mohammad N Uddin
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Tariqul Islam
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Joseph H Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Max Costa
- Department of Environmental Medicine, NYU Langone Medical Center, New York University, New York
| | - Mary V Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| |
Collapse
|
368
|
Mayne BT, Bianco-Miotto T, Buckberry S, Breen J, Clifton V, Shoubridge C, Roberts CT. Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans. Front Genet 2016; 7:183. [PMID: 27790248 PMCID: PMC5062749 DOI: 10.3389/fgene.2016.00183] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/27/2016] [Indexed: 12/29/2022] Open
Abstract
The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analyzed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes), followed by the heart (375 genes), kidney (224 genes), colon (218 genes), and thyroid (163 genes). More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs, and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.
Collapse
Affiliation(s)
- Benjamin T Mayne
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
| | - Tina Bianco-Miotto
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; School of Agriculture, Food and Wine, Waite Research Institute, University of AdelaideAdelaide, SA, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical Research, The University of Western AustraliaPerth, WA, Australia; Plant Energy Biology, Australian Research Council Centre of Excellence, The University of Western AustraliaPerth, WA, Australia
| | - James Breen
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Bioinformatics Hub, School of Biological Sciences, University of AdelaideAdelaide, SA, Australia
| | - Vicki Clifton
- Mater Research Institute, University of Queensland Brisbane, QLD, Australia
| | - Cheryl Shoubridge
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
| | - Claire T Roberts
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
| |
Collapse
|
369
|
Widespread DNA hypomethylation and differential gene expression in Turner syndrome. Sci Rep 2016; 6:34220. [PMID: 27687697 PMCID: PMC5043230 DOI: 10.1038/srep34220] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/08/2016] [Indexed: 01/15/2023] Open
Abstract
Adults with 45,X monosomy (Turner syndrome) reflect a surviving minority since more than 99% of fetuses with 45,X monosomy die in utero. In adulthood 45,X monosomy is associated with increased morbidity and mortality, although strikingly heterogeneous with some individuals left untouched while others suffer from cardiovascular disease, autoimmune disease and infertility. The present study investigates the leukocyte DNAmethylation profile by using the 450K-Illumina Infinium assay and the leukocyte RNA-expression profile in 45,X monosomy compared with karyotypically normal female and male controls. We present results illustrating that genome wide X-chromosome RNA-expression profile, autosomal DNA-methylation profile, and the X-chromosome methylation profile clearly distinguish Turner syndrome from controls. Our results reveal genome wide hypomethylation with most differentially methylated positions showing a medium level of methylation. Contrary to previous studies, applying a single loci specific analysis at well-defined DNA loci, our results indicate that the hypomethylation extend to repetitive elements. We describe novel candidate genes that could be involved in comorbidity in TS and explain congenital urinary malformations (PRKX), premature ovarian failure (KDM6A), and aortic aneurysm formation (ZFYVE9 and TIMP1).
Collapse
|
370
|
Ezaz T, Srikulnath K, Graves JAM. Origin of Amniote Sex Chromosomes: An Ancestral Super-Sex Chromosome, or Common Requirements? J Hered 2016; 108:94-105. [DOI: 10.1093/jhered/esw053] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/22/2016] [Indexed: 12/28/2022] Open
|
371
|
Yoshida K, Makino T, Kitano J. Accumulation of Deleterious Mutations on the Neo-Y Chromosome of Japan Sea Stickleback (Gasterosteus nipponicus). J Hered 2016; 108:63-68. [DOI: 10.1093/jhered/esw054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/22/2016] [Indexed: 12/22/2022] Open
|
372
|
Sanchis-Segura C, Becker JB. Why we should consider sex (and study sex differences) in addiction research. Addict Biol 2016; 21:995-1006. [PMID: 27029841 DOI: 10.1111/adb.12382] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/31/2022]
Abstract
Among mammals, every cell has a biological sex, and the sex of an individual pervades its body and brain. In this review, we describe the processes through which mammals become phenotypically male or female by organizational and activational influences of genes and hormones throughout development. We emphasized that the molecular and cellular changes triggered by sex chromosomes and steroid hormones may generate sex differences in overt physiological functions and behavior, but they may alternatively promote end-point convergences between males and females. Clinical and pre-clinical evidences suggest that sex and gender differences modulate drug consumption as well as of the transition towards drug-promoted pathological states such as dependence and addiction. Additionally, sex differences in drug pharmacokinetics and pharmacodynamics will also influence dependence and addiction as well as side effects of drugs. These effects will further interact with socially gendered factors to result in sex differences in the access to, engagement in and efficacy of any therapeutic attempt. Finally, we maintain that 'sex sameness' is as important as 'sex differences' when building a complete understanding of biology for both males and females and provide a framework with which to classify and guide investigation into the mechanisms mediating sex differences and sex sameness.
Collapse
Affiliation(s)
- Carla Sanchis-Segura
- Departament de Psicologia básica, clínica i psicobiologia. Área de Psicobiología; Universitat Jaume I; Castellón de la Plana Spain
| | - Jill B. Becker
- Department of Psychology and Molecular and Behavioral Neuroscience Institute; University of Michigan; Ann Arbor MI USA
| |
Collapse
|
373
|
Howe CG, Gamble MV. Influence of Arsenic on Global Levels of Histone Posttranslational Modifications: a Review of the Literature and Challenges in the Field. Curr Environ Health Rep 2016; 3:225-37. [PMID: 27352015 PMCID: PMC4967376 DOI: 10.1007/s40572-016-0104-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Arsenic is a human carcinogen and also increases the risk for non-cancer outcomes. Arsenic-induced epigenetic dysregulation may contribute to arsenic toxicity. Although there are several reviews on arsenic and epigenetics, these have largely focused on DNA methylation. Here, we review investigations of the effects of arsenic on global levels of histone posttranslational modifications (PTMs). Multiple studies have observed that arsenic induces higher levels of H3 lysine 9 dimethylation (H3K9me2) and also higher levels of H3 serine 10 phosphorylation (H3S10ph), which regulate chromosome segregation. In contrast, arsenic causes a global loss of H4K16ac, a histone PTM that is a hallmark of human cancers. Although the findings for other histone PTMs have not been entirely consistent across studies, we discuss biological factors which may contribute to these inconsistencies, including differences in the dose, duration, and type of arsenic species examined; the tissue or cell line evaluated; differences by sex; and exposure timing. We also discuss two important considerations for the measurement of histone PTMs: proteolytic cleavage of histones and arsenic-induced alterations in histone expression.
Collapse
Affiliation(s)
- Caitlin G. Howe
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University. Address: 11 Floor, 722 W. 168 Street, New York, New York, 10032. . Phone: 212-305-1205. Fax: 212-305-3857
| | - Mary V. Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University. Address: 11 Floor, 722 W. 168 Street, New York, New York, 10032. . Phone: 212-305-7949. Fax: 212-305-3857
| |
Collapse
|
374
|
Muyle A, Käfer J, Zemp N, Mousset S, Picard F, Marais GA. SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms. Genome Biol Evol 2016; 8:2530-43. [PMID: 27492231 PMCID: PMC5010906 DOI: 10.1093/gbe/evw172] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, and UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U, and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical Silene data show that our method identifies 20-35% more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Approximately 12 individuals are needed for optimal results based on simulations. For species with an unknown sex-determination system, the method can assess the presence and type (XY vs. ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimized for sex chromosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organisms, including non-model ones for which nothing is known a priori, that can be bred in the lab, are suitable for our method. SEX-DETector and its implementation in a Galaxy workflow are made freely available.
Collapse
Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Niklaus Zemp
- Institute of Integrative Biology (IBZ), ETH Zurich, Zürich, Switzerland
| | - Sylvain Mousset
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Gabriel Ab Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| |
Collapse
|
375
|
Mulugeta E, Wassenaar E, Sleddens-Linkels E, van IJcken WFJ, Heard E, Grootegoed JA, Just W, Gribnau J, Baarends WM. Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes. Genome Res 2016; 26:1202-10. [PMID: 27510564 PMCID: PMC5052041 DOI: 10.1101/gr.201665.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/11/2016] [Indexed: 11/24/2022]
Abstract
The X and Y sex chromosomes of placental mammals show hallmarks of a tumultuous evolutionary past. The X Chromosome has a rich and conserved gene content, while the Y Chromosome has lost most of its genes. In the Transcaucasian mole vole Ellobius lutescens, the Y Chromosome including Sry has been lost, and both females and males have a 17,X diploid karyotype. Similarly, the closely related Ellobius talpinus, has a 54,XX karyotype in both females and males. Here, we report the sequencing and assembly of the E. lutescens and E. talpinus genomes. The results indicate that the loss of the Y Chromosome in E. lutescens and E. talpinus occurred in two independent events. Four functional homologs of mouse Y-Chromosomal genes were detected in both female and male E. lutescens, of which three were also detected in the E. talpinus genome. One of these is Eif2s3y, known as the only Y-derived gene that is crucial for successful male meiosis. Female and male E. lutescens can carry one and the same X Chromosome with a largely conserved gene content, including all genes known to function in X Chromosome inactivation. The availability of the genomes of these mole vole species provides unique models to study the dynamics of sex chromosome evolution.
Collapse
Affiliation(s)
- Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands; Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | | | | | - Edith Heard
- Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Walter Just
- Institute of Human Genetics, University of Ulm, 89081, Ulm, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| |
Collapse
|
376
|
Morselli E, Frank AP, Santos RS, Fátima LA, Palmer BF, Clegg DJ. Sex and Gender: Critical Variables in Pre-Clinical and Clinical Medical Research. Cell Metab 2016; 24:203-9. [PMID: 27508869 DOI: 10.1016/j.cmet.2016.07.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/21/2016] [Accepted: 07/22/2016] [Indexed: 01/15/2023]
Abstract
In this Essay, we discuss the critical need to incorporate sex and gender in pre-clinical and clinical research to enhance our understanding of the mechanisms by which metabolic processes differ by sex and gender. This knowledge will allow for development of personalized medicine which will optimize therapies specific for individuals.
Collapse
Affiliation(s)
- Eugenia Morselli
- Faculty of Biological Sciences, Department of Physiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Aaron P Frank
- Department of Biomedical Research, Cedars-Sinai Diabetes and Obesity Research Institute, Los Angeles, CA 90048, USA
| | - Roberta S Santos
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, e Centro de Pesquisa em Obesidade e Comorbidades, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Luciana A Fátima
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo, SP 05508-000, Brazil
| | - Biff F Palmer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Deborah J Clegg
- Department of Biomedical Research, Cedars-Sinai Diabetes and Obesity Research Institute, Los Angeles, CA 90048, USA.
| |
Collapse
|
377
|
Howe CG, Liu X, Hall MN, Slavkovich V, Ilievski V, Parvez F, Siddique AB, Shahriar H, Uddin MN, Islam T, Graziano JH, Costa M, Gamble MV. Associations between Blood and Urine Arsenic Concentrations and Global Levels of Post-Translational Histone Modifications in Bangladeshi Men and Women. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:1234-40. [PMID: 26967670 PMCID: PMC4977054 DOI: 10.1289/ehp.1510412] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/21/2015] [Accepted: 02/22/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Exposure to inorganic arsenic is associated with numerous adverse health outcomes, with susceptibility differing by sex. Although evidence from in vitro studies suggests that arsenic alters post-translational histone modifications (PTHMs), evidence in humans is limited. OBJECTIVES The objectives were to determine: a) if arsenic exposure is associated with global (percent) levels of PTHMs H3K36me2, H3K36me3, and H3K79me2 in a sex-dependent manner, and b) if %PTHMs are stable when arsenic exposure is reduced. METHODS We examined associations between arsenic, measured in blood and urine, and %PTHMs in peripheral blood mononuclear cells from 317 participants enrolled in the Bangladesh Folic Acid and Creatine Trial (FACT). We also examined the stability of %PTHMs after the use of arsenic-removal water filters (n = 60). RESULTS Associations between natural log-transformed (ln) urinary arsenic, adjusted for creatinine (uAsCr), and %H3K36me2 differed significantly between men and women (p = 0.01). ln(uAsCr) was positively associated with %H3K36me2 in men [β = 0.12; 95% confidence interval (CI): 0.01, 0.23, p = 0.03] but was negatively associated with %H3K36me2 in women (β = -0.05; 95% CI: -0.12, 0.02, p = 0.19). The patterns of associations with blood arsenic were similar. On average, water filter use was also associated with reductions in %H3K36me2 (p < 0.01), but this did not differ significantly by sex. Arsenic was not significantly associated with %H3K36me3 or %H3K79me2 in men or women. CONCLUSIONS Arsenic exposure was associated with %H3K36me2 in a sex-specific manner but was not associated with %H3K36me3 or %H3K79me2. Additional studies are needed to assess changes in %H3K36me2 after arsenic removal. CITATION Howe CG, Liu X, Hall MN, Slavkovich V, Ilievski V, Parvez F, Siddique AB, Shahriar H, Uddin MN, Islam T, Graziano JH, Costa M, Gamble MV. 2016. Associations between blood and urine arsenic concentrations and global levels of post-translational histone modifications in Bangladeshi men and women. Environ Health Perspect 124:1234-1240; http://dx.doi.org/10.1289/ehp.1510412.
Collapse
Affiliation(s)
| | | | - Megan N. Hall
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | | | | | - Abu B. Siddique
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Hasan Shahriar
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Mohammad N. Uddin
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Tariqul Islam
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | | | - Max Costa
- Department of Environmental Medicine, Langone Medical Center, New York University, New York, New York, USA
| | - Mary V. Gamble
- Department of Environmental Health Sciences,
- Address correspondence to M.V. Gamble, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 11th Floor, 722 W. 168th St., New York, NY 10032 USA. Telephone: (212) 305-7949. E-mail:
| |
Collapse
|
378
|
Ka S, Ahn H, Seo M, Kim H, Kim JN, Lee HJ. Status of dosage compensation of X chromosome in bovine genome. Genetica 2016; 144:435-44. [PMID: 27376899 DOI: 10.1007/s10709-016-9912-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 06/27/2016] [Indexed: 01/18/2023]
Abstract
Dosage compensation system with X chromosome upregulation and inactivation have evolved to overcome the genetic imbalance between sex chromosomes in both male and female of mammals. Although recent development of chromosome-wide technologies has allowed us to test X upregulation, discrete data processing and analysis methods draw disparate conclusions. A series of expression studies revealed status of dosage compensation in some species belonging to monotremes, marsupials, rodents and primates. However, X upregulation in the Artiodactyla order including cattle have not been studied yet. In this study, we surveyed the genome-wide transcriptional upregulation in X chromosome in cattle RNA-seq data using different gene filtration methods. Overall examination of RNA-seq data revealed that X chromosome in the pituitary gland expressed more genes than in other peripheral tissues, which was consistent with the previous results observed in human and mouse. When analyzed with globally expressed genes, a median X:A expression ratio was 0.94. The ratio of 1-to-1 ortholog genes between chicken and mammals, however, showed considerable reduction to 0.68. These results indicate that status of dosage compensation for cattle is not deviated from those found in rodents and primate, and this is consistent with the evolutionary history of cattle.
Collapse
Affiliation(s)
- Sojeong Ka
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyeonju Ahn
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Minseok Seo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- C&K Genomics Inc., Seoul National University Research Park, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin Nam Kim
- C&K Genomics Inc., Seoul National University Research Park, Seoul, 08826, Republic of Korea.
| | - Hyun-Jeong Lee
- Animal Nutritional Physiology Team, National Institute of Animal Science, Jeonju, Jeollabuk-Do, 55365, Republic of Korea.
| |
Collapse
|
379
|
An Allometric Analysis of Sex and Sex Chromosome Dosage Effects on Subcortical Anatomy in Humans. J Neurosci 2016; 36:2438-48. [PMID: 26911691 DOI: 10.1523/jneurosci.3195-15.2016] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Structural neuroimaging of humans with typical and atypical sex-chromosome complements has established the marked influence of both Yand X-/Y-chromosome dosage on total brain volume (TBV) and identified potential cortical substrates for the psychiatric phenotypes associated with sex-chromosome aneuploidy (SCA). Here, in a cohort of 354 humans with varying karyotypes (XX, XY, XXX, XXY, XYY, XXYY, XXXXY), we investigate sex and SCA effects on subcortical size and shape; focusing on the striatum, pallidum and thalamus. We find large effect-size differences in the volume and shape of all three structures as a function of sex and SCA. We correct for TBV effects with a novel allometric method harnessing normative scaling rules for subcortical size and shape in humans, which we derive here for the first time. We show that all three subcortical volumes scale sublinearly with TBV among healthy humans, mirroring known relationships between subcortical volume and TBV among species. Traditional TBV correction methods assume linear scaling and can therefore invert or exaggerate sex and SCA effects on subcortical anatomy. Allometric analysis restricts sex-differences to: (1) greater pallidal volume (PV) in males, and (2) relative caudate head expansion and ventral striatum contraction in females. Allometric analysis of SCA reveals that supernumerary X- and Y-chromosomes both cause disproportionate reductions in PV, and coordinated deformations of striatopallidal shape. Our study provides a novel understanding of sex and sex-chromosome dosage effects on subcortical organization, using an allometric approach that can be generalized to other basic and clinical structural neuroimaging settings.
Collapse
|
380
|
Murata C, Kuroki Y, Imoto I, Kuroiwa A. Ancestral Y-linked genes were maintained by translocation to the X and Y chromosomes fused to an autosomal pair in the Okinawa spiny rat Tokudaia muenninki. Chromosome Res 2016; 24:407-19. [DOI: 10.1007/s10577-016-9531-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/14/2016] [Indexed: 11/29/2022]
|
381
|
Śliwińska EB, Martyka R, Tryjanowski P. Evolutionary interaction between W/Y chromosome and transposable elements. Genetica 2016; 144:267-78. [PMID: 27000053 PMCID: PMC4879163 DOI: 10.1007/s10709-016-9895-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 03/13/2016] [Indexed: 11/28/2022]
Abstract
The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation.
Collapse
Affiliation(s)
- Ewa B Śliwińska
- Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71C, 60-625, Poznań, Poland.
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Kraków, Poland.
| | - Rafał Martyka
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Kraków, Poland
| | - Piotr Tryjanowski
- Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71C, 60-625, Poznań, Poland
| |
Collapse
|
382
|
Los E, Quezada E, Chen Z, Lapidus J, Silberbach M. Pilot Study of Blood Pressure in Girls With Turner Syndrome: An Awareness Gap, Clinical Associations, and New Hypotheses. Hypertension 2016; 68:133-6. [PMID: 27217413 DOI: 10.1161/hypertensionaha.115.07065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/22/2016] [Indexed: 01/15/2023]
Abstract
Cardiovascular disease is the major factor that reduces lifespan in Turner syndrome. High blood pressure (BP) is common in Turner syndrome and is the most easily treatable cardiovascular risk factor. We studied the prevalence of elevated screening systemic BP, awareness of the problem, and its clinical associations in a large group of girls attending the annual meeting of the Turner Syndrome Society of the United States. Among 168 girls aged 2 to 17 years, 42% had elevated screening BP (systolic and diastolic), yet only 8% reported a previous diagnosis of hypertension. History of aortic coarctation repair (17%) was positively associated with elevated systolic BP (52% versus 32%; P<0.05). Elevated systolic BP was positively associated with obesity (56% versus 31%; P<0.05). Because the prevalence of obesity in the studied population was similar to Center for Disease Control published data for obesity in all girls and the prevalence of increased BP is approximately twice that of the general population, the Turner syndrome phenotype/genotype probably includes an intrinsic risk for hypertension. Obesity and repaired aortic coarctation increase this risk further. There seems to be a BP awareness gap in girls with Turner syndrome. Because girls living with Turner syndrome are a sensitized population for hypertension, further study may provide clues to genetic factors leading to a better understanding of essential hypertension in the general population.
Collapse
Affiliation(s)
- Evan Los
- From the Pediatric Endocrinology (E.L.), Pediatric Cardiology (E.Q., M.S.), and Department of Public Health & Preventive Medicine (Z.C., J.L), Oregon Health & Science University, Portland, OR.
| | - Emilio Quezada
- From the Pediatric Endocrinology (E.L.), Pediatric Cardiology (E.Q., M.S.), and Department of Public Health & Preventive Medicine (Z.C., J.L), Oregon Health & Science University, Portland, OR
| | - Zunqiu Chen
- From the Pediatric Endocrinology (E.L.), Pediatric Cardiology (E.Q., M.S.), and Department of Public Health & Preventive Medicine (Z.C., J.L), Oregon Health & Science University, Portland, OR
| | - Jodi Lapidus
- From the Pediatric Endocrinology (E.L.), Pediatric Cardiology (E.Q., M.S.), and Department of Public Health & Preventive Medicine (Z.C., J.L), Oregon Health & Science University, Portland, OR
| | - Michael Silberbach
- From the Pediatric Endocrinology (E.L.), Pediatric Cardiology (E.Q., M.S.), and Department of Public Health & Preventive Medicine (Z.C., J.L), Oregon Health & Science University, Portland, OR
| |
Collapse
|
383
|
Birchler JA. Parallel Universes for Models of X Chromosome Dosage Compensation in Drosophila: A Review. Cytogenet Genome Res 2016; 148:52-67. [PMID: 27166165 DOI: 10.1159/000445924] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
Dosage compensation in Drosophila involves an approximately 2-fold increase in expression of the single X chromosome in males compared to the per gene expression in females with 2 X chromosomes. Two models have been considered for an explanation. One proposes that the male-specific lethal (MSL) complex that is associated with the male X chromosome brings histone modifiers to the sex chromosome to increase its expression. The other proposes that the inverse effect which results from genomic imbalance would tend to upregulate the genome approximately 2-fold, but the MSL complex sequesters histone modifiers from the autosomes to the X to mute this autosomal male-biased expression. On the X, the MSL complex must override the high level of resulting histone modifications to prevent overcompensation of the X chromosome. Each model is evaluated in terms of fitting classical genetic and recent molecular data. Potential paths toward resolving the models are suggested.
Collapse
Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Mo., USA
| |
Collapse
|
384
|
Abstract
The incidence of many types of cancer arising in organs with non-reproductive functions is significantly higher in male populations than in female populations, with associated differences in survival. Occupational and/or behavioural factors are well-known underlying determinants. However, cellular and molecular differences between the two sexes are also likely to be important. In this Opinion article, we focus on the complex interplay that sex hormones and sex chromosomes can have in intrinsic control of cancer-initiating cell populations, the tumour microenvironment and systemic determinants of cancer development, such as the immune system and metabolism. A better appreciation of these differences between the two sexes could be of substantial value for cancer prevention as well as treatment.
Collapse
Affiliation(s)
- Andrea Clocchiatti
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Elisa Cora
- Department of Biochemistry, University of Lausanne, Epalinges, CH-1066, Switzerland
| | - Yosra Zhang
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; and the Department of Biochemistry, University of Lausanne, Epalinges, CH-1066, Switzerland
| | - G Paolo Dotto
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; and the Department of Biochemistry, University of Lausanne, Epalinges, CH-1066, Switzerland
| |
Collapse
|
385
|
Abstract
Although individuals in most flowering plant species, and in many haploid plants, have both sex functions, dioecious species-in which individuals have either male or female functions only-are scattered across many taxonomic groups, and many species have genetic sex determination. Among these, some have visibly heteromorphic sex chromosomes, and molecular genetic studies are starting to uncover sex-linked markers in others, showing that they too have fully sex-linked regions that are either too small or are located in chromosomes that are too small to be cytologically detectable from lack of pairing, lack of visible crossovers, or accumulation of heterochromatin. Detailed study is revealing that, like animal sex chromosomes, plant sex-linked regions show evidence for accumulation of repetitive sequences and genetic degeneration. Estimating when recombination stopped confirms the view that many plants have young sex-linked regions, making plants of great interest for studying the timescale of these changes.
Collapse
Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
| |
Collapse
|
386
|
Disteche CM. Dosage compensation of the sex chromosomes and autosomes. Semin Cell Dev Biol 2016; 56:9-18. [PMID: 27112542 DOI: 10.1016/j.semcdb.2016.04.013] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/16/2022]
Abstract
Males are XY and females are XX in most mammalian species. Other species such as birds have a different sex chromosome make-up: ZZ in males and ZW in females. In both types of organisms one of the sex chromosomes, Y or W, has degenerated due to lack of recombination with its respective homolog X or Z. Since autosomes are present in two copies in diploid organisms the heterogametic sex has become a natural "aneuploid" with haploinsufficiency for X- or Z-linked genes. Specific mechanisms have evolved to restore a balance between critical gene products throughout the genome and between males and females. Some of these mechanisms were co-opted from and/or added to compensatory processes that alleviate autosomal aneuploidy. Surprisingly, several modes of dosage compensation have evolved. In this review we will consider the evidence for dosage compensation and the molecular mechanisms implicated.
Collapse
Affiliation(s)
- Christine M Disteche
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific St. Seattle, WA 98115, USA; Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific St. Seattle, WA 98115, USA.
| |
Collapse
|
387
|
Abstract
The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
Collapse
|
388
|
Escape Artists of the X Chromosome. Trends Genet 2016; 32:348-359. [PMID: 27103486 DOI: 10.1016/j.tig.2016.03.007] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 01/24/2023]
Abstract
Inactivation of one X chromosome in mammalian females achieves dosage compensation between XX females and XY males; however, over 15% of human X-linked genes continue to be expressed from the inactive X chromosome. New genomic methodologies have improved our identification and characterization of these escape genes, revealing the importance of DNA sequence, chromatin structure, and chromosome ultrastructure in regulating expression from an otherwise inactive chromosome. Study of these exceptions to the rule of silencing highlights the interconnectedness of chromatin and chromosome structure in X-chromosome inactivation (XCI). Recent advances also demonstrate the importance of these genes in sexually dimorphic disease risk, particularly cancer.
Collapse
|
389
|
Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proc Natl Acad Sci U S A 2016; 113:E2114-23. [PMID: 27035980 PMCID: PMC4839409 DOI: 10.1073/pnas.1525164113] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich heterochromatin, knowledge of Y chromosome sequences is limited to a handful of model organisms, constraining our understanding of Y biology across the tree of life. Here, we leverage long single-molecule sequencing to determine the content and structure of the nonrecombining Y chromosome of the primary African malaria mosquito, Anopheles gambiae We find that the An. gambiae Y consists almost entirely of a few massively amplified, tandemly arrayed repeats, some of which can recombine with similar repeats on the X chromosome. Sex-specific genome resequencing in a recent species radiation, the An. gambiae complex, revealed rapid sequence turnover within An. gambiae and among species. Exploiting 52 sex-specific An. gambiae RNA-Seq datasets representing all developmental stages, we identified a small repertoire of Y-linked genes that lack X gametologs and are not Y-linked in any other species except An. gambiae, with the notable exception of YG2, a candidate male-determining gene. YG2 is the only gene conserved and exclusive to the Y in all species examined, yet sequence similarity to YG2 is not detectable in the genome of a more distant mosquito relative, suggesting rapid evolution of Y chromosome genes in this highly dynamic genus of malaria vectors. The extensive characterization of the An. gambiae Y provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.
Collapse
Affiliation(s)
- Andrew Brantley Hall
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Philippos-Aris Papathanos
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Atashi Sharma
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Changde Cheng
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Omar S Akbari
- Department of Entomology, Riverside Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Lauren Assour
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Alessia Cagnetti
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Andrea Crisanti
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Tania Dottorini
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Elisa Fiorentini
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jonathan Hnath
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Xiaofang Jiang
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Diane Radune
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Laboratory of Evolutionary Cytogenetics, Tomsk State University, Tomsk 634050, Russia
| | - Aaron Steele
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Vladimir A Timoshevskiy
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Simo Zhang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405
| | - Matthew W Hahn
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405; Department of Biology, Indiana University, Bloomington, IN 47405
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Igor V Sharakhov
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Laboratory of Evolutionary Cytogenetics, Tomsk State University, Tomsk 634050, Russia;
| | - Zhijian Jake Tu
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556;
| |
Collapse
|
390
|
Galea LAM, Frick KM, Hampson E, Sohrabji F, Choleris E. Why estrogens matter for behavior and brain health. Neurosci Biobehav Rev 2016; 76:363-379. [PMID: 27039345 PMCID: PMC5045786 DOI: 10.1016/j.neubiorev.2016.03.024] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/21/2016] [Accepted: 03/29/2016] [Indexed: 12/22/2022]
Abstract
The National Institutes of Health (NIH) has required the inclusion of women in clinical studies since 1993, which has enhanced our understanding of how biological sex affects certain medical conditions and allowed the development of sex-specific treatment protocols. However, NIH's policy did not previously apply to basic research, and the NIH recently introduced a new policy requiring all new grant applications to explicitly address sex as a biological variable. The policy itself is grounded in the results of numerous investigations in animals and humans illustrating the existence of sex differences in the brain and behavior, and the importance of sex hormones, particularly estrogens, in regulating physiology and behavior. Here, we review findings from our laboratories, and others, demonstrating how estrogens influence brain and behavior in adult females. Research from subjects throughout the adult lifespan on topics ranging from social behavior, learning and memory, to disease risk will be discussed to frame an understanding of why estrogens matter to behavioral neuroscience.
Collapse
Affiliation(s)
- Liisa A M Galea
- Department of Psychology, Centre for Brain Health, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Karyn M Frick
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, United States
| | - Elizabeth Hampson
- Department of Psychology, University of Western Ontario, London, ON N6A 5C2, Canada
| | - Farida Sohrabji
- Department of Neuroscience and Experimental Therapeutics, Texas A&M HSC College of Medicine, Bryan, TX 77807, United States
| | - Elena Choleris
- Department of Psychology and Neuroscience Program, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
391
|
Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PCM, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. Genome Res 2016; 26:530-40. [PMID: 26934921 PMCID: PMC4817776 DOI: 10.1101/gr.199448.115] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/21/2016] [Indexed: 01/25/2023]
Abstract
The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
Collapse
Affiliation(s)
- Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Samarth Rangavittal
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Monika Cechova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Rebeca Campos Sanchez
- Genetics Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Howard W Fescemyer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Danling Ye
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Patricia C M O'Brien
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Rayan Chikhi
- University of Lille 1/CNRS 59655 Villeneuve d'Ascq, France; Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA
| | | | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
392
|
Ghenu AH, Bolker BM, Melnick DJ, Evans BJ. Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 2016; 17:157. [PMID: 26925773 PMCID: PMC4772468 DOI: 10.1186/s12864-015-2187-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022] Open
Abstract
Background The primate Y chromosome is distinguished by a lack of inter-chromosomal recombination along most of its length, extensive gene loss, and a prevalence of repetitive elements. A group of genes on the male-specific portion of the Y chromosome known as the “ampliconic genes” are present in multiple copies that are sometimes part of palindromes, and that undergo a form of intra-chromosomal recombination called gene conversion, wherein the nucleotides of one copy are homogenized by those of another. With the aim of further understanding gene family evolution of these genes, we collected nucleotide sequence and gene copy number information for several species of papionin monkey. We then tested for evidence of gene conversion, and developed a novel statistical framework to evaluate alternative models of gene family evolution using our data combined with other information from a human, a chimpanzee, and a rhesus macaque. Results Our results (i) recovered evidence for several novel examples of gene conversion in papionin monkeys and indicate that (ii) ampliconic gene families evolve faster than autosomal gene families and than single-copy genes on the Y chromosome and that (iii) Y-linked singleton and autosomal gene families evolved faster in humans and chimps than they do in the other Old World Monkey lineages we studied. Conclusions Rapid evolution of ampliconic genes cannot be attributed solely to residence on the Y chromosome, nor to variation between primate lineages in the rate of gene family evolution. Instead other factors, such as natural selection and gene conversion, appear to play a role in driving temporal and genomic evolutionary heterogeneity in primate gene families. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2187-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ana-Hermina Ghenu
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
| | - Benjamin M Bolker
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,Department of Mathematics & Statistics, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th Floor Schermerhorn Extension, New York, 10027, USA
| | - Ben J Evans
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
| |
Collapse
|
393
|
Hallast P, Maisano Delser P, Batini C, Zadik D, Rocchi M, Schempp W, Tyler-Smith C, Jobling MA. Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal. Genome Res 2016; 26:427-39. [PMID: 26883546 PMCID: PMC4817767 DOI: 10.1101/gr.198754.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 12/30/2022]
Abstract
The distribution of genetic diversity in great ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale–multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8–15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times.
Collapse
Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Mariano Rocchi
- Department of Biology, University of Bari, 70124 Bari, Italy
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| |
Collapse
|
394
|
Yamauchi Y, Riel JM, Ruthig VA, Ortega EA, Mitchell MJ, Ward MA. Two genes substitute for the mouse Y chromosome for spermatogenesis and reproduction. Science 2016; 351:514-6. [PMID: 26823431 DOI: 10.1126/science.aad1795] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The mammalian Y chromosome is considered a symbol of maleness, as it encodes a gene driving male sex determination, Sry, as well as a battery of other genes important for male reproduction. We previously demonstrated in the mouse that successful assisted reproduction can be achieved when the Y gene contribution is limited to only two genes, Sry and spermatogonial proliferation factor Eif2s3y. Here, we replaced Sry by transgenic activation of its downstream target Sox9, and Eif2s3y, by transgenic overexpression of its X chromosome-encoded homolog Eif2s3x. The resulting males with no Y chromosome genes produced haploid male gametes and sired offspring after assisted reproduction. Our findings support the existence of functional redundancy between the Y chromosome genes and their homologs encoded on other chromosomes.
Collapse
Affiliation(s)
- Yasuhiro Yamauchi
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, 1960 East-West Road, Honolulu, HI 96822, USA
| | - Jonathan M Riel
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, 1960 East-West Road, Honolulu, HI 96822, USA
| | - Victor A Ruthig
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, 1960 East-West Road, Honolulu, HI 96822, USA
| | - Eglė A Ortega
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, 1960 East-West Road, Honolulu, HI 96822, USA
| | - Michael J Mitchell
- Aix-Marseille Université, INSERM, GMGF UMR_S 910, 13385 Marseille, France
| | - Monika A Ward
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, 1960 East-West Road, Honolulu, HI 96822, USA.
| |
Collapse
|
395
|
Abstract
Male and female differ genetically by their respective sex chromosome composition, that is, XY as male and XX as female. Although both X and Y chromosomes evolved from the same ancestor pair of autosomes, the Y chromosome harbors male-specific genes, which play pivotal roles in male sex determination, germ cell differentiation, and masculinization of various tissues. Deletions or translocation of the sex-determining gene, SRY, from the Y chromosome causes disorders of sex development (previously termed as an intersex condition) with dysgenic gonads. Failure of gonadal development results not only in infertility, but also in increased risks of germ cell tumor (GCT), such as gonadoblastoma and various types of testicular GCT. Recent studies demonstrate that either loss of Y chromosome or ectopic expression of Y chromosome genes is closely associated with various male-biased diseases, including selected somatic cancers. These observations suggest that the Y-linked genes are involved in male health and diseases in more frequently than expected. Although only a small number of protein-coding genes are present in the male-specific region of Y chromosome, the impacts of Y chromosome genes on human diseases are still largely unknown, due to lack of in vivo models and differences between the Y chromosomes of human and rodents. In this review, we highlight the involvement of selected Y chromosome genes in cancer development in men.
Collapse
Affiliation(s)
| | - Yun-Fai Chris Lau
- Division of Cell and Developmental Genetics, Department of Medicine, Veterans Affairs Medical Center, Institute for Human Genetics, University of California, San Francisco, California 94121, USA
| |
Collapse
|
396
|
Koerich LB, Dupim EG, Faria LL, Dias FA, Dias AF, Trindade GS, Mesquita RD, Carvalho AB. First report of Y-linked genes in the kissing bug Rhodnius prolixus. BMC Genomics 2016; 17:100. [PMID: 26861771 PMCID: PMC4746886 DOI: 10.1186/s12864-016-2425-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/01/2016] [Indexed: 12/13/2022] Open
Abstract
Background Due to an abundance of repetitive DNA, the annotation of heterochromatic regions of the genome such as the Y chromosome is problematic. The Y chromosome is involved in key biological functions such as male-fertility and sex-determination and hence, accurate identification of its sequences is vital. The hemipteran insect Rhodnius prolixus is an important vector of Chagas disease, a trypanosomiasis affecting 6–7 million people worldwide. Here we report the identification of the first Y-linked genes of this species. Results The R. prolixus genome was recently sequenced using separate libraries for each sex and the sequences assembled only with male reads are candidates for Y linkage. We found 766 such candidates and PCR tests with the ten largest ones, confirmed Y-linkage for all of them, suggesting that "separate libraries" is a reliable method for the identification of Y-linked sequences. BLAST analyses of the 766 candidate scaffolds revealed that 568 scaffolds contained genes or part of putative genes. We tested Y-linkage for 36 candidates and found that nine of them are Y-linked (the PCR results for the other 25 genes were inconclusive or revealed autosomal/X-linkage). Hence, we describe in this study, for the first time, Y-linked genes in the R. prolixus genome: two zinc finger proteins (Znf-Y1 and Znf-Y2), one metalloproteinase (Met-Y), one aconitase/iron regulatory protein (Aco-Y) and five genes devoid of matches in any database (Rpr-Y1 to Rpr-Y5). Expression profile studies revealed that eight genes are expressed mainly in adult testis (some of which presented a weak expression in the initial developmental stages), while Aco-Y has a gut-restricted expression. Conclusions In this study we showed that the approach used for the R. prolixus genome project (separate sequencing of male and female DNA) is key to easy and fast identification of sex-specific (e.g. Y chromosome sequences). The nine new R. prolixus Y-linked genes reported here provide unique markers for population and phylogenetic analysis and further functional studies of these genes may answer some questions about sex determination, male fertility and Y chromosome evolution in this important species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2425-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Leonardo B Koerich
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. .,Departamento de Parasitologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Eduardo G Dupim
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Leonardo L Faria
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Felipe A Dias
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Ana F Dias
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Gabriela S Trindade
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Rafael D Mesquita
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Antonio B Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| |
Collapse
|
397
|
Prokop JW, Tsaih SW, Faber AB, Boehme S, Underwood AC, Troyer S, Playl L, Milsted A, Turner ME, Ely D, Martins AS, Tutaj M, Lazar J, Dwinell MR, Jacob HJ. The phenotypic impact of the male-specific region of chromosome-Y in inbred mating: the role of genetic variants and gene duplications in multiple inbred rat strains. Biol Sex Differ 2016; 7:10. [PMID: 26848384 PMCID: PMC4740989 DOI: 10.1186/s13293-016-0064-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/26/2016] [Indexed: 12/22/2022] Open
Abstract
Backgound The male-specific region of chromosome-Y (MSY) contributes to phenotypes outside of testis development and has a high rate of evolution between mammalian species. With a lack of genomic crossover, MSY is one of the few genomic areas under similar variation and evolutionary selection in inbred and outbred animal populations, allowing for an assessment of evolutionary mechanisms to translate between the populations. Methods Using next-generation sequencing, MSY consomic strains, molecular characterization, and large-scale phenotyping, we present here regions of MSY that contribute to inbred strain phenotypes. Results We have shown that (1) MSY of rat has nine autosomal gene transposition events with strain-specific selection; (2) sequence variants in MSY occur with a 1.98-fold higher number of variants than other chromosomes in seven sequenced rat strains; (3) Sry, the most studied MSY gene, has undergone extensive gene duplications, driving ubiquitous expression not seen in human or mouse; (4) the expression profile of Sry in the rat is driven by the insertion of the Sry2 copy into an intron of the ubiquitously expressed Kdm5d gene in antisense orientation, but due to several loss of function mutations in the Sry2 protein, nuclear localization and transcriptional control are decreased; (5) expression of Sry copies other than Sry2 in the rat overlaps with the expression profile for human SRY; (6) gene duplications and sequence variants (P76T) of Sry can be selected for phenotypes such as high blood pressure and androgen receptor signaling within inbred mating; and most importantly, (7) per chromosome size, MSY contributes to higher strain-specific phenotypic variation relative to all other chromosomes, with 53 phenotypes showing both a male to female and consomic cross significance. Conclusion The data presented supports a high probability of MSY genetic variation altering a broad range of inbred rat phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s13293-016-0064-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ; Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Shirng-Wern Tsaih
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Allison B Faber
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Shannon Boehme
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Adam C Underwood
- Department of Mathematics and Science, Walsh University, North Canton, OH 44720 USA
| | - Samuel Troyer
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Lauren Playl
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Amy Milsted
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Monte E Turner
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Daniel Ely
- Department of Biology, The University of Akron, Akron, OH 44325 USA
| | - Almir S Martins
- Núcleo de Fisiologia Geral e Genômica Funcional-ICB-Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais Brazil
| | - Marek Tutaj
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Jozef Lazar
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ; Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Melinda R Dwinell
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Howard J Jacob
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ; Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| |
Collapse
|
398
|
Hu YC, Namekawa SH. Functional significance of the sex chromosomes during spermatogenesis. Reproduction 2016; 149:R265-77. [PMID: 25948089 DOI: 10.1530/rep-14-0613] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mammalian sex chromosomes arose from an ordinary pair of autosomes. Over hundreds of millions of years, they have evolved into highly divergent X and Y chromosomes and have become increasingly specialized for male reproduction. Both sex chromosomes have acquired and amplified testis-specific genes, suggestive of roles in spermatogenesis. To understand how the sex chromosome genes participate in the regulation of spermatogenesis, we review genes, including single-copy, multi-copy, and ampliconic genes, whose spermatogenic functions have been demonstrated in mouse genetic studies. Sex chromosomes are subject to chromosome-wide transcriptional silencing in meiotic and postmeiotic stages of spermatogenesis. We also discuss particular sex-linked genes that escape postmeiotic silencing and their evolutionary implications. The unique gene contents and genomic structures of the sex chromosomes reflect their strategies to express genes at various stages of spermatogenesis and reveal the driving forces that shape their evolution.Free Chinese abstract: A Chinese translation of this abstract is freely available at http://www.reproduction-online.org/content/149/6/R265/suppl/DC1.Free Japanese abstract: A Japanese translation of this abstract is freely available at http://www.reproduction-online.org/content/149/6/R265/suppl/DC2.
Collapse
Affiliation(s)
- Yueh-Chiang Hu
- Division of Developmental BiologyDivision of Reproductive SciencesCincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Satoshi H Namekawa
- Division of Developmental BiologyDivision of Reproductive SciencesCincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA Division of Developmental BiologyDivision of Reproductive SciencesCincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| |
Collapse
|
399
|
Clayton JA. Studying both sexes: a guiding principle for biomedicine. FASEB J 2016; 30:519-24. [PMID: 26514164 PMCID: PMC4714546 DOI: 10.1096/fj.15-279554] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/19/2015] [Indexed: 11/11/2022]
Abstract
In May 2014, the U.S. National Institutes of Health (NIH) announced that it will ensure that investigators account for sex as a biological variable (SABV) in NIH-funded preclinical research as part of the agency's rigor and transparency initiative. Herein, I describe in more detail the rationale behind the SABV policy component and provide additional detail about policy goals. In short, studying both sexes is a guiding principle in biomedical research that will expand knowledge toward turning discovery into health. NIH expects that considering SABV in preclinical research will help to build a knowledge base that better informs the design of clinical research and trials in humans. Integrating the practice of studying both sexes in preclinical research will, over time, expand our currently incomplete knowledge base that plays a critical role in informing the development of sex- and gender-appropriate medical care for women and men.
Collapse
Affiliation(s)
- Janine Austin Clayton
- Office of Research on Women's Health, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
400
|
Tuttle EM, Bergland AO, Korody ML, Brewer MS, Newhouse DJ, Minx P, Stager M, Betuel A, Cheviron ZA, Warren WC, Gonser RA, Balakrishnan CN. Divergence and Functional Degradation of a Sex Chromosome-like Supergene. Curr Biol 2016; 26:344-50. [PMID: 26804558 DOI: 10.1016/j.cub.2015.11.069] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/12/2015] [Accepted: 11/25/2015] [Indexed: 11/18/2022]
Abstract
A major challenge in biology is to understand the genetic basis of adaptation. One compelling idea is that groups of tightly linked genes (i.e., "supergenes" [1, 2]) facilitate adaptation in suites of traits that determine fitness. Despite their likely importance, little is known about how alternate supergene alleles arise and become differentiated, nor their ultimate fate within species. Herein we address these questions by investigating the evolutionary history of a supergene in white-throated sparrows, Zonotrichia albicollis. This species comprises two morphs, tan and white, that differ in pigmentation and components of social behavior [3-5]. Morph is determined by alternative alleles at a balanced >100-Mb inversion-based supergene, providing a unique system for studying gene-behavior relationships. Using over two decades of field data, we document near-perfect disassortative mating among morphs, as well as the fitness consequences of rare assortative mating. We use de novo whole-genome sequencing coupled with population- and phylogenomic data to show that alternate supergene alleles are highly divergent at over 1,000 genes and that these alleles originated prior to the split of Z. albicollis from its sister species and may be polymorphic in Z. albicollis due to a past hybridization event. We provide evidence that the "white" allele may be degrading, similar to neo-Y/W sex chromosomes. We further show that the "tan" allele has surprisingly low levels of genetic diversity yet does not show several canonical signatures of recurrent positive selection. We discuss these results in the context of the origin, molecular evolution, and possible fate of this remarkable polymorphism.
Collapse
Affiliation(s)
- Elaina M Tuttle
- Department of Biology and The Center for Genomic Advocacy, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA.
| | - Alan O Bergland
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305-5020, USA
| | - Marisa L Korody
- Department of Biology and The Center for Genomic Advocacy, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA
| | - Michael S Brewer
- Department of Biology, East Carolina University, Howell Science Complex, Greenville, NC 27858, USA
| | - Daniel J Newhouse
- Department of Biology, East Carolina University, Howell Science Complex, Greenville, NC 27858, USA
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108, USA
| | - Maria Stager
- Department of Animal Biology, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Adam Betuel
- Department of Biology and The Center for Genomic Advocacy, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA
| | - Zachary A Cheviron
- Department of Animal Biology, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108, USA
| | - Rusty A Gonser
- Department of Biology and The Center for Genomic Advocacy, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA
| | | |
Collapse
|