1
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Courret C, Larracuente AM. High levels of intra-strain structural variation in Drosophila simulans X pericentric heterochromatin. Genetics 2023; 225:iyad176. [PMID: 37768175 PMCID: PMC10697818 DOI: 10.1093/genetics/iyad176] [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: 08/12/2023] [Revised: 08/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Large genome structural variations can impact genome regulation and integrity. Repeat-rich regions like pericentric heterochromatin are vulnerable to structural rearrangements although we know little about how often these rearrangements occur over evolutionary time. Repetitive genome regions are particularly difficult to study with genomic approaches, as they are missing from most genome assemblies. However, cytogenetic approaches offer a direct way to detect large rearrangements involving pericentric heterochromatin. Here, we use a cytogenetic approach to reveal large structural rearrangements associated with the X pericentromeric region of Drosophila simulans. These rearrangements involve large blocks of satellite DNA-the 500-bp and Rsp-like satellites-which colocalize in the X pericentromeric heterochromatin. We find that this region is polymorphic not only among different strains, but between isolates of the same strain from different labs, and even within individual isolates. On the one hand, our observations raise questions regarding the potential impact of such variation at the phenotypic level and our ability to control for such genetic variability. On the other hand, this highlights the very rapid turnover of the pericentric heterochromatin most likely associated with genomic instability of the X pericentromere. It represents a unique opportunity to study the dynamics of pericentric heterochromatin, the evolution of associated satellites on a very short time scale, and to better understand how structural variation arises.
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Affiliation(s)
- Cécile Courret
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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2
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Murphy PJ, Berger F. The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations. Development 2023; 150:dev201989. [PMID: 38771301 PMCID: PMC10629678 DOI: 10.1242/dev.201989] [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: 05/13/2023] [Accepted: 09/12/2023] [Indexed: 11/05/2023]
Abstract
We propose that several chromatin-mediated regulatory processes are dominated by source-sink relationships in which factors operate as 'sources' to produce or provide a resource and compete with each other to occupy separate 'sinks'. In this model, large portions of genomic DNA operate as 'sinks', which are filled by 'sources', such as available histone variants, covalent modifications to histones, the readers of these modifications and non-coding RNAs. Competing occupation for the sinks by different sources leads to distinct states of genomic equilibrium in differentiated cells. During dynamic developmental events, such as sexual reproduction, we propose that dramatic and rapid reconfiguration of source-sink relationships modifies chromatin states. We envision that re-routing of sources could occur by altering the dimensions of the sink, by reconfiguration of existing sink occupation or by varying the size of the source, providing a central mechanism to explain a plethora of epigenetic phenomena, which contribute to phenotypic variegation, zygotic genome activation and nucleolar dominance.
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Affiliation(s)
- Patrick J. Murphy
- University of Rochester, Department of Biomedical Genetics and Department of Biology, 601 Elmwood Ave., Rochester NY 14620, USA
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter; Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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3
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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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4
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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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5
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Nanni AV, Martinez N, Graze R, Morse A, Newman JRB, Jain V, Vlaho S, Signor S, Nuzhdin SV, Renne R, McIntyre LM. Sex-biased expression is associated with chromatin state in D. melanogaster and D. simulans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523946. [PMID: 36711631 PMCID: PMC9882225 DOI: 10.1101/2023.01.13.523946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We propose a new model for the association of chromatin state and sex-bias in expression. We hypothesize enrichment of open chromatin in the sex where we see expression bias (OS) and closed chromatin in the opposite sex (CO). In this study of D. melanogaster and D. simulans head tissue, sex-bias in expression is associated with H3K4me3 (open mark) in males for male-biased genes and in females for female-biased genes in both species. Sex-bias in expression is also largely conserved in direction and magnitude between the two species on the X and autosomes. In male-biased orthologs, the sex-bias ratio is more divergent between species if both species have H3K27me2me3 marks in females compared to when either or neither species has H3K27me2me3 in females. H3K27me2me3 marks in females are associated with male-bias in expression on the autosomes in both species, but on the X only in D. melanogaster . In female-biased orthologs the relationship between the species for the sex-bias ratio is similar regardless of the H3K27me2me3 marks in males. Female-biased orthologs are more similar in the ratio of sex-bias than male-biased orthologs and there is an excess of male-bias in expression in orthologs that gain/lose sex-bias. There is an excess of male-bias in sex-limited expression in both species suggesting excess male-bias is due to rapid evolution between the species. The X chromosome has an enrichment in male-limited H3K4me3 in both species and an enrichment of sex-bias in expression compared to the autosomes.
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Affiliation(s)
- Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Natalie Martinez
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Rita Graze
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Alison Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jeremy R B Newman
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Vaibhav Jain
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Srna Vlaho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Sarah Signor
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
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6
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Cechova M, Miga KH. Satellite DNAs and human sex chromosome variation. Semin Cell Dev Biol 2022; 128:15-25. [PMID: 35644878 DOI: 10.1016/j.semcdb.2022.04.022] [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: 03/15/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022]
Abstract
Satellite DNAs are present on every chromosome in the cell and are typically enriched in repetitive, heterochromatic parts of the human genome. Sex chromosomes represent a unique genomic and epigenetic context. In this review, we first report what is known about satellite DNA biology on human X and Y chromosomes, including repeat content and organization, as well as satellite variation in typical euploid individuals. Then, we review sex chromosome aneuploidies that are among the most common types of aneuploidies in the general population, and are better tolerated than autosomal aneuploidies. This is demonstrated also by the fact that aging is associated with the loss of the X, and especially the Y chromosome. In addition, supernumerary sex chromosomes enable us to study general processes in a cell, such as analyzing heterochromatin dosage (i.e. additional Barr bodies and long heterochromatin arrays on Yq) and their downstream consequences. Finally, genomic and epigenetic organization and regulation of satellite DNA could influence chromosome stability and lead to aneuploidy. In this review, we argue that the complete annotation of satellite DNA on sex chromosomes in human, and especially in centromeric regions, will aid in explaining the prevalence and the consequences of sex chromosome aneuploidies.
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Affiliation(s)
- Monika Cechova
- Faculty of Informatics, Masaryk University, Czech Republic
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA; UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA 95064, USA
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7
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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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8
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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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9
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Munasinghe M, Haller BC, Clark AG. Migration restores hybrid incompatibility driven by mitochondrial-nuclear sexual conflict. Proc Biol Sci 2022; 289:20212561. [PMID: 35078356 PMCID: PMC8790342 DOI: 10.1098/rspb.2021.2561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In the mitochondrial genome, sexual asymmetry in transmission allows the accumulation of male-harming mutations since selection acts only on the effect of the mutation in females. Called the 'Mother's Curse', this phenomenon induces a selective pressure for nuclear variants that compensate for this reduction in male fitness. Previous work has demonstrated the existence of these interactions and their potential to act as Dobzhansky-Muller incompatibilities, contributing to reproductive isolation between populations. However, it is not clear how readily they would give rise to and sustain hybrid incompatibilities. Here, we use computer simulations in SLiM 3 to investigate the consequences of sexually antagonistic mitochondrial-nuclear interactions in a subdivided population. We consider distinct migration schemes and vary the chromosomal location, and consequently the transmission pattern, of nuclear restorers. Disrupting these co-evolved interactions results in less-fit males, skewing the sex ratio toward females. Restoration of male fitness depends on both the chromosomal location of nuclear restorer loci and the migration scheme. Our results show that these interactions may act as Dobzhansky-Muller incompatibilities, but their strength is not enough to drive population isolation. Overall, this model shows the varied ways in which populations can respond to migration's disruption of co-evolved mitochondrial-nuclear interactions.
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Affiliation(s)
- Manisha Munasinghe
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Benjamin C. Haller
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Andrew G. Clark
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14583, USA
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10
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Shohat S, Vol E, Shifman S. Gene essentiality in cancer cell lines is modified by the sex chromosomes. Genome Res 2022; 32:1993-2002. [PMID: 36418059 PMCID: PMC9808629 DOI: 10.1101/gr.276488.121] [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: 12/14/2021] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Abstract
Human sex differences arise from gonadal hormones and sex chromosomes. Studying the direct effects of sex chromosomes in humans is still challenging. Here we studied how the sex chromosomes can modulate gene expression and the outcome of mutations across the genome by exploiting the tendency of cancer cell lines to lose or gain sex chromosomes. We inferred the dosage of the sex chromosomes in 355 female and 408 male cancer cell lines and used it to dissect the contributions of the Y and X Chromosomes to sex-biased gene expression. Furthermore, based on genome-wide CRISPR screens, we identified genes whose essentiality is different between male and female cells depending on the sex chromosomes. The most significant genes were X-linked genes compensated by Y-linked paralogs. Our sex-based analysis identifies genes that, when mutated, can affect male and female cells differently and reinforces the roles of the X and Y Chromosomes in sex-specific cell function.
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11
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Edwards MM, Zuccaro MV, Sagi I, Ding Q, Vershkov D, Benvenisty N, Egli D, Koren A. Delayed DNA replication in haploid human embryonic stem cells. Genome Res 2021; 31:2155-2169. [PMID: 34810218 PMCID: PMC8647822 DOI: 10.1101/gr.275953.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Ido Sagi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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12
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Lawlor MA, Cao W, Ellison CE. A transposon expression burst accompanies the activation of Y-chromosome fertility genes during Drosophila spermatogenesis. Nat Commun 2021; 12:6854. [PMID: 34824217 PMCID: PMC8617248 DOI: 10.1038/s41467-021-27136-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/04/2021] [Indexed: 11/09/2022] Open
Abstract
Transposable elements (TEs) must replicate in germline cells to pass novel insertions to offspring. In Drosophila melanogaster ovaries, TEs can exploit specific developmental windows of opportunity to evade host silencing and increase their copy numbers. However, TE activity and host silencing in the distinct cell types of Drosophila testis are not well understood. Here, we reanalyze publicly available single-cell RNA-seq datasets to quantify TE expression in the distinct cell types of the Drosophila testis. We develop a method for identification of TE and host gene expression modules and find that a distinct population of early spermatocytes expresses a large number of TEs at much higher levels than other germline and somatic components of the testes. This burst of TE expression coincides with the activation of Y chromosome fertility factors and spermatocyte-specific transcriptional regulators, as well as downregulation of many components of the piRNA pathway. The TEs expressed by this cell population are specifically enriched on the Y chromosome and depleted on the X chromosome, relative to other active TEs. These data suggest that some TEs may achieve high insertional activity in males by exploiting a window of opportunity for mobilization created by the activation of spermatocyte-specific and Y chromosome-specific transcriptional programs.
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Affiliation(s)
- Matthew A Lawlor
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Christopher E Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA.
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13
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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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14
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Kuhn GCS, Heringer P, Dias GB. Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:27-56. [PMID: 34386871 DOI: 10.1007/978-3-030-74889-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The fact that satellite DNAs (satDNAs) in eukaryotes are abundant genomic components, can perform functional roles, but can also change rapidly across species while being homogenous within a species, makes them an intriguing and fascinating genomic component to study. It is also becoming clear that satDNAs represent an important piece in genome architecture and that changes in their structure, organization, and abundance can affect the evolution of genomes and species in many ways. Since the discovery of satDNAs more than 50 years ago, species from the Drosophila genus have continuously been used as models to study several aspects of satDNA biology. These studies have been largely concentrated in D. melanogaster and closely related species from the Sophophora subgenus, even though the vast majority of all Drosophila species belong to the Drosophila subgenus. This chapter highlights some studies on the satDNA structure, organization, and evolution in two species groups from the Drosophila subgenus: the repleta and virilis groups. We also discuss and review the classification of other abundant tandem repeats found in these species in the light of the current information available.
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Affiliation(s)
- Gustavo C S Kuhn
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
| | - Pedro Heringer
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Guilherme Borges Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
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15
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Mutzel V, Schulz EG. Dosage Sensing, Threshold Responses, and Epigenetic Memory: A Systems Biology Perspective on Random X-Chromosome Inactivation. Bioessays 2021; 42:e1900163. [PMID: 32189388 DOI: 10.1002/bies.201900163] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/27/2020] [Indexed: 02/06/2023]
Abstract
X-chromosome inactivation ensures dosage compensation between the sexes in mammals by randomly choosing one out of the two X chromosomes in females for inactivation. This process imposes a plethora of questions: How do cells count their X chromosome number and ensure that exactly one stays active? How do they randomly choose one of two identical X chromosomes for inactivation? And how do they stably maintain this state of monoallelic expression? Here, different regulatory concepts and their plausibility are evaluated in the context of theoretical studies that have investigated threshold behavior, ultrasensitivity, and bistability through mathematical modeling. It is discussed how a twofold difference between a single and a double dose of X-linked genes might be converted to an all-or-nothing response and how mutually exclusive expression can be initiated and maintained. Finally, candidate factors that might mediate the proposed regulatory principles are reviewed.
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Affiliation(s)
- Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
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16
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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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17
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Brown EJ, Nguyen AH, Bachtrog D. The Drosophila Y Chromosome Affects Heterochromatin Integrity Genome-Wide. Mol Biol Evol 2021; 37:2808-2824. [PMID: 32211857 PMCID: PMC7530609 DOI: 10.1093/molbev/msaa082] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Drosophila Y chromosome is gene poor and mainly consists of silenced, repetitive DNA. Nonetheless, the Y influences expression of hundreds of genes genome-wide, possibly by sequestering key components of the heterochromatin machinery away from other positions in the genome. To test the influence of the Y chromosome on the genome-wide chromatin landscape, we assayed the genomic distribution of histone modifications associated with gene activation (H3K4me3) or heterochromatin (H3K9me2 and H3K9me3) in fruit flies with varying sex chromosome complements (X0, XY, and XYY males; XX and XXY females). Consistent with the general deficiency of active chromatin modifications on the Y, we find that Y gene dose has little influence on the genomic distribution of H3K4me3. In contrast, both the presence and the number of Y chromosomes strongly influence genome-wide enrichment patterns of repressive chromatin modifications. Highly repetitive regions such as the pericentromeres, the dot, and the Y chromosome (if present) are enriched for heterochromatic modifications in wildtype males and females, and even more strongly in X0 flies. In contrast, the additional Y chromosome in XYY males and XXY females diminishes the heterochromatic signal in these normally silenced, repeat-rich regions, which is accompanied by an increase in expression of Y-linked repeats. We find hundreds of genes that are expressed differentially between individuals with aberrant sex chromosome karyotypes, many of which also show sex-biased expression in wildtype Drosophila. Thus, Y chromosomes influence heterochromatin integrity genome-wide, and differences in the chromatin landscape of males and females may also contribute to sex-biased gene expression and sexual dimorphisms.
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Affiliation(s)
- Emily J Brown
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Alison H Nguyen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
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18
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Anifandis G, Tempest HG, Oliva R, Swanson GM, Simopoulou M, Easley CA, Primig M, Messini CI, Turek PJ, Sutovsky P, Ory SJ, Krawetz SA. COVID-19 and human reproduction: A pandemic that packs a serious punch. Syst Biol Reprod Med 2021; 67:3-23. [PMID: 33719829 DOI: 10.1080/19396368.2020.1855271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic has led to a worldwide health emergency that has impacted 188 countries at last count. The rapid community transmission and relatively high mortality rates with COVID-19 in modern times are relatively unique features of this flu pandemic and have resulted in an unparalleled global health crisis. SARS-CoV-2, being a respiratory virus, mainly affects the lungs, but is capable of infecting other vital organs, such as brain, heart and kidney. Emerging evidence suggests that the virus also targets male and female reproductive organs that express its main receptor ACE2, although it is as yet unclear if this has any implications for human fertility. Furthermore, professional bodies have recommended discontinuing fertility services during the pandemic such that reproductive services have also been affected. Although increased safety measures have helped to mitigate the propagation of COVID-19 in a number of countries, it seems that there is no predictable timeline to containment of the virus, a goal likely to remain elusive until an effective vaccine becomes available and widely distributed across the globe. In parallel, research on reproduction has been postponed for obvious reasons, while diagnostic tests that detect the virus or antibodies against it are of vital importance to support public health policies, such as social distancing and our obligation to wear masks in public spaces. This review aims to provide an overview of critical research and ethics issues that have been continuously emerging in the field of reproductive medicine as the COVID-19 pandemic tragically unfolds.Abbreviations: ACE2: angiotensin- converting enzyme 2; ART: Assisted reproductive technology; ASRM: American Society for Reproductive Medicine; CCR9: C-C Motif Chemokine Receptor 9; CDC: Centers for Disease Control and Prevention; COVID-19: Coronavirus disease 2019; Ct: Cycle threshold; CXCR6: C-X-C Motif Chemokine Receptor 6; ELISA: enzyme-linked immunosorbent assay; ESHRE: European Society of Human Reproduction and Embryology; ET: Embryo transfer; FSH: Follicle Stimulating Hormone; FFPE: formalin fixed paraffin embedded; FYCO1: FYVE And Coiled-Coil Domain Autophagy Adaptor 1; IFFS: International Federation of Fertility Societies; IUI: Intrauterine insemination; IVF: In vitro fertilization; LH: Luteinizing Hormone; LZTFL1: Leucine Zipper Transcription Factor Like 1; MAR: medically assisted reproduction services; MERS: Middle East Respiratory syndrome; NGS: Next Generation Sequencing; ORF: Open Reading Frame; PPE: personal protective equipment; RE: RNA Element; REDa: RNA Element Discovery algorithm; RT-PCR: Reverse=trascriptase transcriptase-polymerase chain reaction; SARS: Severe acute respiratory syndrome; SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus 2; SLC6A20: Solute Carrier Family 6 Member 20; SMS: Single Molecule Sequencing; T: Testosterone; TMPRSS2: transmembrane serine protease 2; WHO: World Health Organization; XCR1: X-C Motif Chemokine Receptor.
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Affiliation(s)
- George Anifandis
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, Larisa, Greece
| | - Helen G Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat De Barcelona, and Hospital Clinic from Barcelona, Spain
| | - Grace M Swanson
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Mara Simopoulou
- Department of Experimental Physiology, School of Health Sciences, Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece, Athens, Greece
| | - Charles A Easley
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Michael Primig
- Inserm, EHESP, Irset (Institut De Recherche En Santé, Environnement Et Travail), Rennes, France
| | - Christina I Messini
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, Larisa, Greece
| | - Paul J Turek
- It is a private Clinic, The Turek Clinic, Beverly Hills, CA, USA
| | - Peter Sutovsky
- Division of Animal Sciences and the Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
| | - Steve J Ory
- It is a private Clinic, IVF Florida Reproductive Institutes, Margate, FL, USA.,Department of Obstetrics and Gynecology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology and Center of Molecular Medicine and Genetics, C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI, USA
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19
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Kulikov AM, Sorokina SY, Melnikov AI, Gornostaev NG, Seleznev DG, Lazebny OE. The effects of the sex chromosomes on the inheritance of species-specific traits of the copulatory organ shape in Drosophila virilis and Drosophila lummei. PLoS One 2020; 15:e0244339. [PMID: 33373382 PMCID: PMC7771703 DOI: 10.1371/journal.pone.0244339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
The shape of the male genitalia in many taxa is the most rapidly evolving morphological structure, often driving reproductive isolation, and is therefore widely used in systematics as a key character to distinguish between sibling species. However, only a few studies have used the genital arch of the male copulatory organ as a model to study the genetic basis of species-specific differences in the Drosophila copulatory system. Moreover, almost nothing is known about the effects of the sex chromosomes on the shape of the male mating organ. In our study, we used a set of crosses between D. virilis and D. lummei and applied the methods of quantitative genetics to assess the variability of the shape of the male copulatory organ and the effects of the sex chromosomes and autosomes on its variance. Our results showed that the male genital shape depends on the species composition of the sex chromosomes and autosomes. Epistatic interactions of the sex chromosomes with autosomes and the species origin of the Y-chromosome in a male in interspecific crosses also influenced the expression of species-specific traits in the shape of the male copulatory system. Overall, the effects of sex chromosomes were comparable to the effects of autosomes despite the great differences in gene numbers between them. It may be reasonably considered that sexual selection for specific genes associated with the shape of the male mating organ prevents the demasculinization of the X chromosome.
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Affiliation(s)
- Alex M. Kulikov
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Svetlana Yu. Sorokina
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Anton I. Melnikov
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Nick G. Gornostaev
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy G. Seleznev
- Department of Ecology of Aquatic Invertebrates, Papanin Institute for Biology of Inland Waters of the Russian Academy of Sciences, Borok village, Yaroslavl Region, Russia
| | - Oleg E. Lazebny
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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20
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Hellmann JK, Carlson ER, Bell AM. Sex-specific plasticity across generations II: Grandpaternal effects are lineage specific and sex specific. J Anim Ecol 2020; 89:2800-2812. [PMID: 33191513 PMCID: PMC7902365 DOI: 10.1111/1365-2656.13365] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Transgenerational plasticity (TGP) occurs when the environment encountered by one generation (F0) alters the phenotypes of one or more future generations (e.g. F1 and F2). Sex selective TGP, via specific lineages or to only male or female descendants, has been underexplored in natural systems, and may be adaptive if it allows past generations to fine-tune the phenotypes of future generations in response to sex-specific life-history strategies. We sought to understand if exposing males to predation risk can influence grandoffspring via sperm in three-spined stickleback Gasterosteus aculeatus. We specifically tested the hypothesis that grandparental effects are transmitted in a sex-specific way down the male lineage, from paternal grandfathers to F2 males. We reared F1 offspring of unexposed and predator-exposed F0 males under 'control' conditions and used them to generate F2s with control grandfathers, a predator-exposed maternal grandfather (i.e. predator-exposed F0 males to F1 daughters to F2s), a predator-exposed paternal grandfather (i.e. predator-exposed F0 males to F1 sons to F2s) or two predator-exposed grandfathers. We then assayed male and female F2s for a variety of traits related to antipredator defence. We found little evidence that transgenerational effects were mediated to only male descendants via the paternal lineage. Instead, grandpaternal effects depended on lineage and were mediated largely across sexes, from F1 males to F2 females and from F1 females to F2 males. When their paternal grandfather was exposed to predation risk, female F2s were heavier and showed a reduced change in behaviour in response to a simulated predator attack relative to grandoffspring of control, unexposed grandparents. In contrast, male F2s showed reduced antipredator behaviour when their maternal grandfather was exposed to predation risk. However, these patterns were only evident when one grandfather, but not both grandfathers, was exposed to predation risk, suggesting the potential for non-additive interactions across lineages. If sex-specific and lineage effects are common, then grandparental effects are likely underestimated in the literature. These results draw attention to the importance of sex-selective inheritance of environmental effects and raise new questions about the proximate and ultimate causes of selective transmission across generations.
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Affiliation(s)
- Jennifer K Hellmann
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
| | - Erika R Carlson
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
| | - Alison M Bell
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
- Program in Ecology, Evolution and Conservation, University of Illinois Urbana-Champaign, Urbana, Illinois, USA, 61801
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21
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Kasinathan B, Colmenares SU, McConnell H, Young JM, Karpen GH, Malik HS. Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila. eLife 2020; 9:e63368. [PMID: 33169670 PMCID: PMC7655104 DOI: 10.7554/elife.63368] [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: 09/23/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Contrary to dogma, evolutionarily young and dynamic genes can encode essential functions. We find that evolutionarily dynamic ZAD-ZNF genes, which encode the most abundant class of insect transcription factors, are more likely to encode essential functions in Drosophila melanogaster than ancient, conserved ZAD-ZNF genes. We focus on the Nicknack ZAD-ZNF gene, which is evolutionarily young, poorly retained in Drosophila species, and evolves under strong positive selection. Yet we find that it is necessary for larval development in D. melanogaster. We show that Nicknack encodes a heterochromatin-localizing protein like its paralog Oddjob, also an evolutionarily dynamic yet essential ZAD-ZNF gene. We find that the divergent D. simulans Nicknack protein can still localize to D. melanogaster heterochromatin and rescue viability of female but not male Nicknack-null D. melanogaster. Our findings suggest that innovation for rapidly changing heterochromatin functions might generally explain the essentiality of many evolutionarily dynamic ZAD-ZNF genes in insects.
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Affiliation(s)
- Bhavatharini Kasinathan
- Medical Scientist Training Program, University of Washington School of MedicineSeattleUnited States
- Molecular and Cellular Biology Graduate program, University of Washington School of MedicineSeattleUnited States
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Serafin U Colmenares
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteBerkeleyUnited States
| | - Hannah McConnell
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Gary H Karpen
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteBerkeleyUnited States
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research CenterSeattleUnited States
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22
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Liu J, Ali M, Zhou Q. Establishment and evolution of heterochromatin. Ann N Y Acad Sci 2020; 1476:59-77. [PMID: 32017156 PMCID: PMC7586837 DOI: 10.1111/nyas.14303] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome is packaged into transcriptionally active euchromatin and silent heterochromatin, with most studies focused on the former encompassing the majority of protein-coding genes. The recent development of various sequencing techniques has refined this classic dichromatic partition and has better illuminated the composition, establishment, and evolution of this genomic and epigenomic "dark matter" in the context of topologically associated domains and phase-separated droplets. Heterochromatin includes genomic regions that can be densely stained by chemical dyes, which have been shown to be enriched for repetitive elements and epigenetic marks, including H3K9me2/3 and H3K27me3. Heterochromatin is usually replicated late, concentrated at the nuclear periphery or around nucleoli, and usually lacks highly expressed genes; and now it is considered to be as neither genetically inert nor developmentally static. Heterochromatin guards genome integrity against transposon activities and exerts important regulatory functions by targeting beyond its contained genes. Both its nucleotide sequences and regulatory proteins exhibit rapid coevolution between species. In addition, there are dynamic transitions between euchromatin and heterochromatin during developmental and evolutionary processes. We summarize here the ever-changing characteristics of heterochromatin and propose models and principles for the evolutionary transitions of heterochromatin that have been mainly learned from studies of Drosophila and yeast. Finally, we highlight the role of sex chromosomes in studying heterochromatin evolution.
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Affiliation(s)
- Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Mujahid Ali
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouChina
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23
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Kloc M, Ghobrial RM, Kubiak JZ. The Role of Genetic Sex and Mitochondria in Response to COVID-19 Infection. Int Arch Allergy Immunol 2020; 181:629-634. [PMID: 32564017 PMCID: PMC7360490 DOI: 10.1159/000508560] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/08/2020] [Indexed: 12/14/2022] Open
Abstract
The difference between the female and male immune response to COVID-19 infection, and infections in general, is multifactorial. The well-known determiners of the immune response, such as X and Y chromosomes, sex hormones, and microbiota, are functionally interconnected and influence each other in shaping the organism's immunity. We focus our commentary on the interplay between the genetic sex and mitochondria and how this may affect a sex-dependent immune response in COVID-19 infection. Realizing the existence of these interactions may help in designing novel methods or fine-tuning the existing and routine therapies to fight COVID-19 and other infections.
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Affiliation(s)
- Malgorzata Kloc
- The Houston Methodist Research Institute, Houston, Texas, USA,
- Department of Surgery, The Houston Methodist Hospital, Houston, Texas, USA,
- Department of Genetics, M.D. Anderson Cancer Center, The University of Texas, Houston, Texas, USA,
| | - Rafik Mark Ghobrial
- The Houston Methodist Research Institute, Houston, Texas, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, Texas, USA
| | - Jacek Z Kubiak
- Laboratory of Regenerative Medicine and Cell Biology, Military Institute of Hygiene and Epidemiology (WIHE), Warsaw, Poland
- UnivRennes, UMR 6290, CNRS, Institute of Genetics and Development of Rennes, Cell Cycle Group, Faculty of Medicine, Rennes, France
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24
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Sharma A, Kinney NA, Timoshevskiy VA, Sharakhova MV, Sharakhov IV. Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex. Genes (Basel) 2020; 11:E327. [PMID: 32204543 PMCID: PMC7140835 DOI: 10.3390/genes11030327] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
Heterochromatin is identified as a potential factor driving diversification of species. To understand the magnitude of heterochromatin variation within the Anopheles gambiae complex of malaria mosquitoes, we analyzed metaphase chromosomes in An. arabiensis, An. coluzzii, An. gambiae, An. merus, and An. quadriannulatus. Using fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA), a highly repetitive fraction of DNA, and heterochromatic Bacterial Artificial Chromosome (BAC) clones, we established the correspondence of pericentric heterochromatin between the metaphase and polytene X chromosomes of An. gambiae. We then developed chromosome idiograms and demonstrated that the X chromosomes exhibit qualitative differences in their pattern of heterochromatic bands and position of satellite DNA (satDNA) repeats among the sibling species with postzygotic isolation, An. arabiensis, An. merus, An. quadriannulatus, and An. coluzzii or An. gambiae. The identified differences in the size and structure of the X chromosome heterochromatin point to a possible role of repetitive DNA in speciation of mosquitoes. We found that An. coluzzii and An. gambiae, incipient species with prezygotic isolation, share variations in the relative positions of the satDNA repeats and the proximal heterochromatin band on the X chromosomes. This previously unknown genetic polymorphism in malaria mosquitoes may be caused by a differential amplification of DNA repeats or an inversion in the sex chromosome heterochromatin.
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Affiliation(s)
- Atashi Sharma
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
| | - Nicholas A. Kinney
- Genomics Bioinformatics and Computational Biology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA;
| | - Vladimir A. Timoshevskiy
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
| | - Maria V. Sharakhova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
- Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 634050 Tomsk, Russia
| | - Igor V. Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
- Genomics Bioinformatics and Computational Biology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA;
- Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Cytology and Genetics, Tomsk State University, 634050 Tomsk, Russia
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Helleu Q, Courret C, Ogereau D, Burnham KL, Chaminade N, Chakir M, Aulard S, Montchamp-Moreau C. Sex-Ratio Meiotic Drive Shapes the Evolution of the Y Chromosome in Drosophila simulans. Mol Biol Evol 2020; 36:2668-2681. [PMID: 31290972 DOI: 10.1093/molbev/msz160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The recent emergence and spread of X-linked segregation distorters-called "Paris" system-in the worldwide species Drosophila simulans has elicited the selection of drive-resistant Y chromosomes. Here, we investigate the evolutionary history of 386 Y chromosomes originating from 29 population samples collected over a period of 20 years, showing a wide continuum of phenotypes when tested against the Paris distorters, from high sensitivity to complete resistance (males sire ∼95% to ∼40% female progeny). Analyzing around 13 kb of Y-linked gene sequences in a representative subset of nine Y chromosomes, we identified only three polymorphic sites resulting in three haplotypes. Remarkably, one of the haplotypes is associated with resistance. This haplotype is fixed in all samples from Sub-Saharan Africa, the region of origin of the drivers. Exceptionally, with the spread of the drivers in Egypt and Morocco, we were able to record the replacement of the sensitive lineage by the resistant haplotype in real time, within only a few years. In addition, we performed in situ hybridization, using satellite DNA probes, on a subset of 21 Y chromosomes from six locations. In contrast to the low molecular polymorphism, this revealed extensive structural variation suggestive of rapid evolution, either neutral or adaptive. Moreover, our results show that intragenomic conflicts can drive astonishingly rapid replacement of Y chromosomes and suggest that the emergence of Paris segregation distorters in East Africa occurred less than half a century ago.
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Affiliation(s)
- Quentin Helleu
- Évolution Génomes Comportement et Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Cécile Courret
- Évolution Génomes Comportement et Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - David Ogereau
- Évolution Génomes Comportement et Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Katie L Burnham
- Évolution Génomes Comportement et Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicole Chaminade
- Évolution Génomes Comportement et Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mohamed Chakir
- Laboratoire Aliments, environnement et Santé, Faculté des Sciences et Techniques Université Cadi Ayyad, Marrakech, Morocco
| | - Sylvie Aulard
- Évolution Génomes Comportement et Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Faculté des Sciences et Ingénierie, UFR des Sciences de la Vie, UPMC, Sorbonne Université, Paris, France
| | - Catherine Montchamp-Moreau
- Évolution Génomes Comportement et Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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Lea JK, Unckless RL. An assessment of the immune costs associated with meiotic drive elements in Drosophila. Proc Biol Sci 2019; 286:20191534. [PMID: 31530140 PMCID: PMC6784720 DOI: 10.1098/rspb.2019.1534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022] Open
Abstract
Most organisms are constantly adapting to pathogens and parasites that exploit their host for their own benefit. Less studied, but perhaps more ubiquitous, are intragenomic parasites or selfish genetic elements. These include transposable elements, selfish B chromosomes and meiotic drivers that promote their own replication without regard to fitness effects on hosts. Therefore, intragenomic parasites are also a constant evolutionary pressure on hosts. Gamete-killing meiotic drive elements are often associated with large chromosomal inversions that reduce recombination between the drive and wild-type chromosomes. This reduced recombination is thought to reduce the efficacy of selection on the drive chromosome and allow for the accumulation of deleterious mutations. We tested whether gamete-killing meiotic drive chromosomes were associated with reduced immune defence against two bacterial pathogens in three species of Drosophila. We found little evidence of reduced immune defence in lines with meiotic drive. One line carrying the Drosophila melanogaster autosomal Segregation Distorter did show reduced defence, but we were unable to attribute that reduced defence to either genotype or immune gene expression differences. Our results suggest that though gamete-killing meiotic drive chromosomes probably accumulate deleterious mutations, those mutations do not result in reduced capacity for immune defence.
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Affiliation(s)
| | - Robert L. Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
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Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice. Sci Rep 2019; 9:13057. [PMID: 31506492 PMCID: PMC6736928 DOI: 10.1038/s41598-019-49440-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023] Open
Abstract
Exposure to environmental stressors is known to increase disease susceptibility in unexposed descendants in the absence of detectable genetic mutations. The mechanisms mediating environmentally-induced transgenerational disease susceptibility are poorly understood. We showed that great-great-grandsons of female mice exposed to tributyltin (TBT) throughout pregnancy and lactation were predisposed to obesity due to altered chromatin organization that subsequently biased DNA methylation and gene expression. Here we analyzed DNA methylomes and transcriptomes from tissues of animals ancestrally exposed to TBT spanning generations, sexes, ontogeny, and cell differentiation state. We found that TBT elicited concerted alterations in the expression of “chromatin organization” genes and inferred that TBT-disrupted chromatin organization might be able to self-reconstruct transgenerationally. We also found that the location of “chromatin organization” and “metabolic” genes is biased similarly in mouse and human genomes, suggesting that exposure to environmental stressors in different species could elicit similar phenotypic effects via self-reconstruction of disrupted chromatin organization.
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Kutch IC, Fedorka KM. Y-chromosomes can constrain adaptive evolution via epistatic interactions with other chromosomes. BMC Evol Biol 2018; 18:204. [PMID: 30587105 PMCID: PMC6307184 DOI: 10.1186/s12862-018-1327-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/12/2018] [Indexed: 01/28/2023] Open
Abstract
Background Variation in the non-coding regions of Y-chromosomes have been shown to influence gene regulation throughout the genome in some systems; a phenomenon termed Y-linked regulatory variation (YRV). This type of sex-specific genetic variance could have important implications for the evolution of male and female traits. If YRV contributes to the additive genetic variation of an autosomally coded trait shared between the sexes (e.g. body size), then selection could facilitate sexually dimorphic evolution via the Y-chromosome. In contrast, if YRV is entirely non-additive (i.e. interacts epistatically with other chromosomes), then Y-chromosomes could constrain trait evolution in both sexes whenever they are selected for the same trait value. The ability for this phenomenon to influence such fundamental evolutionary dynamics remains unexplored. Results Here we address the evolutionary contribution of Y-linked variance by selecting for improved male geotaxis in populations possessing multiple Y-chromosomes (i.e. possessed Y-linked additive and/or epistatic variation) or a single Y-chromosome variant (i.e. possessed no Y-linked variation). We found that males from populations possessing Y-linked variation did not significantly respond to selection; however, males from populations with no Y-linked variation did respond. These patterns suggest the presence of a large quantity of Y-linked epistatic variance in the multi-Y population that dramatically slowed its response. Conclusions Our results imply that YRV is unlikely to facilitate the evolution of sexually dimorphic traits (at least for the trait examined here), but can interfere with the rate of trait evolution in both males and females. This result could have real biological implications as it suggests that YRV can affect how quickly a population responds to new selective pressures (e.g. invasive species, novel pathogens, or climate change). Considering that YRV influences hundreds of genes and is likely typical of other independently-evolved hemizygous chromosomes, YRV-like phenomena may represent common and significant costs to hemizygous sex determination.
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Affiliation(s)
- Ian C Kutch
- Biological Sciences Building, University of Central Florida, 4110 Libra Dr, Orlando, FL, 32816, USA.
| | - Kenneth M Fedorka
- Biological Sciences Building, University of Central Florida, 4110 Libra Dr, Orlando, FL, 32816, USA
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Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome. Genetics 2018; 211:333-348. [PMID: 30420487 PMCID: PMC6325706 DOI: 10.1534/genetics.118.301765] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022] Open
Abstract
Heterochromatic regions of the genome are repeat-rich and poor in protein coding genes, and are therefore underrepresented in even the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9 Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family, crystal-Stellate While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of the crystal-Stellate gene family, Su(Ste), and PCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.
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Branco AT, Brito RM, Lemos B. Sex-specific adaptation and genomic responses to Y chromosome presence in female reproductive and neural tissues. Proc Biol Sci 2018; 284:rspb.2017.2062. [PMID: 29237855 DOI: 10.1098/rspb.2017.2062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
Y chromosomes typically harbour a small number of genes and an abundance of repetitive sequences. In Drosophila, the Y chromosome comprises multimegabase long segments of repetitive DNA and a handful of protein-coding genes. In mammals, the Y chromosome also harbours a disproportionally high abundance of repeats. Here, we built on a Drosophila melanogaster model in which the Y chromosome is decoupled from sexual determination. Genotypes were genetically identical for the autosomes, X chromosome, and mitochondria, but differ by the presence or dose of the Y chromosome. Addition of an extra Y chromosome had limited impact in males. However, the presence of a Y chromosome in females induced a disproportionate response in genes expressed in the ovaries as well as genes encoded by the mitochondrial genome. Furthermore, the data revealed significant consequences of Y chromosome presence in larvae neuronal tissue. This included the repression of genes implicated in reproductive behaviour, courtship, mating and synaptic function. Our findings exhibit the Y chromosome as a hotspot for sex-specific adaptation. They suggest roles for natural selection on Y-linked genetic elements exerting impact on sex-specific tissues as well as somatic tissues shared by males and females.
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Affiliation(s)
- Alan T Branco
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, 02115, Boston, MA, USA
| | - Rute M Brito
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, 02115, Boston, MA, USA
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, 02115, Boston, MA, USA
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Hill T, Betancourt AJ. Extensive exchange of transposable elements in the Drosophila pseudoobscura group. Mob DNA 2018; 9:20. [PMID: 29946370 PMCID: PMC6006672 DOI: 10.1186/s13100-018-0123-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/01/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND As species diverge, so does their transposable element (TE) content. Within a genome, TE families may eventually become dormant due to host-silencing mechanisms, natural selection and the accumulation of inactive copies. The transmission of active copies from a TE families, both vertically and horizontally between species, can allow TEs to escape inactivation if it occurs often enough, as it may allow TEs to temporarily escape silencing in a new host. Thus, the contribution of horizontal exchange to TE persistence has been of increasing interest. RESULTS Here, we annotated TEs in five species with sequenced genomes from the D. pseudoobscura species group, and curated a set of TE families found in these species. We found that, compared to host genes, many TE families showed lower neutral divergence between species, consistent with recent transmission of TEs between species. Despite these transfers, there are differences in the TE content between species in the group. CONCLUSIONS The TE content is highly dynamic in the D. pseudoobscura species group, frequently transferring between species, keeping TEs active. This result highlights how frequently transposable elements are transmitted between sympatric species and, despite these transfers, how rapidly species TE content can diverge.
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Affiliation(s)
- Tom Hill
- The Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS 66045 USA
| | - Andrea J. Betancourt
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
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32
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Same-Sex Twin Pair Phenotypic Correlations are Consistent with Human Y Chromosome Promoting Phenotypic Heterogeneity. Evol Biol 2018. [DOI: 10.1007/s11692-018-9454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Rajpathak SN, Deobagkar DD. Aneuploidy: an important model system to understand salient aspects of functional genomics. Brief Funct Genomics 2018; 17:181-190. [PMID: 29228117 DOI: 10.1093/bfgp/elx041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Maintaining a balance in gene dosage and protein activity is essential to sustain normal cellular functions. Males and females have a wide range of genetic as well as epigenetic differences, where X-linked gene dosage is an essential regulatory factor. Basic understanding of gene dosage maintenance has emerged from the studies carried out using mouse models with FCG (four core genotype) and chromosomal aneuploidy as well as from mono-chromosomal hybrid cells. In mammals, aneuploidy often leads to embryonic lethality particularly in early development with major developmental and structural abnormalities. Thus, in-depth analysis of the causes and consequences of gene dosage alterations is needed to unravel its effects on basic cellular and developmental functions as well as in understanding its medical implications. Cells isolated from individuals with naturally occurring chromosomal aneuploidy can be considered as true representatives, as these cells have stable chromosomal alterations/gene dosage imbalance, which have occurred by modulation of the basic molecular machinery. Therefore, innovative use of these natural aneuploidy cells/organisms with recent molecular and high-throughput techniques will provide an understanding of the basic mechanisms involved in gene dosage balance and the related consequences for functional genomics.
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McGurk MP, Barbash DA. Double insertion of transposable elements provides a substrate for the evolution of satellite DNA. Genome Res 2018; 28:714-725. [PMID: 29588362 PMCID: PMC5932611 DOI: 10.1101/gr.231472.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/22/2018] [Indexed: 02/06/2023]
Abstract
Eukaryotic genomes are replete with repeated sequences in the form of transposable elements (TEs) dispersed across the genome or as satellite arrays, large stretches of tandemly repeated sequences. Many satellites clearly originated as TEs, but it is unclear how mobile genetic parasites can transform into megabase-sized tandem arrays. Comprehensive population genomic sampling is needed to determine the frequency and generative mechanisms of tandem TEs, at all stages from their initial formation to their subsequent expansion and maintenance as satellites. The best available population resources, short-read DNA sequences, are often considered to be of limited utility for analyzing repetitive DNA due to the challenge of mapping individual repeats to unique genomic locations. Here we develop a new pipeline called ConTExt that demonstrates that paired-end Illumina data can be successfully leveraged to identify a wide range of structural variation within repetitive sequence, including tandem elements. By analyzing 85 genomes from five populations of Drosophila melanogaster, we discover that TEs commonly form tandem dimers. Our results further suggest that insertion site preference is the major mechanism by which dimers arise and that, consequently, dimers form rapidly during periods of active transposition. This abundance of TE dimers has the potential to provide source material for future expansion into satellite arrays, and we discover one such copy number expansion of the DNA transposon hobo to approximately 16 tandem copies in a single line. The very process that defines TEs—transposition—thus regularly generates sequences from which new satellites can arise.
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Affiliation(s)
- Michael P McGurk
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Daniel A Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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The Y Chromosome Modulates Splicing and Sex-Biased Intron Retention Rates in Drosophila. Genetics 2017; 208:1057-1067. [PMID: 29263027 DOI: 10.1534/genetics.117.300637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023] Open
Abstract
The Drosophila Y chromosome is a 40-Mb segment of mostly repetitive DNA; it harbors a handful of protein-coding genes and a disproportionate amount of satellite repeats, transposable elements, and multicopy DNA arrays. Intron retention (IR) is a type of alternative splicing (AS) event by which one or more introns remain within the mature transcript. IR recently emerged as a deliberate cellular mechanism to modulate gene expression levels and has been implicated in multiple biological processes. However, the extent of sex differences in IR and the contribution of the Y chromosome to the modulation of AS and IR rates has not been addressed. Here we showed pervasive IR in the fruit fly Drosophila melanogaster with thousands of novel IR events, hundreds of which displayed extensive sex bias. The data also revealed an unsuspected role for the Y chromosome in the modulation of AS and IR. The majority of sex-biased IR events introduced premature termination codons and the magnitude of sex bias was associated with gene expression differences between the sexes. Surprisingly, an extra Y chromosome in males (X^YY genotype) or the presence of a Y chromosome in females (X^XY genotype) significantly modulated IR and recapitulated natural differences in IR between the sexes. Our results highlight the significance of sex-biased IR in tuning sex differences and the role of the Y chromosome as a source of variable IR rates between the sexes. Modulation of splicing and IR rates across the genome represent new and unexpected outcomes of the Drosophila Y chromosome.
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Lakhotia SC. Non-coding RNAs demystify constitutive heterochromatin as essential modulator of epigenotype. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0221-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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The New RNA World: Growing Evidence for Long Noncoding RNA Functionality. Trends Genet 2017; 33:665-676. [DOI: 10.1016/j.tig.2017.08.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/18/2022]
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Variation in Position Effect Variegation Within a Natural Population. Genetics 2017; 207:1157-1166. [PMID: 28931559 DOI: 10.1534/genetics.117.300306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/31/2017] [Indexed: 01/11/2023] Open
Abstract
Changes in chromatin state may drive changes in gene expression, and it is of growing interest to understand the population genetic forces that drive differences in chromatin state. Here, we use the phenomenon of position effect variegation (PEV), a well-studied proxy for chromatin state, to survey variation in PEV among a naturally derived population. Further, we explore the genetic architecture of natural variation in factors that modify PEV. While previous mutation screens have identified over 150 suppressors and enhancers of PEV, it remains unknown to what extent allelic variation in these modifiers mediate interindividual variation in PEV. Is natural variation in PEV mediated by segregating genetic variation in known Su(var) and E(var) genes, or is the trait polygenic, with many variants mapping elsewhere in the genome? We designed a dominant mapping study that directly answers this question and suggests that the bulk of the variance in PEV does not map to genes with prior annotated impact to PEV. Instead, we find enrichment of top P-value ranked associations that suggest impact to active promoter and transcription start site proximal regions. This work highlights extensive variation in PEV within a population, and provides a quantitative view of the role naturally segregating autosomal variants play in modifying PEV-a phenomenon that continues to shape our understanding of chromatin state and epigenetics.
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40
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Kutch IC, Fedorka KM. A test for Y-linked additive and epistatic effects on surviving bacterial infections in Drosophila melanogaster. J Evol Biol 2017; 30:1400-1408. [DOI: 10.1111/jeb.13118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/11/2017] [Indexed: 02/03/2023]
Affiliation(s)
- I. C. Kutch
- University of Central Florida; Orlando FL USA
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Tomaszkiewicz M, Medvedev P, Makova KD. Y and W Chromosome Assemblies: Approaches and Discoveries. Trends Genet 2017; 33:266-282. [DOI: 10.1016/j.tig.2017.01.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 01/19/2023]
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Dias GB, Heringer P, Svartman M, Kuhn GCS. Helitrons shaping the genomic architecture of Drosophila: enrichment of DINE-TR1 in α- and β-heterochromatin, satellite DNA emergence, and piRNA expression. Chromosome Res 2016; 23:597-613. [PMID: 26408292 DOI: 10.1007/s10577-015-9480-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drosophila INterspersed Elements (DINEs) constitute an abundant but poorly understood group of Helitrons present in several Drosophila species. The general structure of DINEs includes two conserved blocks that may or not contain a region with tandem repeats in between. These central tandem repeats (CTRs) are similar within species but highly divergent between species. It has been assumed that CTRs have independent origins. Herein, we identify a subset of DINEs, termed DINE-TR1, which contain homologous CTRs of approximately 150 bp. We found DINE-TR1 in the sequenced genomes of several Drosophila species and in Bactrocera tryoni (Acalyptratae, Diptera). However, interspecific high sequence identity (∼ 88 %) is limited to the first ∼ 30 bp of each tandem repeat, implying that evolutionary constraints operate differently over the monomer length. DINE-TR1 is unevenly distributed across the Drosophila phylogeny. Nevertheless, sequence analysis suggests vertical transmission. We found that CTRs within DINE-TR1 have independently expanded into satellite DNA-like arrays at least twice within Drosophila. By analyzing the genome of Drosophila virilis and Drosophila americana, we show that DINE-TR1 is highly abundant in pericentromeric heterochromatin boundaries, some telomeric regions and in the Y chromosome. It is also present in the centromeric region of one autosome from D. virilis and dispersed throughout several euchromatic sites in both species. We further found that DINE-TR1 is abundant at piRNA clusters, and small DINE-TR1-derived RNA transcripts (∼25 nt) are predominantly expressed in the testes and the ovaries, suggesting active targeting by the piRNA machinery. These features suggest potential piRNA-mediated regulatory roles for DINEs at local and genome-wide scales in Drosophila.
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Affiliation(s)
- Guilherme B Dias
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro Heringer
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marta Svartman
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gustavo C S Kuhn
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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Araripe LO, Tao Y, Lemos B. Interspecific Y chromosome variation is sufficient to rescue hybrid male sterility and is influenced by the grandparental origin of the chromosomes. Heredity (Edinb) 2016; 116:516-22. [PMID: 26980343 DOI: 10.1038/hdy.2016.11] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/25/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022] Open
Abstract
Y chromosomes display population variation within and between species. Co-evolution within populations is expected to produce adaptive interactions between Y chromosomes and the rest of the genome. One consequence is that Y chromosomes from disparate populations could disrupt harmonious interactions between co-evolved genetic elements and result in reduced male fertility, sterility or inviability. Here we address the contribution of 'heterospecific Y chromosomes' to fertility in hybrid males carrying a homozygous region of Drosophila mauritiana introgressed in the Drosophila simulans background. In order to detect Y chromosome-autosome interactions, which may go unnoticed in a single-species background of autosomes, we constructed hybrid genotypes involving three sister species: Drosophila simulans, D. mauritiana, and D. sechellia. These engineered strains varied due to: (i) species origin of the Y chromosome (D. simulans or D. sechellia); (ii) location of the introgressed D. mauritiana segment on the D. simulans third chromosome, and (iii) grandparental genomic background (three genotypes of D. simulans). We find complex interactions between the species origin of the Y chromosome, the identity of the D. mauritiana segment and the grandparental genetic background donating the chromosomes. Unexpectedly, the interaction of the Y chromosome and one segment of D. mauritiana drastically reduced fertility in the presence of Ysim, whereas the fertility is partially rescued by the Y chromosome of D. sechellia when it descends from a specific grandparental genotype. The restoration of fertility occurs in spite of an autosomal and X-linked genome that is mostly of D. simulans origin. These results illustrate the multifactorial basis of genetic interactions involving the Y chromosome. Our study supports the hypothesis that the Y chromosome can contribute significantly to the evolution of reproductive isolation and highlights the conditional manifestation of infertility in specific genotypic combinations.
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Affiliation(s)
- L O Araripe
- Laboratório de Biologia Molecular de Insetos, Fundação Oswaldo Cruz, IOC, Rio de Janeiro, Brasil
| | - Y Tao
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA, USA
| | - B Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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Cousminer DL, Widén E, Palmert MR. The genetics of pubertal timing in the general population: recent advances and evidence for sex-specificity. Curr Opin Endocrinol Diabetes Obes 2016; 23:57-65. [PMID: 26574646 PMCID: PMC4734379 DOI: 10.1097/med.0000000000000213] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW This article overviews advances in the genetics of puberty based on studies in the general population, describes evidence for sex-specific genetic effects on pubertal timing, and briefly reviews possible mechanisms mediating sexually dimorphic genetic effects. RECENT FINDINGS Pubertal timing is highly polygenic, and many loci are conserved among ethnicities. A number of identified loci underlie both pubertal timing and related traits such as height and BMI. It is increasingly apparent that understanding the factors modulating the onset of puberty is important because the timing of this developmental stage is associated with a wider range of adult health outcomes than previously appreciated. Although most of the genetic effects underlying the timing of puberty are common between boys and girls, some effects show sex-specificity and many are epigenetically modulated. Several potential mechanisms, including hormone-independent ones, may be responsible for observed sex differences. SUMMARY Studies of pubertal timing in the general population have provided new knowledge about the genetic architecture of this complex trait. Increasing attention paid to sex-specific effects may provide key insights into the sexual dimorphism in pubertal timing and even into the associations between puberty and adult health risks by identifying common underlying biological pathways.
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Affiliation(s)
- Diana L. Cousminer
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elisabeth Widén
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | - Mark R. Palmert
- Division of Endocrinology, the Hospital for Sick Children
- The Departments of Pediatrics and Physiology, University of Toronto, Canada
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Forger NG, Strahan JA, Castillo-Ruiz A. Cellular and molecular mechanisms of sexual differentiation in the mammalian nervous system. Front Neuroendocrinol 2016; 40:67-86. [PMID: 26790970 PMCID: PMC4897775 DOI: 10.1016/j.yfrne.2016.01.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/31/2015] [Accepted: 01/09/2016] [Indexed: 01/16/2023]
Abstract
Neuroscientists are likely to discover new sex differences in the coming years, spurred by the National Institutes of Health initiative to include both sexes in preclinical studies. This review summarizes the current state of knowledge of the cellular and molecular mechanisms underlying sex differences in the mammalian nervous system, based primarily on work in rodents. Cellular mechanisms examined include neurogenesis, migration, the differentiation of neurochemical and morphological cell phenotype, and cell death. At the molecular level we discuss evolving roles for epigenetics, sex chromosome complement, the immune system, and newly identified cell signaling pathways. We review recent findings on the role of the environment, as well as genome-wide studies with some surprising results, causing us to re-think often-used models of sexual differentiation. We end by pointing to future directions, including an increased awareness of the important contributions of tissues outside of the nervous system to sexual differentiation of the brain.
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Affiliation(s)
- Nancy G Forger
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States.
| | - J Alex Strahan
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, United States.
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Kutch IC, Fedorka KM. Y-linked variation for autosomal immune gene regulation has the potential to shape sexually dimorphic immunity. Proc Biol Sci 2015; 282:20151301. [PMID: 26631557 PMCID: PMC4685771 DOI: 10.1098/rspb.2015.1301] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/05/2015] [Indexed: 01/09/2023] Open
Abstract
Sexually dimorphic phenotypes arise from the differential expression of male and female shared genes throughout the genome. Unfortunately, the underlying molecular mechanisms by which dimorphic regulation manifests and evolves are unclear. Recent work suggests that Y-chromosomes may play an important role, given that Drosophila melanogaster Ys were shown to influence the regulation of hundreds of X and autosomal genes. For Y-linked regulatory variation (YRV) to facilitate sexually dimorphic evolution, however, it must exist within populations (where selection operates) and influence male fitness. These criteria have seldom been investigated, leaving the potential for dimorphic evolution via YRV unclear. Interestingly, male and female D. melanogaster differ in immune gene regulation. Furthermore, immune gene regulation appears to be influenced by the Y-chromosome, suggesting it may contribute to dimorphic immune evolution. We address this possibility by introgressing Y-chromosomes from a single wild population into an isogenic background (to create Y-lines) and assessing immune gene regulation and bacterial defence. We found that Y-line males differed in their immune gene regulation and their ability to defend against Serratia marcescens. Moreover, gene expression and bacterial defence were positively genetically correlated. These data indicate that the Y-chromosome has the potential to shape the evolution of sexually dimorphic immunity in this system.
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Affiliation(s)
- Ian C Kutch
- Department of Biology, University of Central Florida, Biological Sciences Building, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Kenneth M Fedorka
- Department of Biology, University of Central Florida, Biological Sciences Building, 4110 Libra Drive, Orlando, FL 32816, USA
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Griffin RM, Le Gall D, Schielzeth H, Friberg U. Within-population Y-linked genetic variation for lifespan inDrosophila melanogaster. J Evol Biol 2015; 28:1940-7. [DOI: 10.1111/jeb.12708] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/24/2015] [Accepted: 07/24/2015] [Indexed: 12/12/2022]
Affiliation(s)
- R. M. Griffin
- Department of Evolutionary Biology; Uppsala University; Uppsala Sweden
| | - D. Le Gall
- Department of Evolutionary Biology; Uppsala University; Uppsala Sweden
- Department of Biology; Ecole Normale Supérieure de Cachan; Cachan France
| | - H. Schielzeth
- Department of Evolutionary Biology; Bielefeld University; Bielefeld Germany
| | - U. Friberg
- Department of Evolutionary Biology; Uppsala University; Uppsala Sweden
- IFM Biology; AVIAN Behavioural Genomics and Physiology Group; Linköping University; Linköping Sweden
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Case LK, Teuscher C. Y genetic variation and phenotypic diversity in health and disease. Biol Sex Differ 2015; 6:6. [PMID: 25866616 PMCID: PMC4392626 DOI: 10.1186/s13293-015-0024-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/22/2015] [Indexed: 11/10/2022] Open
Abstract
Sexually dimorphic traits arise through the combined effects of sex hormones and sex chromosomes on sex-biased gene expression, and experimental mouse models have been instrumental in determining their relative contribution in modulating sex differences. A role for the Y chromosome (ChrY) in mediating sex differences outside of development and reproduction has historically been overlooked due to its unusual genetic composition and the predominant testes-specific expression of ChrY-encoded genes. However, ample evidence now exists supporting ChrY as a mediator of other physiological traits in males, and genetic variation in ChrY has been linked to several diseases, including heart disease, cancer, and autoimmune diseases in experimental animal models, as well as humans. The genetic and molecular mechanisms by which ChrY modulates phenotypic variation in males remain unknown but may be a function of copy number variation between homologous X-Y multicopy genes driving differential gene expression. Here, we review the literature identifying an association between ChrY polymorphism and phenotypic variation and present the current evidence depicting the mammalian ChrY as a member of the regulatory genome in males and as a factor influencing paternal parent-of-origin effects in female offspring.
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Affiliation(s)
- Laure K Case
- Department of Medicine, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA
| | - Cory Teuscher
- Department of Medicine, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA ; Department of Pathology, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA ; University of Vermont, Given Medical Building C317, Burlington, VT 05405 USA
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A novel electronic assessment strategy to support applied Drosophila genetics training in university courses. G3-GENES GENOMES GENETICS 2015; 5:689-98. [PMID: 25717150 PMCID: PMC4426358 DOI: 10.1534/g3.115.017509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The advent of "omic" technologies has revolutionized genetics and created a demand to focus classical genetics on its present-day applications (Redfield, 2012, PLoS Biol 10: e1001356). This demand can be met by training students in Drosophila mating scheme design, which is an important problem-solving skill routinely applied in many modern research laboratories. It promotes a thorough understanding and application of classical genetics rules and introduces to transgenic technologies and the use of model organisms. As we show here, such training can be implemented as a flexible and concise module (~1-day home study, ~8-hour course time) on university courses by using our previously published training package designed for fly researchers (Roote and Prokop, 2013, G3 (Bethesda) 3: 353-358). However, assessing this training to make it an accredited course element is difficult, especially in large courses. Here, we present a powerful assessment strategy based on a novel hybrid concept in which students solve crossing tasks initially on paper and then answer automatically marked questions on the computer (1.5 hours total). This procedure can be used to examine student performance on more complex tasks than conventional e-assessments and is more versatile, time-saving, and fairer than standard paper-based assignments. Our evaluation shows that the hybrid assessment is effective and reliably detects varying degrees of understanding among students. It also may be applicable in other disciplines requiring complex problem solving, such as mathematics, chemistry, physics, or informatics. Here, we describe our strategies in detail and provide all resources needed for their implementation.
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