1
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Flynn JM, Yamashita YM. The implications of satellite DNA instability on cellular function and evolution. Semin Cell Dev Biol 2024; 156:152-159. [PMID: 37852904 DOI: 10.1016/j.semcdb.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Abundant tandemly repeated satellite DNA is present in most eukaryotic genomes. Previous limitations including a pervasive view that it was uninteresting junk DNA, combined with challenges in studying it, are starting to dissolve - and recent studies have found important functions for satellite DNAs. The observed rapid evolution and implied instability of satellite DNA now has important significance for their functions and maintenance within the genome. In this review, we discuss the processes that lead to satellite DNA copy number instability, and the importance of mechanisms to manage the potential negative effects of instability. Satellite DNA is vulnerable to challenges during replication and repair, since it forms difficult-to-process secondary structures and its homology within tandem arrays can result in various types of recombination. Satellite DNA instability may be managed by DNA or chromatin-binding proteins ensuring proper nuclear localization and repair, or by proteins that process aberrant structures that satellite DNAs tend to form. We also discuss the pattern of satellite DNA mutations from recent mutation accumulation (MA) studies that have tracked changes in satellite DNA for up to 1000 generations with minimal selection. Finally, we highlight examples of satellite evolution from studies that have characterized satellites across millions of years of Drosophila fruit fly evolution, and discuss possible ways that selection might act on the satellite DNA composition.
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Affiliation(s)
- Jullien M Flynn
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Muralidhar P, Coop G. Polygenic response of sex chromosomes to sexual antagonism. Evolution 2024; 78:539-554. [PMID: 38153370 PMCID: PMC10903542 DOI: 10.1093/evolut/qpad231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/30/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
Sexual antagonism occurs when males and females differ in their phenotypic fitness optima but are constrained in their evolution to these optima because of their shared genome. The sex chromosomes, which have distinct evolutionary "interests" relative to the autosomes, are theorized to play an important role in sexually antagonistic conflict. However, the evolutionary responses of sex chromosomes and autosomes have usually been considered independently, that is, via contrasting the response of a gene located on either an X chromosome or an autosome. Here, we study the coevolutionary response of the X chromosome and autosomes to sexually antagonistic selection acting on a polygenic phenotype. We model a phenotype initially under stabilizing selection around a single optimum, followed by a sudden divergence of the male and female optima. We find that, in the absence of dosage compensation, the X chromosome promotes evolution toward the female optimum, inducing coevolutionary male-biased responses on the autosomes. Dosage compensation obscures the female-biased interests of the X, causing it to contribute equally to male and female phenotypic change. We further demonstrate that fluctuations in an adaptive landscape can generate prolonged intragenomic conflict and accentuate the differential responses of the X and autosomes to this conflict.
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Affiliation(s)
- Pavitra Muralidhar
- Center for Population Biology, University of California, Davis, CA, United States
- Department of Evolution and Ecology, University of California, Davis, CA, United States
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA, United States
- Department of Evolution and Ecology, University of California, Davis, CA, United States
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3
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Clot C, Hudry B, Delanoue R. [The Y chromosome has no impact on sex-specific longevity]. Med Sci (Paris) 2024; 40:143-145. [PMID: 38411420 DOI: 10.1051/medsci/2023203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Affiliation(s)
- Charlène Clot
- Université Côte d'Azur, CNRS, Inserm, Institut de biologie Valrose, Nice, France
| | - Bruno Hudry
- Université Côte d'Azur, CNRS, Inserm, Institut de biologie Valrose, Nice, France
| | - Rénald Delanoue
- Université Côte d'Azur, CNRS, Inserm, Institut de biologie Valrose, Nice, France
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4
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Zeidan RS, McElroy T, Rathor L, Martenson MS, Lin Y, Mankowski RT. Sex differences in frailty among older adults. Exp Gerontol 2023; 184:112333. [PMID: 37993077 DOI: 10.1016/j.exger.2023.112333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
By definition, aging is a natural, gradual and continuous process. On the other hand, frailty reflects the increase in vulnerability to stressors and shortens the time without disease (health span) while longevity refers to the length of life (lifespan). The average life expectancy has significantly increased during the last few decades. A longer lifespan has been accompanied by an increase in frailty and decreased independence in older adults, with major differences existing between men and women. For example, women tend to live longer than men but also experience higher rates of frailty and disability. Sex differences prevent optimization of lifestyle interventions and therapies to effectively prevent frailty. Sex differences in frailty and aging are rooted in a complex interplay between uncontrollable (genetic, epigenetic, physiological), and controllable factors (psychosocial and lifestyle factors). Thus, understanding the underlying causes of sex differences in frailty and aging is essential for developing personalized interventions to promote healthy aging and improve quality of life in older men and women. In this review, we have discussed the key contributors and knowledge gaps related to sex differences in aging and frailty.
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Affiliation(s)
- Rola S Zeidan
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America; Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Taylor McElroy
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America; Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Laxmi Rathor
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Matthew S Martenson
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Yi Lin
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Robert T Mankowski
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
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5
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Li S, Vazquez JM, Sudmant PH. The evolution of aging and lifespan. Trends Genet 2023; 39:830-843. [PMID: 37714733 PMCID: PMC11147682 DOI: 10.1016/j.tig.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Aging is a nearly inescapable trait among organisms yet lifespan varies tremendously across different species and spans several orders of magnitude in vertebrates alone. This vast phenotypic diversity is driven by distinct evolutionary trajectories and tradeoffs that are reflected in patterns of diversification and constraint in organismal genomes. Age-specific impacts of selection also shape allele frequencies in populations, thus impacting disease susceptibility and environment-specific mortality risk. Further, the mutational processes that spawn this genetic diversity in both germline and somatic cells are strongly influenced by age and life history. We discuss recent advances in our understanding of the evolution of aging and lifespan at organismal, population, and cellular scales, and highlight outstanding questions that remain unanswered.
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Affiliation(s)
- Stacy Li
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA
| | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA.
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6
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Xu A, Teefy BB, Lu RJ, Nozownik S, Tyers AM, Valenzano DR, Benayoun BA. Transcriptomes of aging brain, heart, muscle, and spleen from female and male African turquoise killifish. Sci Data 2023; 10:695. [PMID: 37828039 PMCID: PMC10570339 DOI: 10.1038/s41597-023-02609-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
The African turquoise killifish is an emerging vertebrate model organism with great potential for aging research due to its naturally short lifespan. Thus far, turquoise killifish aging 'omic' studies have examined a single organ, single sex and/or evaluated samples from non-reference strains. Here, we describe a resource dataset of ribosomal RNA-depleted RNA-seq libraries generated from the brain, heart, muscle, and spleen from both sexes, as well as young and old animals, in the reference GRZ turquoise killifish strain. We provide basic quality control steps and demonstrate the utility of our dataset by performing differential gene expression and gene ontology analyses by age and sex. Importantly, we show that age has a greater impact than sex on transcriptional landscapes across probed tissues. Finally, we confirm transcription of transposable elements (TEs), which are highly abundant and increase in expression with age in brain tissue. This dataset will be a useful resource for exploring gene and TE expression as a function of both age and sex in a powerful naturally short-lived vertebrate model.
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Affiliation(s)
- Alan Xu
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, 90089, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ryan J Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, USA
| | - Séverine Nozownik
- Unit of Forensic Genetics, University Center of Legal Medicine, Lausanne, Switzerland
| | - Alexandra M Tyers
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Strasse 9b, 50931, Cologne, Germany
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
| | - Dario R Valenzano
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Strasse 9b, 50931, Cologne, Germany
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, 90089, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, 90089, USA.
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA.
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7
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Delanoue R, Clot C, Leray C, Pihl T, Hudry B. Y chromosome toxicity does not contribute to sex-specific differences in longevity. Nat Ecol Evol 2023; 7:1245-1256. [PMID: 37308701 PMCID: PMC10406604 DOI: 10.1038/s41559-023-02089-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/14/2023] [Indexed: 06/14/2023]
Abstract
While sex chromosomes carry sex-determining genes, they also often differ from autosomes in size and composition, consisting mainly of silenced heterochromatic repetitive DNA. Even though Y chromosomes show structural heteromorphism, the functional significance of such differences remains elusive. Correlative studies suggest that the amount of Y chromosome heterochromatin might be responsible for several male-specific traits, including sex-specific differences in longevity observed across a wide spectrum of species, including humans. However, experimental models to test this hypothesis have been lacking. Here we use the Drosophila melanogaster Y chromosome to investigate the relevance of sex chromosome heterochromatin in somatic organs in vivo. Using CRISPR-Cas9, we generated a library of Y chromosomes with variable levels of heterochromatin. We show that these different Y chromosomes can disrupt gene silencing in trans, on other chromosomes, by sequestering core components of the heterochromatin machinery. This effect is positively correlated to the level of Y heterochromatin. However, we also find that the ability of the Y chromosome to affect genome-wide heterochromatin does not generate physiological sex differences, including sexual dimorphism in longevity. Instead, we discovered that it is the phenotypic sex, female or male, that controls sex-specific differences in lifespan, rather than the presence of a Y chromosome. Altogether, our findings dismiss the 'toxic Y' hypothesis that postulates that the Y chromosome leads to reduced lifespan in XY individuals.
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Affiliation(s)
- Rénald Delanoue
- Institut de Biologie Valrose, Université Côte d'Azur, CNRS, INSERM, Nice, France.
| | - Charlène Clot
- Institut de Biologie Valrose, Université Côte d'Azur, CNRS, INSERM, Nice, France
| | - Chloé Leray
- Institut de Biologie Valrose, Université Côte d'Azur, CNRS, INSERM, Nice, France
| | - Thomas Pihl
- Institut de Biologie Valrose, Université Côte d'Azur, CNRS, INSERM, Nice, France
| | - Bruno Hudry
- Institut de Biologie Valrose, Université Côte d'Azur, CNRS, INSERM, Nice, France.
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8
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Yamashita YM. Why Ys are not necessarily toxic. Nat Ecol Evol 2023; 7:1177-1178. [PMID: 37308702 DOI: 10.1038/s41559-023-02079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, MA, USA.
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9
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Lin YC, Zhang M, Chang YJ, Kuo TH. Comparisons of lifespan and stress resistance between sexes in Drosophila melanogaster. Heliyon 2023; 9:e18178. [PMID: 37576293 PMCID: PMC10415617 DOI: 10.1016/j.heliyon.2023.e18178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Animals exhibit different extents of sexual dimorphism in a variety of phenotypes. Sex differences in longevity, one of the most complex life history traits, have also been reported. Although lifespan regulation has been studied extensively in the fruit fly, Drosophila melanogaster, the sex differences in lifespan have not been consistent in previous studies. To explore this issue, we revisited this question by examining the lifespan and stress resistance of both sexes among 15 inbred strains. We first found positive correlations between males and females from the same strain in terms of lifespan and resistance to starvation and desiccation stress. Although the lifespan difference between male and female flies varied greatly depending on the strain, males across all strains collectively had a longer lifespan. In contrast, females showed better resistance to starvation and desiccation stress. We also observed greater variation in lifespan and resistance to starvation and desiccation stress in females. Unexpectedly, there was no notable correlation observed between lifespan and the three types of stress resistance in either males or females. Overall, our study provides new data regarding sexual dimorphism in fly lifespan and stress resistance; this information may promote the investigation of mechanisms underlying longevity in future research.
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Affiliation(s)
- Yu-Chiao Lin
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | - MingYang Zhang
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Tsung-Han Kuo
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan
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10
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Wodrich APK, Scott AW, Giniger E. What do we mean by "aging"?: Questions and perspectives revealed by studies in Drosophila. Mech Ageing Dev 2023:111839. [PMID: 37354919 DOI: 10.1016/j.mad.2023.111839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
What is the nature of aging, and how best can we study it? Here, using a series of questions that highlight differing perspectives about the nature of aging, we ask how data from Drosophila melanogaster at the organismal, tissue, cellular, and molecular levels shed light on the complex interactions among the phenotypes associated with aging. Should aging be viewed as an individual's increasing probability of mortality over time or as a progression of physiological states? Are all age-correlated changes in physiology detrimental to vigor or are some compensatory changes that maintain vigor? Why do different age-correlated functions seem to change at different rates in a single individual as it ages? Should aging be considered as a single, integrated process across the scales of biological resolution, from organismal to molecular, or must we consider each level of biological scale as a separate, distinct entity? Viewing aging from these differing perspectives yields distinct but complementary interpretations about the properties and mechanisms of aging and may offer a path through the complexities related to understanding the nature of aging.
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Affiliation(s)
- Andrew P K Wodrich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States; Interdisciplinary Program in Neuroscience, Georgetown University, Washington, DC, United States; College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Andrew W Scott
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States.
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11
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Flynn JM, Hu KB, Clark AG. Three recent sex chromosome-to-autosome fusions in a Drosophila virilis strain with high satellite DNA content. Genetics 2023; 224:iyad062. [PMID: 37052958 PMCID: PMC10213488 DOI: 10.1093/genetics/iyad062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/02/2022] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
The karyotype, or number and arrangement of chromosomes, has varying levels of stability across both evolution and disease. Karyotype changes often originate from DNA breaks near the centromeres of chromosomes, which generally contain long arrays of tandem repeats or satellite DNA. Drosophila virilis possesses among the highest relative satellite abundances of studied species, with almost half its genome composed of three related 7 bp satellites. We discovered a strain of D. virilis that we infer recently underwent three independent chromosome fusion events involving the X and Y chromosomes, in addition to one subsequent fission event. Here, we isolate and characterize the four different karyotypes we discovered in this strain which we believe demonstrates remarkable genome instability. We discovered that one of the substrains with an X-autosome fusion has an X-to-Y chromosome nondisjunction rate 20 × higher than the D. virilis reference strain (21% vs 1%). Finally, we found an overall higher rate of DNA breakage in the substrain with higher satellite DNA compared to a genetically similar substrain with less satellite DNA. This suggests that satellite DNA abundance may play a role in the risk of genome instability. Overall, we introduce a novel system consisting of a single strain with four different karyotypes, which we believe will be useful for future studies of genome instability, centromere function, and sex chromosome evolution.
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Affiliation(s)
- Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building Room 227, Ithaca, NY 14853, USA
| | - Kevin B Hu
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building Room 227, Ithaca, NY 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building Room 227, Ithaca, NY 14853, USA
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12
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Aging and memory are altered by genetically manipulating lactate dehydrogenase in the neurons or glia of flies. Aging (Albany NY) 2023; 15:947-981. [PMID: 36849157 PMCID: PMC10008500 DOI: 10.18632/aging.204565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/20/2023] [Indexed: 03/01/2023]
Abstract
The astrocyte-neuron lactate shuttle hypothesis posits that glial-generated lactate is transported to neurons to fuel metabolic processes required for long-term memory. Although studies in vertebrates have revealed that lactate shuttling is important for cognitive function, it is uncertain if this form of metabolic coupling is conserved in invertebrates or is influenced by age. Lactate dehydrogenase (Ldh) is a rate limiting enzyme that interconverts lactate and pyruvate. Here we genetically manipulated expression of Drosophila melanogaster lactate dehydrogenase (dLdh) in neurons or glia to assess the impact of altered lactate metabolism on invertebrate aging and long-term courtship memory at different ages. We also assessed survival, negative geotaxis, brain neutral lipids (the core component of lipid droplets) and brain metabolites. Both upregulation and downregulation of dLdh in neurons resulted in decreased survival and memory impairment with age. Glial downregulation of dLdh expression caused age-related memory impairment without altering survival, while upregulated glial dLdh expression lowered survival without disrupting memory. Both neuronal and glial dLdh upregulation increased neutral lipid accumulation. We provide evidence that altered lactate metabolism with age affects the tricarboxylic acid (TCA) cycle, 2-hydroxyglutarate (2HG), and neutral lipid accumulation. Collectively, our findings indicate that the direct alteration of lactate metabolism in either glia or neurons affects memory and survival but only in an age-dependent manner.
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13
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Sultanova Z, Downing PA, Carazo P. Genetic sex determination, sex chromosome size and sex-specific lifespans across tetrapods. J Evol Biol 2023; 36:480-494. [PMID: 36537352 PMCID: PMC10107984 DOI: 10.1111/jeb.14130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
Sex differences in lifespan are ubiquitous across the tree of life and exhibit broad taxonomic patterns that remain a puzzle, such as males living longer than females in birds and vice versa in mammals. The prevailing unguarded X hypothesis explains sex differences in lifespan by differential expression of recessive mutations on the X or Z chromosome of the heterogametic sex, but has only received indirect support to date. An alternative hypothesis is that the accumulation of deleterious mutations and repetitive elements on the Y or W chromosome might lower the survival of the heterogametic sex ('toxic Y' hypothesis). Here, we use a new database to report lower survival of the heterogametic relative to the homogametic sex across 136 species of birds, mammals, reptiles and amphibians, as expected if sex chromosomes shape sex-specific lifespans, and consistent with previous findings. We also found that the relative sizes of both the X and the Y chromosomes in mammals (but not the Z or the W chromosomes in birds) are associated with sex differences in lifespan, as predicted by the unguarded X and the 'toxic Y'. Furthermore, we report that the relative size of the Y is negatively associated with male lifespan in mammals, so that small Y size correlates with increased male lifespan. In theory, toxic Y effects are expected to be particularly strong in mammals, and we did not find similar effects in birds. Our results confirm the role of sex chromosomes in explaining sex differences in lifespan across tetrapods and further suggest that, at least in mammals, 'toxic Y' effects may play an important part in this role.
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Affiliation(s)
- Zahida Sultanova
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Philip A Downing
- Department of Biology, Lund University, Lund, Sweden.,Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Pau Carazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
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14
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Lushchak O, Strilbytska O, Storey KB. Gender-specific effects of pro-longevity interventions in Drosophila. Mech Ageing Dev 2023; 209:111754. [PMID: 36375654 DOI: 10.1016/j.mad.2022.111754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022]
Abstract
Sex differences in lifespan are well recognized in the majority of animal species. For example, in male versus female Drosophila melanogaster there are significant differences in behavior and physiology. However, little is known about the underlying mechanisms of gender differences in responses to pro-longevity interventions in this model organism. Here we summarize the existing data on the effects of nutritional and pharmacological anti-aging interventions such as nutrition regimens, diet and dietary supplementation on the lifespan of male and female Drosophila. We demonstrate that males and females have different sensitivities to interventions and that the effects are highly dependent on genetic background, mating, dose and exposure duration. Our work highlights the importance of understanding the mechanisms that underlie the gender-specific effect of anti-aging manipulations. This will provide insight into how these benefits may be valuable for elucidating the primary physiological and molecular targets involved in aging and lifespan determination.
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Affiliation(s)
- Oleh Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka str., Ivano-Frankivsk 76018, Ukraine; Research and Development University, 13a Shota Rustaveli Str., Ivano-Frankivsk 76018, Ukraine.
| | - Olha Strilbytska
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka str., Ivano-Frankivsk 76018, Ukraine
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
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15
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Meisel RP. Ecology and the evolution of sex chromosomes. J Evol Biol 2022; 35:1601-1618. [PMID: 35950939 DOI: 10.1111/jeb.14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes are common features of animal genomes, often carrying a sex determination gene responsible for initiating the development of sexually dimorphic traits. The specific chromosome that serves as the sex chromosome differs across taxa as a result of fusions between sex chromosomes and autosomes, along with sex chromosome turnover-autosomes becoming sex chromosomes and sex chromosomes 'reverting' back to autosomes. In addition, the types of genes on sex chromosomes frequently differ from the autosomes, and genes on sex chromosomes often evolve faster than autosomal genes. Sex-specific selection pressures, such as sexual antagonism and sexual selection, are hypothesized to be responsible for sex chromosome turnovers, the unique gene content of sex chromosomes and the accelerated evolutionary rates of genes on sex chromosomes. Sex-specific selection has pronounced effects on sex chromosomes because their sex-biased inheritance can tilt the balance of selection in favour of one sex. Despite the general consensus that sex-specific selection affects sex chromosome evolution, most population genetic models are agnostic as to the specific sources of these sex-specific selection pressures, and many of the details about the effects of sex-specific selection remain unresolved. Here, I review the evidence that ecological factors, including variable selection across heterogeneous environments and conflicts between sexual and natural selection, can be important determinants of sex-specific selection pressures that shape sex chromosome evolution. I also explain how studying the ecology of sex chromosome evolution can help us understand important and unresolved aspects of both sex chromosome evolution and sex-specific selection.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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16
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Schield DR, Perry BW, Card DC, Pasquesi GIM, Westfall AK, Mackessy SP, Castoe TA. The rattlesnake W chromosome: A GC-rich retroelement refugium with retained gene function across ancient evolutionary strata. Genome Biol Evol 2022; 14:6648526. [PMID: 35867356 PMCID: PMC9447483 DOI: 10.1093/gbe/evac116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 11/18/2022] Open
Abstract
Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limited Y and W chromosomes contain valuable information about the evolutionary transition from autosomes to sex chromosomes, yet detailed characterizations of the structure, composition, and gene content of sex-limited chromosomes are lacking for many species. In this study, we characterize the female-specific W chromosome of the prairie rattlesnake (Crotalus viridis) and evaluate how recombination suppression and other processes have shaped sex chromosome evolution in ZW snakes. Our analyses indicate that the rattlesnake W chromosome is over 80% repetitive and that an abundance of GC-rich mdg4 elements has driven an overall high degree of GC-richness despite a lack of recombination. The W chromosome is also highly enriched for repeat sequences derived from endogenous retroviruses and likely acts as a “refugium” for these and other retroelements. We annotated 219 putatively functional W-linked genes across at least two evolutionary strata identified based on estimates of sequence divergence between Z and W gametologs. The youngest of these strata is relatively gene-rich, however gene expression across strata suggests retained gene function amidst a greater degree of degeneration following ancient recombination suppression. Functional annotation of W-linked genes indicates a specialization of the W chromosome for reproductive and developmental function since recombination suppression from the Z chromosome.
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Affiliation(s)
- Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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17
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Cīrulis A, Hansson B, Abbott JK. Sex-limited chromosomes and non-reproductive traits. BMC Biol 2022; 20:156. [PMID: 35794589 PMCID: PMC9261002 DOI: 10.1186/s12915-022-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 06/22/2022] [Indexed: 12/03/2022] Open
Abstract
Sex chromosomes are typically viewed as having originated from a pair of autosomes, and differentiated as the sex-limited chromosome (e.g. Y) has degenerated by losing most genes through cessation of recombination. While often thought that degenerated sex-limited chromosomes primarily affect traits involved in sex determination and sex cell production, accumulating evidence suggests they also influence traits not sex-limited or directly involved in reproduction. Here, we provide an overview of the effects of sex-limited chromosomes on non-reproductive traits in XY, ZW or UV sex determination systems, and discuss evolutionary processes maintaining variation at sex-limited chromosomes and molecular mechanisms affecting non-reproductive traits.
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Affiliation(s)
- Aivars Cīrulis
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Bengt Hansson
- Department of Biology, Lund University, 223 62, Lund, Sweden
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18
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Connallon T, Beasley IJ, MDonough Y, Ruzicka F. How much does the unguarded X contribute to sex differences in life span? Evol Lett 2022; 6:319-329. [PMID: 35937469 PMCID: PMC9346086 DOI: 10.1002/evl3.292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/22/2022] [Accepted: 06/12/2022] [Indexed: 11/09/2022] Open
Abstract
Females and males often have markedly different mortality rates and life spans, but it is unclear why these forms of sexual dimorphism evolve. The unguarded X hypothesis contends that dimorphic life spans arise from sex differences in X or Z chromosome copy number (i.e., one copy in the “heterogametic” sex; two copies in the “homogametic” sex), which leads to a disproportionate expression of deleterious mutations by the heterogametic sex (e.g., mammalian males; avian females). Although data on adult sex ratios and sex‐specific longevity are consistent with predictions of the unguarded X hypothesis, direct experimental evidence remains scant, and alternative explanations are difficult to rule out. Using a simple population genetic model, we show that the unguarded X effect on sex differential mortality is a function of several reasonably well‐studied evolutionary parameters, including the proportion of the genome that is sex linked, the genomic deleterious mutation rate, the mean dominance of deleterious mutations, the relative rates of mutation and strengths of selection in each sex, and the average effect of mutations on survival and longevity relative to their effects on fitness. We review published estimates of these parameters, parameterize our model with them, and show that unguarded X effects are too small to explain observed sex differences in life span across species. For example, sex differences in mean life span are known to often exceed 20% (e.g., in mammals), whereas our parameterized models predict unguarded X effects of a few percent (e.g., 1–3% in Drosophila and mammals). Indeed, these predicted unguarded X effects fall below statistical thresholds of detectability in most experiments, potentially explaining why direct tests of the hypothesis have generated little support for it. Our results suggest that evolution of sexually dimorphic life spans is predominantly attributable to other mechanisms, potentially including “toxic Y” effects and sexual dimorphism for optimal investment in survival versus reproduction. Females and males are dimorphic for a wide range of traits, including the average lengths of their life spans. Sex differences in life span are both conspicuous and variable among species. For example, in mammals, females live ∼20% longer than males (on average), whereas in birds, males live ∼10% longer than females. One leading explanation for these patterns—the unguarded X hypothesis—argues that sex differences in life span emerge from the distinct sex chromosomes that females and males inherit. For many species, one sex (e.g., female mammals; male birds) carries two copies of each X‐linked gene, whereas the other carries one. Because harmful mutations are partially recessive, the sex with only one copy of the X is more prone to expressing them, and that sex should therefore have a shorter average life span. This prediction of the unguarded X hypothesis is qualitatively consistent with observations of sex‐ratio bias in adults and sexual dimorphism for longevity (e.g., mammalian males have one copy of the X and have shorter lives than females). However, there are other possible explanations for these patterns, making it unclear how much the unguarded X explains species diversity for sex‐specific longevity. We developed a mathematical model for the contribution of unguarded X effects to sex differences in survival and life span, and used data on mutation rates and their effects on survival and fitness to quantify the importance of the unguarded X across species. The model, when combined with current data, suggests that the unguarded X hypothesis cannot explain the conspicuous sex differences in life span that are commonly reported in animal species, particularly vertebrates. Our results suggest that the unguarded X is an unlikely general explanation for the evolution of sexually dimorphic life spans, which gives weight to alternative mechanisms, including “toxic Y” effects and sex differential selection via trade‐offs between survival and reproduction.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences Monash University Clayton VIC 3800 Australia
| | - Isobel J. Beasley
- School of BioSciences The University of Melbourne Parkville VIC 3010 Australia
- Melbourne Integrative Genomics The University of Melbourne Parkville VIC 3010 Australia
- St. Vincent's Institute of Medical Research Fitzroy VIC 3065 Australia
| | - Yasmine MDonough
- School of Biological Sciences Monash University Clayton VIC 3800 Australia
| | - Filip Ruzicka
- School of Biological Sciences Monash University Clayton VIC 3800 Australia
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19
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Shenoi VN, Brengdahl MI, Grace JL, Eriksson B, Rydén P, Friberg U. A genome-wide test for paternal indirect genetic effects on lifespan in Drosophila melanogaster. Proc Biol Sci 2022; 289:20212707. [PMID: 35538781 PMCID: PMC9091837 DOI: 10.1098/rspb.2021.2707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Exposing sires to various environmental manipulations has demonstrated that paternal effects can be non-trivial also in species where male investment in offspring is almost exclusively limited to sperm. Whether paternal effects also have a genetic component (i.e. paternal indirect genetic effects (PIGEs)) in such species is however largely unknown, primarily because of methodological difficulties separating indirect from direct effects of genes. PIGEs may nevertheless be important since they have the capacity to contribute to evolutionary change. Here we use Drosophila genetics to construct a breeding design that allows testing nearly complete haploid genomes (more than 99%) for PIGEs. Using this technique, we estimate the variance in male lifespan due to PIGEs among four populations and compare this to the total paternal genetic variance (the sum of paternal indirect and direct genetic effects). Our results indicate that a substantial part of the total paternal genetic variance results from PIGEs. A screen of 38 haploid genomes, randomly sampled from a single population, suggests that PIGEs also influence variation in lifespan within populations. Collectively, our results demonstrate that PIGEs may constitute an underappreciated source of phenotypic variation.
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Affiliation(s)
| | | | - Jaime L. Grace
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Björn Eriksson
- Unit of Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 14, Box 102, 230 53 Alnarp, Sweden
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, 901 87 Umeå, Sweden,Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden
| | - Urban Friberg
- IFM Biology, Linköping University, 581 83 Linköping, Sweden
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20
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Marais GAB, Lemaître JF. Sex chromosomes, sex ratios and sex gaps in longevity in plants. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210219. [PMID: 35306888 PMCID: PMC8935291 DOI: 10.1098/rstb.2021.0219] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In animals, males and females can display markedly different longevity (also called sex gaps in longevity, SGL). Sex chromosomes contribute to establishing these SGLs. X-hemizygosity and toxicity of the Y chromosomes are two mechanisms that have been suggested to reduce male longevity (Z-hemizygosity and W toxicity in females in ZW systems). In plants, SGLs are known to exist, but the role of sex chromosomes remains to be established. Here, by using adult sex ratio as a proxy for measuring SGLs, we explored the relationship between sex chromosomes and SGLs across 43 plant species. Based on the knowledge accumulated in animals, we specifically asked whether: (i) species with XY systems tend to have female-biased sex ratios (reduced male longevity) and species with ZW ones tend to have male-biased sex ratios (reduced female longevity); and (ii) this pattern was stronger in heteromorphic systems compared to homomorphic ones. Our results tend to support these predictions although we lack statistical power because of a small number of ZW systems and the absence of any heteromorphic ZW system in the dataset. We discuss the implications of these findings, which we hope will stimulate further research on sex differences in lifespan and ageing across plants. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Gabriel A B Marais
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.,LBBE, CNRS/Univ. Lyon 1, Campus de la Doua, Villeurbanne, France
| | - J-F Lemaître
- LBBE, CNRS/Univ. Lyon 1, Campus de la Doua, Villeurbanne, France
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21
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Nguyen A, Wang W, Chong E, Chatla K, Bachtrog D. Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila. Genome Res 2022; 32:1074-1088. [PMID: 35501131 DOI: 10.1101/gr.275996.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022]
Abstract
Y Chromosomes of many species are gene poor and show low levels of nucleotide variation, yet often display high amounts of structural diversity. Dobzhansky cataloged several morphologically distinct Y Chromosomes in Drosophila pseudoobscura that differ in size and shape, but the molecular causes of their dramatic size differences are unclear. Here we use cytogenetics and long-read sequencing to study the sequence content of polymorphic Y Chromosomes in D. pseudoobscura We show that Y Chromosomes differ almost 2-fold in size, ranging from 30 to 60 Mb. Most of this size difference is caused by a handful of active transposable elements (TEs) that have recently expanded on the largest Y Chromosome, with different elements being responsible for Y expansion on differently sized D. pseudoobscura Y's. We show that Y Chromosomes differ in their heterochromatin enrichment, expression of Y-enriched TEs, and also influence expression of dozens of autosomal and X-linked genes. The same helitron element that showed the most drastic amplification on the largest Y in D. pseudoobscura independently amplified on a polymorphic large Y Chromosome in D. affinis, suggesting that some TEs are inherently more prone to become deregulated on Y Chromosomes.
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22
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Yang N, Srivastav SP, Rahman R, Ma Q, Dayama G, Li S, Chinen M, Lei EP, Rosbash M, Lau NC. Transposable element landscapes in aging Drosophila. PLoS Genet 2022; 18:e1010024. [PMID: 35239675 PMCID: PMC8893327 DOI: 10.1371/journal.pgen.1010024] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/10/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic mechanisms that repress transposable elements (TEs) in young animals decline during aging, as reflected by increased TE expression in aged animals. Does increased TE expression during aging lead to more genomic TE copies in older animals? To address this question, we quantified TE Landscapes (TLs) via whole genome sequencing of young and aged Drosophila strains of wild-type and mutant backgrounds. We quantified TLs in whole flies and dissected brains and validated the feasibility of our approach in detecting new TE insertions in aging Drosophila genomes when small RNA and RNA interference (RNAi) pathways are compromised. We also describe improved sequencing methods to quantify extra-chromosomal DNA circles (eccDNAs) in Drosophila as an additional source of TE copies that accumulate during aging. Lastly, to combat the natural progression of aging-associated TE expression, we show that knocking down PAF1, a conserved transcription elongation factor that antagonizes RNAi pathways, may bolster suppression of TEs during aging and extend lifespan. Our study suggests that in addition to a possible influence by different genetic backgrounds, small RNA and RNAi mechanisms may mitigate genomic TL expansion despite the increase in TE transcripts during aging. Transposable elements, also called transposons, are genetic parasites found in all animal genomes. Normally, transposons are compacted away in silent chromatin in young animals. But, as animals age and transposon-silencing defense mechanisms break down, transposon RNAs accumulate to significant levels in old animals like fruit flies. An open question is whether the increased levels of transposon RNAs in older animals also correspond to increased genomic copies of transposons. This study approached this question by sequencing the whole genomes of young and old wild-type and mutant flies lacking a functional RNA interference (RNAi) pathway, which naturally silences transposon RNAs. Although the wild-type flies with intact RNAi activity had little new accumulation of transposon copies, the sequencing approach was able to detect several transposon accumulation occurrences in some RNAi mutants. In addition, we found that some fly transposon families can also accumulate as extra-chromosomal circular DNA copies. Lastly, we showed that genetically augmenting the expression of RNAi factors can counteract the rising transposon RNA levels in aging and promote longevity. This study improves our understanding of the animal host genome relationship with transposons during natural aging processes.
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Affiliation(s)
- Nachen Yang
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Satyam P. Srivastav
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Reazur Rahman
- Brandeis University, Department of Biology and Howard Hughes Medical Institute, Waltham, Massachusetts, United States of America
| | - Qicheng Ma
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Gargi Dayama
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Sizheng Li
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Madoka Chinen
- Nuclear Organization and Gene Expression Section, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Michael Rosbash
- Brandeis University, Department of Biology and Howard Hughes Medical Institute, Waltham, Massachusetts, United States of America
| | - Nelson C. Lau
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
- Boston University Genome Science Institute, Boston, Massachusetts, United States of America
- * E-mail:
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23
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Warmuth VM, Weissensteiner MH, Wolf J. Ineffective silencing of transposable elements on an avian W Chromosome. Genome Res 2022; 32:671-681. [PMID: 35149543 PMCID: PMC8997356 DOI: 10.1101/gr.275465.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 02/08/2022] [Indexed: 11/24/2022]
Abstract
One of the defining features of transposable elements (TEs) is their ability to move to new locations in the host genome. To minimise the potentially deleterious effects of de novo TE insertions, hosts have evolved several mechanisms to control TE activity, including recombination-mediated removal and epigenetic silencing; however, increasing evidence suggests that silencing of TEs is often incomplete. The crow family experienced a recent radiation of LTR retrotransposons (LTRs), offering an opportunity to gain insight into the regulatory control of young, potentially still active TEs. We quantified the abundance of TE-derived transcripts across several tissues in 15 Eurasian crows (Corvus (corone) spp.) raised under common garden conditions and find evidence for ineffective TE suppression on the female-specific W Chromosome. Using RNA-seq data, we show that ~ 9.5% of all transcribed TEs had considerably greater (average: 16-fold) transcript abundance in female crows, and that more than 85% of these female-biased TEs originated on the W Chromosome. After accounting for differences in TE density among chromosomal classes, W-linked TEs were significantly more highly expressed than TEs residing on other chromosomes, consistent with ineffective silencing on the former. Together, our results suggest that the crow W Chromosome acts as a source of transcriptionally active TEs, with possible negative fitness consequences for female birds analogous to Drosophila (an X/Y system), where overexpression of Y-linked TEs is associated with male-specific aging and fitness loss ('toxic Y').
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24
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Bronikowski AM, Meisel RP, Biga PR, Walters J, Mank JE, Larschan E, Wilkinson GS, Valenzuela N, Conard AM, de Magalhães JP, Duan J, Elias AE, Gamble T, Graze R, Gribble KE, Kreiling JA, Riddle NC. Sex-specific aging in animals: Perspective and future directions. Aging Cell 2022; 21:e13542. [PMID: 35072344 PMCID: PMC8844111 DOI: 10.1111/acel.13542] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/15/2021] [Accepted: 12/11/2021] [Indexed: 12/14/2022] Open
Abstract
Sex differences in aging occur in many animal species, and they include sex differences in lifespan, in the onset and progression of age-associated decline, and in physiological and molecular markers of aging. Sex differences in aging vary greatly across the animal kingdom. For example, there are species with longer-lived females, species where males live longer, and species lacking sex differences in lifespan. The underlying causes of sex differences in aging remain mostly unknown. Currently, we do not understand the molecular drivers of sex differences in aging, or whether they are related to the accepted hallmarks or pillars of aging or linked to other well-characterized processes. In particular, understanding the role of sex-determination mechanisms and sex differences in aging is relatively understudied. Here, we take a comparative, interdisciplinary approach to explore various hypotheses about how sex differences in aging arise. We discuss genomic, morphological, and environmental differences between the sexes and how these relate to sex differences in aging. Finally, we present some suggestions for future research in this area and provide recommendations for promising experimental designs.
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Affiliation(s)
- Anne M. Bronikowski
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | - Richard P. Meisel
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
| | - Peggy R. Biga
- Department of BiologyThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - James R. Walters
- Department of Ecology and Evolutionary BiologyThe University of KansasLawrenceKansasUSA
| | - Judith E. Mank
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of BioscienceUniversity of ExeterPenrynUK
| | - Erica Larschan
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
| | | | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | - Ashley Mae Conard
- Department of Computer ScienceCenter for Computational and Molecular BiologyBrown UniversityProvidenceRhode IslandUSA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing GroupInstitute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | | | - Amy E. Elias
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
| | - Tony Gamble
- Department of Biological SciencesMarquette UniversityMilwaukeeWisconsinUSA
- Milwaukee Public MuseumMilwaukeeWisconsinUSA
- Bell Museum of Natural HistoryUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Rita M. Graze
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
| | - Kristin E. Gribble
- Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMassachusettsUSA
| | - Jill A. Kreiling
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
| | - Nicole C. Riddle
- Department of BiologyThe University of Alabama at BirminghamBirminghamAlabamaUSA
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25
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Cayuela H, Lemaître JF, Léna JP, Ronget V, Martínez-Solano I, Muths E, Pilliod DS, Schmidt BR, Sánchez-Montes G, Gutiérrez-Rodríguez J, Pyke G, Grossenbacher K, Lenzi O, Bosch J, Beard KH, Woolbright LL, Lambert BA, Green DM, Jreidini N, Garwood JM, Fisher RN, Matthews K, Dudgeon D, Lau A, Speybroeck J, Homan R, Jehle R, Başkale E, Mori E, Arntzen JW, Joly P, Stiles RM, Lannoo MJ, Maerz JC, Lowe WH, Valenzuela-Sánchez A, Christiansen DG, Angelini C, Thirion JM, Merilä J, Colli GR, Vasconcellos MM, Boas TCV, Arantes ÍDC, Levionnois P, Reinke BA, Vieira C, Marais GAB, Gaillard JM, Miller DAW. Sex-related differences in aging rate are associated with sex chromosome system in amphibians. Evolution 2021; 76:346-356. [PMID: 34878663 PMCID: PMC9304222 DOI: 10.1111/evo.14410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/03/2022]
Abstract
Sex‐related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex‐specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat‐rich Y/W chromosome (the “toxic Y/W effect”) could accelerate aging in the heterogametic sex in some vertebrate clades.
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Affiliation(s)
- Hugo Cayuela
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Jean-François Lemaître
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, F-769622, France
| | - Jean-Paul Léna
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, F-69622, France
| | - Victor Ronget
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, F-75016, France
| | - Iñigo Martínez-Solano
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - Erin Muths
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, 80526, USA
| | - David S Pilliod
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 970 Lusk Street, Boise, ID, 83706, USA
| | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, 8057, Switzerland.,Info fauna karch, Neuchâtel, 2000, Switzerland
| | - Gregorio Sánchez-Montes
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - Jorge Gutiérrez-Rodríguez
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, Madrid, 28006, Spain.,Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Graham Pyke
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China.,Department of Biological Sciences, Macquarie University, Ryde, NSW, 2109, Australia
| | - Kurt Grossenbacher
- Abteilung Wirbeltiere, Naturhistorisches Museum, Bernastrasse 15, Bern, 3005, Switzerland
| | - Omar Lenzi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, 8057, Switzerland
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, Madrid, 28006, Spain.,UMIB-Research Unit of Biodiversity (CSIC, UO, PA), Universidad de Oviedo, Campus de Mieres, Mieres, 33600, Spain.,Centro de Investigación, Seguimiento y Evaluación, Sierra de Guadarrama National Park, Cta. M-604, Km 27.6, Rascafría, 28740, Spain
| | - Karen H Beard
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, Utah, 84322, USA
| | - Lawrence L Woolbright
- Biology Department, Siena College, 515 Loudon Road, Loudonville, New York, 12211, USA
| | - Brad A Lambert
- Colorado Natural Heritage Program, Colorado State University, Fort Collins, Colorado, 80523-1475, USA
| | - David M Green
- Redpath Museum, McGill University, Montreal, QC, H3A 0C4, Canada
| | | | - Justin M Garwood
- California Department of Fish and Wildlife, 5341 Ericson Way, Arcata, CA, 95521, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, 92101, USA
| | - Kathleen Matthews
- USDA Forest Service, Pacific Southwest Research Station, Albany, California, USA
| | - David Dudgeon
- Division of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR
| | - Anthony Lau
- Science Unit, Lingnan University, Hong Kong, China
| | - Jeroen Speybroeck
- Research Institute for Nature and Forest, Havenlaan 88 bus 73, Brussel, 1000, Belgium
| | - Rebecca Homan
- Biology Department, Denison University, Granville, Ohio, USA
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Eyup Başkale
- Department of Biology, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Emiliano Mori
- Consiglio Nazionale delle Ricerche, Istituto di Ricerca sugli Ecosistemi Terrestri, Via Madonna del Piano 10, Sesto Fiorentino, 50019, Italy
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Pierre Joly
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, F-69622, France
| | - Rochelle M Stiles
- San Francisco Zoological Society, 1 Zoo Road, San Francisco, California, 94132, USA
| | - Michael J Lannoo
- Indiana University School of Medicine-TH, 620 Chestnut Street, Terre Haute, Indiana, 47809, USA
| | - John C Maerz
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| | - Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, USA
| | - Andrés Valenzuela-Sánchez
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile.,ONG Ranita de Darwin, Valdivia, 5112144, Chile
| | - Ditte G Christiansen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, 8057, Switzerland
| | - Claudio Angelini
- Salamandrina Sezzese Search Society, via G. Marconi 30, Sezze, 04018, Italy
| | - Jean-Marc Thirion
- Objectifs Biodiversité, 22 rue du Dr. Gilbert, Pont-l'Abbé-d'Arnoult, 17250, France
| | - Juha Merilä
- Division of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR.,Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | - Mariana M Vasconcellos
- Department of Biology, City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Taissa C V Boas
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | - Ísis da C Arantes
- Department of Biology, University of Mississippi, Oxford, MS, 38677, USA
| | - Pauline Levionnois
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, F-69622, France
| | - Beth A Reinke
- Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL, 60625, USA
| | - Cristina Vieira
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, F-769622, France
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, F-769622, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
| | - Jean-Michel Gaillard
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, F-769622, France
| | - David A W Miller
- Department of Ecosystem Sciences and Management, The Pennsylvania State University, University Park, Pennsylvania, USA
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26
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Ruchert JM, Brady MM, McMahan S, Lacey KJ, Latta LC, Sekelsky J, Stoffregen EP. Blm helicase facilitates rapid replication of repetitive DNA sequences in early Drosophila development. Genetics 2021; 220:6407149. [PMID: 34849849 DOI: 10.1093/genetics/iyab169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/18/2021] [Indexed: 11/12/2022] Open
Abstract
The absence of functional BLM DNA helicase, a member of the RecQ family of helicases, is responsible for the rare human disorder Bloom Syndrome, which results in developmental abnormalities, DNA repair defects, genomic instability, and a predisposition to cancer. In Drosophila melanogaster, the orthologous Blm protein is essential during early development when the embryo is under the control of maternal gene products. We show that lack of functional maternal Blm during the syncytial cell cycles of Drosophila embryonic development results in severe nuclear defects and lethality. Amongst the small fraction of embryos from Blm mutant mothers that survive to adulthood, a prominent sex-bias favors the class that inherits less repetitive DNA content, which serves as an endogenous source of replication stress. This selection against repetitive DNA content reflects a role for Blm in facilitating replication through repetitive sequences during the rapid S-phases of syncytial cell cycles. During these syncytial cycles, Blm is not required for complex DNA double-strand break repair; however, the progeny sex-bias resulting from the absence of maternal Blm is exacerbated by repetitive DNA sequences and by the slowing of replication fork progression, suggesting that the essential role for Blm during this stage is to manage replication fork stress brought about by impediments to fork progression. Additionally, our data suggest that Blm is only required to manage this replication stress during embryonic development, and likely only during the early, rapid syncytial cell cycles, and not at later developmental stages. These results provide novel insights into Blm function throughout development.
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Affiliation(s)
- Jolee M Ruchert
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Morgan M Brady
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Susan McMahan
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karly J Lacey
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Leigh C Latta
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Jeff Sekelsky
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric P Stoffregen
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.,SPIRE Postdoctoral Fellowship Program, University of North Carolina, Chapel Hill, NC 27599, USA
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27
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Ricchio J, Uno F, Carvalho AB. New Genes in the Drosophila Y Chromosome: Lessons from D. willistoni. Genes (Basel) 2021; 12:genes12111815. [PMID: 34828421 PMCID: PMC8623413 DOI: 10.3390/genes12111815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 01/05/2023] Open
Abstract
Y chromosomes play important roles in sex determination and male fertility. In several groups (e.g., mammals) there is strong evidence that they evolved through gene loss from a common X-Y ancestor, but in Drosophila the acquisition of new genes plays a major role. This conclusion came mostly from studies in two species. Here we report the identification of the 22 Y-linked genes in D. willistoni. They all fit the previously observed pattern of autosomal or X-linked testis-specific genes that duplicated to the Y. The ratio of gene gains to gene losses is ~25 in D. willistoni, confirming the prominent role of gene gains in the evolution of Drosophila Y chromosomes. We also found four large segmental duplications (ranging from 62 kb to 303 kb) from autosomal regions to the Y, containing ~58 genes. All but four of these duplicated genes became pseudogenes in the Y or disappeared. In the GK20609 gene the Y-linked copy remained functional, whereas its original autosomal copy degenerated, demonstrating how autosomal genes are transferred to the Y chromosome. Since the segmental duplication that carried GK20609 contained six other testis-specific genes, it seems that chance plays a significant role in the acquisition of new genes by the Drosophila Y chromosome.
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28
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Peona V, Palacios-Gimenez OM, Blommaert J, Liu J, Haryoko T, Jønsson KA, Irestedt M, Zhou Q, Jern P, Suh A. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200186. [PMID: 34304594 PMCID: PMC8310711 DOI: 10.1098/rstb.2020.0186] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Julie Blommaert
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, People's Republic of China
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
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29
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Kratochvíl L, Stöck M, Rovatsos M, Bullejos M, Herpin A, Jeffries DL, Peichel CL, Perrin N, Valenzuela N, Pokorná MJ. Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200097. [PMID: 34304593 PMCID: PMC8310716 DOI: 10.1098/rstb.2020.0097] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Las Lagunillas Campus S/N, 23071 Jaén, Spain
| | - Amaury Herpin
- INRAE, LPGP, 35000 Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Catherine L. Peichel
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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30
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Cayuela H, Dorant Y, Forester BR, Jeffries DL, Mccaffery RM, Eby LA, Hossack BR, Gippet JMW, Pilliod DS, Chris Funk W. Genomic signatures of thermal adaptation are associated with clinal shifts of life history in a broadly distributed frog. J Anim Ecol 2021; 91:1222-1238. [PMID: 34048026 PMCID: PMC9292533 DOI: 10.1111/1365-2656.13545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Abstract
Temperature is a critical driver of ectotherm life‐history strategies, whereby a warmer environment is associated with increased growth, reduced longevity and accelerated senescence. Increasing evidence indicates that thermal adaptation may underlie such life‐history shifts in wild populations. Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) can help uncover the molecular mechanisms of temperature‐driven variation in growth, longevity and senescence. However, our understanding of these mechanisms is still limited, which reduces our ability to predict the response of non‐model ectotherms to global temperature change. In this study, we examined the potential role of thermal adaptation in clinal shifts of life‐history traits (i.e. life span, senescence rate and recruitment) in the Columbia spotted frog Rana luteiventris along a broad temperature gradient in the western United States. We took advantage of extensive capture–recapture datasets of 20,033 marked individuals from eight populations surveyed annually for 14–18 years to examine how mean annual temperature and precipitation influenced demographic parameters (i.e. adult survival, life span, senescence rate, recruitment and population growth). After showing that temperature was the main climatic predictor influencing demography, we used RAD‐seq data (50,829 SNPs and 6,599 putative CNVs) generated for 352 individuals from 31 breeding sites to identify the genomic signatures of thermal adaptation. Our results showed that temperature was negatively associated with annual adult survival and reproductive life span and positively associated with senescence rate. By contrast, recruitment increased with temperature, promoting the long‐term viability of most populations. These temperature‐dependent demographic changes were associated with strong genomic signatures of thermal adaptation. We identified 148 SNP candidates associated with temperature including three SNPs located within protein‐coding genes regulating resistance to cold and hypoxia, immunity and reproduction in ranids. We also identified 39 CNV candidates (including within 38 transposable elements) for which normalized read depth was associated with temperature. Our study indicates that both SNPs and structural variants are associated with temperature and could eventually be found to play a functional role in clinal shifts in senescence rate and life‐history strategies in R. luteiventris. These results highlight the potential role of different sources of molecular variation in the response of ectotherms to environmental temperature variation in the context of global warming.
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Affiliation(s)
- Hugo Cayuela
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Brenna R Forester
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Dan L Jeffries
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Rebecca M Mccaffery
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Port Angeles, WA, USA
| | - Lisa A Eby
- Wildlife Biology Program, W. A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Blake R Hossack
- US Geological Survey, Northern Rocky Mountain Science Center, Missoula, MT, USA
| | - Jérôme M W Gippet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - David S Pilliod
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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31
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Meisel RP. The maintenance of polygenic sex determination depends on the dominance of fitness effects which are predictive of the role of sexual antagonism. G3 (BETHESDA, MD.) 2021; 11:6261074. [PMID: 33930135 PMCID: PMC8496315 DOI: 10.1093/g3journal/jkab149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/23/2021] [Indexed: 12/18/2022]
Abstract
In species with polygenic sex determination (PSD), multiple male- and female-determining loci on different proto-sex chromosomes segregate as polymorphisms within populations. The extent to which these polymorphisms are at stable equilibria is not yet resolved. Previous work demonstrated that PSD is most likely to be maintained as a stable polymorphism when the proto-sex chromosomes have opposite (sexually antagonistic) fitness effects in males and females. However, these models usually consider PSD systems with only two proto-sex chromosomes, or they do not broadly consider the dominance of the alleles under selection. To address these shortcomings, I used forward population genetic simulations to identify selection pressures that can maintain PSD under different dominance scenarios in a system with more than two proto-sex chromosomes (modeled after the house fly). I found that overdominant fitness effects of male-determining proto-Y chromosomes are more likely to maintain PSD than dominant, recessive, or additive fitness effects. The overdominant fitness effects that maintain PSD tend to have proto-Y chromosomes with sexually antagonistic effects (male-beneficial and female-detrimental). In contrast, dominant fitness effects that maintain PSD tend to have sexually antagonistic multi-chromosomal genotypes, but the individual proto-sex chromosomes do not have sexually antagonistic effects. These results demonstrate that sexual antagonism can be an emergent property of the multi-chromosome genotype without individual sexually antagonistic chromosomes. My results further illustrate how the dominance of fitness effects has consequences for both the likelihood that PSD will be maintained as well as the role sexually antagonistic selection is expected to play in maintaining the polymorphism.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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32
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Muyle A, Bachtrog D, Marais GAB, Turner JMA. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200124. [PMID: 33866802 DOI: 10.1098/rstb.2020.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Aline Muyle
- University of California Irvine, Irvine, CA 92697, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
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33
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Nguyen AH, Bachtrog D. Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome. PLoS Genet 2021; 17:e1009438. [PMID: 33886541 PMCID: PMC8061872 DOI: 10.1371/journal.pgen.1009438] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Sex-specific differences in lifespan are prevalent across the tree of life and influenced by heteromorphic sex chromosomes. In species with XY sex chromosomes, females often outlive males. Males and females can differ in their overall repeat content due to the repetitive Y chromosome, and repeats on the Y might lower survival of the heterogametic sex (toxic Y effect). Here, we take advantage of the well-assembled young Y chromosome of Drosophila miranda to study the sex-specific dynamics of chromatin structure and repeat expression during aging in male and female flies. Male D. miranda have about twice as much repetitive DNA compared to females, and live shorter than females. Heterochromatin is crucial for silencing of repetitive elements, yet old D. miranda flies lose H3K9me3 modifications in their pericentromere, with heterochromatin loss being more severe during aging in males than females. Satellite DNA becomes de-repressed more rapidly in old vs. young male flies relative to females. In contrast to what is observed in D. melanogaster, we find that transposable elements (TEs) are expressed at higher levels in male D. miranda throughout their life. We show that epigenetic silencing via heterochromatin formation is ineffective on the TE-rich neo-Y chromosome, presumably due to active transcription of a large number of neo-Y linked genes, resulting in up-regulation of Y-linked TEs already in young males. This is consistent with an interaction between the evolutionary age of the Y chromosome and the genomic effects of aging. Our data support growing evidence that "toxic Y chromosomes" can diminish male fitness and a reduction in heterochromatin can contribute to sex-specific aging.
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Affiliation(s)
- Alison H. Nguyen
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
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34
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Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ. Evolution of genome structure in the Drosophila simulans species complex. Genome Res 2021; 31:380-396. [PMID: 33563718 PMCID: PMC7919458 DOI: 10.1101/gr.263442.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022]
Abstract
The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Ching-Ho Chang
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Danielle E Khost
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
- FAS Informatics and Scientific Applications, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jeffrey R Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | | | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
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Proshkina E, Yushkova E, Koval L, Zemskaya N, Shchegoleva E, Solovev I, Yakovleva D, Pakshina N, Ulyasheva N, Shaposhnikov M, Moskalev A. Tissue-Specific Knockdown of Genes of the Argonaute Family Modulates Lifespan and Radioresistance in Drosophila Melanogaster. Int J Mol Sci 2021; 22:2396. [PMID: 33673647 PMCID: PMC7957547 DOI: 10.3390/ijms22052396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Small RNAs are essential to coordinate many cellular processes, including the regulation of gene expression patterns, the prevention of genomic instability, and the suppression of the mutagenic transposon activity. These processes determine the aging, longevity, and sensitivity of cells and an organism to stress factors (particularly, ionizing radiation). The biogenesis and activity of small RNAs are provided by proteins of the Argonaute family. These proteins participate in the processing of small RNA precursors and the formation of an RNA-induced silencing complex. However, the role of Argonaute proteins in regulating lifespan and radioresistance remains poorly explored. We studied the effect of knockdown of Argonaute genes (AGO1, AGO2, AGO3, piwi) in various tissues on the Drosophila melanogaster lifespan and survival after the γ-irradiation at a dose of 700 Gy. In most cases, these parameters are reduced or did not change significantly in flies with tissue-specific RNA interference. Surprisingly, piwi knockdown in both the fat body and the nervous system causes a lifespan increase. But changes in radioresistance depend on the tissue in which the gene was knocked out. In addition, analysis of changes in retrotransposon levels and expression of stress response genes allow us to determine associated molecular mechanisms.
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Affiliation(s)
- Ekaterina Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Liubov Koval
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Nadezhda Zemskaya
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Evgeniya Shchegoleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Ilya Solovev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Daria Yakovleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Natalya Pakshina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Natalia Ulyasheva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Mikhail Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Laboratory of Post-Genomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia
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Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM. Transposable Element Landscape in Drosophila Populations Selected for Longevity. Genome Biol Evol 2021; 13:6141024. [PMID: 33595657 PMCID: PMC8355499 DOI: 10.1093/gbe/evab031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) inflict numerous negative effects on health and fitness as they replicate by integrating into new regions of the host genome. Even though organisms employ powerful mechanisms to demobilize TEs, transposons gradually lose repression during aging. The rising TE activity causes genomic instability and was implicated in age-dependent neurodegenerative diseases, inflammation, and the determination of lifespan. It is therefore conceivable that long-lived individuals have improved TE silencing mechanisms resulting in reduced TE expression relative to their shorter-lived counterparts and fewer genomic insertions. Here, we test this hypothesis by performing the first genome-wide analysis of TE insertions and expression in populations of Drosophila melanogaster selected for longevity through late-life reproduction for 50–170 generations from four independent studies. Contrary to our expectation, TE families were generally more abundant in long-lived populations compared with nonselected controls. Although simulations showed that this was not expected under neutrality, we found little evidence for selection driving TE abundance differences. Additional RNA-seq analysis revealed a tendency for reducing TE expression in selected populations, which might be more important for lifespan than regulating genomic insertions. We further find limited evidence of parallel selection on genes related to TE regulation and transposition. However, telomeric TEs were genomically and transcriptionally more abundant in long-lived flies, suggesting improved telomere maintenance as a promising TE-mediated mechanism for prolonging lifespan. Our results provide a novel viewpoint indicating that reproduction at old age increases the opportunity of TEs to be passed on to the next generation with little impact on longevity.
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Affiliation(s)
- Daniel K Fabian
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
- Corresponding author: E-mail:
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Matías Fuentealba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Linda Partridge
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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An 8.22 Mb Assembly and Annotation of the Alpaca ( Vicugna pacos) Y Chromosome. Genes (Basel) 2021; 12:genes12010105. [PMID: 33467186 PMCID: PMC7830431 DOI: 10.3390/genes12010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.
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Wei KHC, Gibilisco L, Bachtrog D. Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males. Nat Commun 2020; 11:5537. [PMID: 33139741 PMCID: PMC7608633 DOI: 10.1038/s41467-020-19134-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/24/2020] [Indexed: 01/04/2023] Open
Abstract
Large portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity in Drosophila. Repeat-rich Y chromosomes can act as reservoirs for TEs ('toxic' Y effect), and incomplete epigenomic defenses during early development can lead to deleterious TE mobilization. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different ages. Zygotic TE expression is elevated in male embryos relative to females in both species, mostly due to expression of Y-linked TEs. Interestingly, male-biased TE expression diminishes across development in D. pseudoobscura, but remains elevated in D. miranda, the species with the younger and larger Y chromosome. The repeat-rich Y of D. miranda still contains many actively transcribed genes, which compromise the formation of silencing heterochromatin. Elevated TE expression results in more de novo insertions of repeats in males compared to females. This lends support to the idea that the 'toxic' Y chromosome can create a mutational burden in males when genome-wide defense mechanisms are compromised, and suggests a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA.
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Affiliation(s)
- Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Lauren Gibilisco
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
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Ågren JA, Munasinghe M, Clark AG. Mitochondrial-Y chromosome epistasis in Drosophila melanogaster. Proc Biol Sci 2020; 287:20200469. [PMID: 33081607 DOI: 10.1098/rspb.2020.0469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The coordination between mitochondrial and nuclear genes is crucial to eukaryotic organisms. Predicting the nature of these epistatic interactions can be difficult because of the transmission asymmetry of the genes involved. While autosomes and X-linked genes are transmitted through both sexes, genes on the Y chromosome and in the mitochondrial genome are uniparentally transmitted through males and females, respectively. Here, we generate 36 otherwise isogenic Drosophila melanogaster strains differing only in the geographical origin of their mitochondrial genome and Y chromosome, to experimentally examine the effects of the uniparentally inherited parts of the genome, as well as their interaction, in males. We assay longevity and gene expression through RNA-sequencing. We detect an important role for both mitochondrial and Y-linked genes, as well as extensive mitochondrial-Y chromosome epistasis. In particular, genes involved in male reproduction appear to be especially sensitive to such interactions, and variation on the Y chromosome is associated with differences in longevity. Despite these interactions, we find no evidence that the mitochondrial genome and Y chromosome are co-adapted within a geographical region. Overall, our study demonstrates a key role for the uniparentally inherited parts of the genome for male biology, but also that mito-nuclear interactions are complex and not easily predicted from simple transmission asymmetries.
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Affiliation(s)
- J Arvid Ågren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Manisha Munasinghe
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.,Department of Computational Biology, Cornell University, Ithaca, NY, USA
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40
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Credendino SC, Neumayer C, Cantone I. Genetics and Epigenetics of Sex Bias: Insights from Human Cancer and Autoimmunity. Trends Genet 2020; 36:650-663. [PMID: 32736810 DOI: 10.1016/j.tig.2020.06.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
High-throughput sequencing and genome-wide association studies have revealed a sex bias in human diseases. The underlying molecular mechanisms remain, however, unknown. Here, we cover recent advances in cancer and autoimmunity focusing on intrinsic genetic and epigenetic differences underlying sex biases in human disease. These studies reveal a central role of genome regulatory mechanisms including genome repair, chromosome folding, and epigenetic regulation in dictating the sex bias. These highlight the importance of considering sex as a variable in both basic science and clinical investigations. Understanding the molecular mechanisms underlying sex bias in human diseases will be instrumental in making a first step forwards into the era of personalized medicine.
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Affiliation(s)
- Sara Carmela Credendino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Christoph Neumayer
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Irene Cantone
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; Institute of Experimental Endocrinology and Oncology 'G. Salvatore', National Research Council (CNR), 80131 Naples, Italy.
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41
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Yost RT, Robinson JW, Baxter CM, Scott AM, Brown LP, Aletta MS, Hakimjavadi R, Lone A, Cumming RC, Dukas R, Mozer B, Simon AF. Abnormal Social Interactions in a Drosophila Mutant of an Autism Candidate Gene: Neuroligin 3. Int J Mol Sci 2020; 21:E4601. [PMID: 32610435 PMCID: PMC7370170 DOI: 10.3390/ijms21134601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/20/2022] Open
Abstract
Social interactions are typically impaired in neuropsychiatric disorders such as autism, for which the genetic underpinnings are very complex. Social interactions can be modeled by analysis of behaviors, including social spacing, sociability, and aggression, in simpler organisms such as Drosophila melanogaster. Here, we examined the effects of mutants of the autism-related gene neuroligin 3 (nlg3) on fly social and non-social behaviors. Startled-induced negative geotaxis is affected by a loss of function nlg3 mutation. Social space and aggression are also altered in a sex- and social-experience-specific manner in nlg3 mutant flies. In light of the conserved roles that neuroligins play in social behavior, our results offer insight into the regulation of social behavior in other organisms, including humans.
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Affiliation(s)
- Ryley T. Yost
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada; (R.T.Y.); (J.W.R.); (L.P.B.); (M.S.A.); (R.H.); (A.L.); (R.C.C.)
| | - J. Wesley Robinson
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada; (R.T.Y.); (J.W.R.); (L.P.B.); (M.S.A.); (R.H.); (A.L.); (R.C.C.)
| | - Carling M. Baxter
- Animal Behaviour Group, Department of Psychology, Neuroscience and Behaviour (PNB) McMaster University, Hamilton, ON L8S 4K1, Canada; (C.M.B.); (A.M.S.); (R.D.)
| | - Andrew M. Scott
- Animal Behaviour Group, Department of Psychology, Neuroscience and Behaviour (PNB) McMaster University, Hamilton, ON L8S 4K1, Canada; (C.M.B.); (A.M.S.); (R.D.)
| | - Liam P. Brown
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada; (R.T.Y.); (J.W.R.); (L.P.B.); (M.S.A.); (R.H.); (A.L.); (R.C.C.)
| | - M. Sol Aletta
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada; (R.T.Y.); (J.W.R.); (L.P.B.); (M.S.A.); (R.H.); (A.L.); (R.C.C.)
| | - Ramtin Hakimjavadi
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada; (R.T.Y.); (J.W.R.); (L.P.B.); (M.S.A.); (R.H.); (A.L.); (R.C.C.)
| | - Asad Lone
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada; (R.T.Y.); (J.W.R.); (L.P.B.); (M.S.A.); (R.H.); (A.L.); (R.C.C.)
| | - Robert C. Cumming
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada; (R.T.Y.); (J.W.R.); (L.P.B.); (M.S.A.); (R.H.); (A.L.); (R.C.C.)
| | - Reuven Dukas
- Animal Behaviour Group, Department of Psychology, Neuroscience and Behaviour (PNB) McMaster University, Hamilton, ON L8S 4K1, Canada; (C.M.B.); (A.M.S.); (R.D.)
| | - Brian Mozer
- Office of Research Integrity, Office of the Assistant Secretary for Health, Rockville, MD 20889, USA;
| | - Anne F. Simon
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada; (R.T.Y.); (J.W.R.); (L.P.B.); (M.S.A.); (R.H.); (A.L.); (R.C.C.)
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