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Santos AS, Ramos ES, Valente-Gaiesky VLS, de Melo Sene F, Manfrin MH. Evidences of differential methylation in the genome during development in the cactophilic Drosophila species. Genesis 2024; 62:e23554. [PMID: 37750176 DOI: 10.1002/dvg.23554] [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: 07/04/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023]
Abstract
DNA methylation with 5-methylcytosine (5mC) has been reported in the genome of several eukaryotes, with marked differences between vertebrates and invertebrates. DNA methylation is poorly understood as its role in evolution in insects. Drosophila gouveai (cluster Drosophila buzzatii) presents larvae that develop obligatorily in necrotic tissues of cacti in nature, with the distribution of populations in South America, and plasticity of phenotypes in insect-plant interaction. We characterize organisms at developmental stages and analyze variations at multiple methylation-sensitive loci in pupae, and adult flies using methylation sensitive amplification polymorphism. We obtained 326 loci with CCGG targets in the genome of D. gouveai. Genomic regions with molecular lengths from 100 to 700 pb were most informative about methylation states. Multiple loci show differences in methylation-sensitive sites (MSL) concerning developmental stages, such as in pupae (MSL = 40), female reproductive tissue (MSL = 76), and male reproductive tissues (MSL = 58). Our results are the first evidence of genome-wide methylation in D. gouveai organisms.
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Affiliation(s)
- Adriano S Santos
- Programa de Pós-Graduação em Genética, Departamento de Genética, da Faculdade de Medicina de Ribeirão Preto, FMRP-USP, São Paulo, Brazil
| | - Ester S Ramos
- Programa de Pós-Graduação em Genética, Departamento de Genética, da Faculdade de Medicina de Ribeirão Preto, FMRP-USP, São Paulo, Brazil
| | - Vera L S Valente-Gaiesky
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fábio de Melo Sene
- Programa de Pós-Graduação em Genética, Departamento de Genética, da Faculdade de Medicina de Ribeirão Preto, FMRP-USP, São Paulo, Brazil
| | - Maura H Manfrin
- Programa de Pós-Graduação em Genética, Departamento de Genética, da Faculdade de Medicina de Ribeirão Preto, FMRP-USP, São Paulo, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências, e Letras de Ribeirão preto, FFCLRP-USP, São Paulo, Brazil
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Kangassalo K, Sorvari J, Nousiainen I, Pölkki M, Valtonen TM, Krams I, Rantala MJ. Intra- and Trans-Generational Phenotypic Responses of the Greater Wax Moth, Galleria mellonella, to a Low-Nutrition Larval Diet. ANN ZOOL FENN 2020. [DOI: 10.5735/086.057.0111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Katariina Kangassalo
- Department of Biology, Section of Ecology, FI-20014 University of Turku, Finland
| | - Jouni Sorvari
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Ilkka Nousiainen
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, EE-51014 Tartu, Estonia
| | - Mari Pölkki
- Department of Biology, Section of Ecology, FI-20014 University of Turku, Finland
| | - Terhi M. Valtonen
- Department of Biology, Section of Ecology, FI-20014 University of Turku, Finland
| | - Indrikis Krams
- Latvian Biomedical Research and Study Center, Rātsupītes iela 1, LV-1067 Rīga, Latvia
| | - Markus J. Rantala
- Department of Biology, Section of Ecology, FI-20014 University of Turku, Finland
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Affiliation(s)
- Kenji Matsuura
- Laboratory of Insect Ecology, Graduate School of AgricultureKyoto University Kyoto Japan
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Saravanan K, Kumar H, Chhotaray S, Preethi AL, Talokar AJ, Natarajan A, Parida S, Bhushan B, Panigrahi M. Drosophila melanogaster: a promising model system for epigenetic research. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1685216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- K.A. Saravanan
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Supriya Chhotaray
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - A. Latha Preethi
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Amol J. Talokar
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - A. Natarajan
- Division of Animal Nutrition, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
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Kangassalo K, Valtonen TM, Roff D, Pölkki M, Dubovskiy IM, Sorvari J, Rantala MJ. Intra- and trans-generational effects of larval diet on susceptibility to an entomopathogenic fungus, Beauveria bassiana
, in the greater wax moth, Galleria mellonella. J Evol Biol 2015; 28:1453-64. [DOI: 10.1111/jeb.12666] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 05/11/2015] [Indexed: 11/30/2022]
Affiliation(s)
- K. Kangassalo
- Department of Biology; Section of Ecology; University of Turku; Turku Finland
| | - T. M. Valtonen
- Department of Biology; Section of Ecology; University of Turku; Turku Finland
| | - D. Roff
- Department of Biology; University of California; Riverside CA USA
| | - M. Pölkki
- Department of Biology; Section of Ecology; University of Turku; Turku Finland
| | - I. M. Dubovskiy
- Institute of Animal Systematics and Ecology; Siberian Branch of Russian Academy of Science; Novosibirsk Russia
| | - J. Sorvari
- Department of Environmental Science; University of Eastern Finland; Kuopio Finland
| | - M. J. Rantala
- Department of Biology; Section of Ecology; University of Turku; Turku Finland
- Turku Brain and Mind Center; University of Turku; Turku Finland
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6
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Endogenously imprinted genes in Drosophila melanogaster. Mol Genet Genomics 2014; 289:653-73. [DOI: 10.1007/s00438-014-0840-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 03/04/2014] [Indexed: 12/21/2022]
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Genome-wide gene expression effects of sex chromosome imprinting in Drosophila. G3-GENES GENOMES GENETICS 2014; 4:1-10. [PMID: 24318925 PMCID: PMC3887524 DOI: 10.1534/g3.113.008029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Imprinting is well-documented in both plant and animal species. In Drosophila, the Y chromosome is differently modified when transmitted through the male and female germlines. Here, we report genome-wide gene expression effects resulting from reversed parent-of-origin of the X and Y chromosomes. We found that hundreds of genes are differentially expressed between adult male Drosophila melanogaster that differ in the maternal and paternal origin of the sex chromosomes. Many of the differentially regulated genes are expressed specifically in testis and midgut cells, suggesting that sex chromosome imprinting might globally impact gene expression in these tissues. In contrast, we observed much fewer Y-linked parent-of-origin effects on genome-wide gene expression in females carrying a Y chromosome, indicating that gene expression in females is less sensitive to sex chromosome parent-of-origin. Genes whose expression differs between females inheriting a maternal or paternal Y chromosome also show sex chromosome parent-of-origin effects in males, but the direction of the effects on gene expression (overexpression or underexpression) differ between the sexes. We suggest that passage of sex chromosome chromatin through male meiosis may be required for wild-type function in F1 progeny, whereas disruption of Y-chromosome function through passage in the female germline likely arises because the chromosome is not adapted to the female germline environment.
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Affiliation(s)
- Alison M. Triggs
- School of Biological and Chemical Sciences, Queen Mary; University of London; Mile End Road London E14NS UK
| | - Robert J. Knell
- School of Biological and Chemical Sciences, Queen Mary; University of London; Mile End Road London E14NS UK
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Genomic imprinting absent in Drosophila melanogaster adult females. Cell Rep 2012; 2:69-75. [PMID: 22840398 DOI: 10.1016/j.celrep.2012.06.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/27/2012] [Accepted: 06/12/2012] [Indexed: 12/15/2022] Open
Abstract
Genomic imprinting occurs when expression of an allele differs based on the sex of the parent that transmitted the allele. In D. melanogaster, imprinting can occur, but its impact on allelic expression genome-wide is unclear. Here, we search for imprinted genes in D. melanogaster using RNA-seq to compare allele-specific expression between pools of 7- to 10-day-old adult female progeny from reciprocal crosses. We identified 119 genes with allelic expression consistent with imprinting, and these genes showed significant clustering within the genome. Surprisingly, additional analysis of several of these genes showed that either genomic heterogeneity or high levels of intrinsic noise caused imprinting-like allelic expression. Consequently, our data provide no convincing evidence of imprinting for D. melanogaster genes in their native genomic context. Elucidating sources of false-positive signals for imprinting in allele-specific RNA-seq data, as done here, is critical given the growing popularity of this method for identifying imprinted genes.
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Epigenetic mechanisms of genomic imprinting: common themes in the regulation of imprinted regions in mammals, plants, and insects. GENETICS RESEARCH INTERNATIONAL 2012; 2012:585024. [PMID: 22567394 PMCID: PMC3335465 DOI: 10.1155/2012/585024] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 09/26/2011] [Indexed: 01/08/2023]
Abstract
Genomic imprinting is a form of epigenetic inheritance whereby the regulation of a gene or chromosomal region is dependent on the sex of the transmitting parent. During gametogenesis, imprinted regions of DNA are differentially marked in accordance to the sex of the parent, resulting in parent-specific expression. While mice are the primary research model used to study genomic imprinting, imprinted regions have been described in a broad variety of organisms, including other mammals, plants, and insects. Each of these organisms employs multiple, interrelated, epigenetic mechanisms to maintain parent-specific expression. While imprinted genes and imprint control regions are often species and locus-specific, the same suites of epigenetic mechanisms are often used to achieve imprinted expression. This review examines some examples of the epigenetic mechanisms responsible for genomic imprinting in mammals, plants, and insects.
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Frías-Lasserre D. Non coding RNAs and viruses in the framework of the phylogeny of the genes, epigenesis and heredity. Int J Mol Sci 2012; 13:477-490. [PMID: 22312265 PMCID: PMC3269699 DOI: 10.3390/ijms13010477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 01/21/2023] Open
Abstract
The origin of genes is one of the most enigmatic events in the origin of life. It has been suggested that noncoding (nc) RNA was probably a precursor in the formation of the first polypeptide, and also at the origin of the first manifestation of life and genes. ncRNAs are also becoming central for understanding gene expression and silencing. Indeed, before the discovery of ncRNAs, proteins were viewed as the major molecules in the regulation of gene expression and gene silencing; however, recent findings suggest that ncRNA also plays an important role in gene expression. Reverse transcription of RNA viruses and their integration into the genome of eukaryotes and also their relationship with the ncRNA suggest that their origin is basal in genome evolution, and also probably constitute the first mechanism of gene regulation. I am to review the different roles of ncRNAs in the framework of gene evolution, as well as the importance of ncRNAs and viruses in the epigenesis and in the non-Mendelian model of heredity and evolution.
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Affiliation(s)
- Daniel Frías-Lasserre
- Institute of Entomology, Metropolitan University of Educational Sciences, Avenue J.P. Alessandri 774 Ñuñoa, Código Postal 7760197, Santiago, Chile; E-Mail: ; Tel.: +56-2-2412457; Fax: +56-2-2412699
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Abstract
Chromosomes acquire different epigenetic marks during oogenesis and spermatogenesis. After fertilization, if retained and selected, these differences may result in imprinting effects. Rather than being an oddity, imprinting effects have been found in many sexually reproducing organisms. Interestingly, imprinting can result in disparate effects under different selective forces. At the same time, epigenetic mechanisms and selective pressures shared by sexually reproducing organisms could underlie common imprinting effects. Large-scale studies are revealing that parent-of-origin effects are more common than previously thought and supporting the important contribution of imprinting to many traits and diseases.
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Kaneda M. Genomic imprinting in mammals—Epigenetic parental memories. Differentiation 2011; 82:51-6. [DOI: 10.1016/j.diff.2011.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 04/05/2011] [Accepted: 05/09/2011] [Indexed: 01/12/2023]
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MacDonald WA, Menon D, Bartlett NJ, Sperry GE, Rasheva V, Meller V, Lloyd VK. The Drosophila homolog of the mammalian imprint regulator, CTCF, maintains the maternal genomic imprint in Drosophila melanogaster. BMC Biol 2010; 8:105. [PMID: 20673338 PMCID: PMC2922095 DOI: 10.1186/1741-7007-8-105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 07/30/2010] [Indexed: 11/28/2022] Open
Abstract
Background CTCF is a versatile zinc finger DNA-binding protein that functions as a highly conserved epigenetic transcriptional regulator. CTCF is known to act as a chromosomal insulator, bind promoter regions, and facilitate long-range chromatin interactions. In mammals, CTCF is active in the regulatory regions of some genes that exhibit genomic imprinting, acting as insulator on only one parental allele to facilitate parent-specific expression. In Drosophila, CTCF acts as a chromatin insulator and is thought to be actively involved in the global organization of the genome. Results To determine whether CTCF regulates imprinting in Drosophila, we generated CTCF mutant alleles and assayed gene expression from the imprinted Dp(1;f)LJ9 mini-X chromosome in the presence of reduced CTCF expression. We observed disruption of the maternal imprint when CTCF levels were reduced, but no effect was observed on the paternal imprint. The effect was restricted to maintenance of the imprint and was specific for the Dp(1;f)LJ9 mini-X chromosome. Conclusions CTCF in Drosophila functions in maintaining parent-specific expression from an imprinted domain as it does in mammals. We propose that Drosophila CTCF maintains an insulator boundary on the maternal X chromosome, shielding genes from the imprint-induced silencing that occurs on the paternally inherited X chromosome. See commentary: http://www.biomedcentral.com/1741-7007/8/104
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Vargas AO. Did Paul Kammerer discover epigenetic inheritance? A modern look at the controversial midwife toad experiments. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312:667-78. [DOI: 10.1002/jez.b.21319] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Imprinting of the Y chromosome influences dosage compensation in roX1 roX2 Drosophila melanogaster. Genetics 2009; 183:811-20. [PMID: 19704014 DOI: 10.1534/genetics.109.107219] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Drosophila melanogaster males have a well-characterized regulatory system that increases X-linked gene expression. This essential process restores the balance between X-linked and autosomal gene products in males. A complex composed of the male-specific lethal (MSL) proteins and RNA is recruited to the body of transcribed X-linked genes where it modifies chromatin to increase expression. The RNA components of this complex, roX1 and roX2 (RNA on the X1, RNA on the X2), are functionally redundant. Males mutated for both roX genes have dramatically reduced survival. We show that reversal of sex chromosome inheritance suppresses lethality in roX1 roX2 males. Genetic tests indicate that the effect on male survival depends upon the presence and source of the Y chromosome, revealing a germ line imprint that influences dosage compensation. Conventional paternal transmission of the Y chromosome enhances roX1 roX2 lethality, while maternal transmission of the Y chromosome suppresses lethality. roX1 roX2 males with both maternal and paternal Y chromosomes have very low survival, indicating dominance of the paternal imprint. In an otherwise wild-type male, the Y chromosome does not appreciably affect dosage compensation. The influence of the Y chromosome, clearly apparent in roX1 roX2 mutants, thus requires a sensitized genetic background. We believe that the Y chromosome is likely to act through modulation of a process that is defective in roX1 roX2 mutants: X chromosome recognition or chromatin modification by the MSL complex.
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