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Escudeiro A, Ferreira D, Mendes-da-Silva A, Heslop-Harrison JS, Adega F, Chaves R. Bovine satellite DNAs – a history of the evolution of complexity and its impact in the Bovidae family. THE EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2018.1558294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- A. Escudeiro
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - D. Ferreira
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - A. Mendes-da-Silva
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | | | - F. Adega
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - R. Chaves
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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Perrier JP, Sellem E, Prézelin A, Gasselin M, Jouneau L, Piumi F, Al Adhami H, Weber M, Fritz S, Boichard D, Le Danvic C, Schibler L, Jammes H, Kiefer H. A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features. BMC Genomics 2018; 19:404. [PMID: 29843609 PMCID: PMC5975405 DOI: 10.1186/s12864-018-4764-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/07/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Spermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. Accordingly, perturbations in the establishment of DNA methylation patterns during male germ cell differentiation have been associated with infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bull spermatozoa is still scarce. The purpose of this study was therefore to characterize the bull sperm methylome relative to both bovine somatic cells and the sperm of other mammals through a multiscale analysis. RESULTS The quantification of DNA methylation at CCGG sites using luminometric methylation assay (LUMA) highlighted the undermethylation of bull sperm compared to the sperm of rams, stallions, mice, goats and men. Total blood cells displayed a similarly high level of methylation in bulls and rams, suggesting that undermethylation of the bovine genome was specific to sperm. Annotation of CCGG sites in different species revealed no striking bias in the distribution of genome features targeted by LUMA that could explain undermethylation of bull sperm. To map DNA methylation at a genome-wide scale, bull sperm was compared with bovine liver, fibroblasts and monocytes using reduced representation bisulfite sequencing (RRBS) and immunoprecipitation of methylated DNA followed by microarray hybridization (MeDIP-chip). These two methods exhibited differences in terms of genome coverage, and consistently, two independent sets of sequences differentially methylated in sperm and somatic cells were identified for RRBS and MeDIP-chip. Remarkably, in the two sets most of the differentially methylated sequences were hypomethylated in sperm. In agreement with previous studies in other species, the sequences that were specifically hypomethylated in bull sperm targeted processes relevant to the germline differentiation program (piRNA metabolism, meiosis, spermatogenesis) and sperm functions (cell adhesion, fertilization), as well as satellites and rDNA repeats. CONCLUSIONS These results highlight the undermethylation of bull spermatozoa when compared with both bovine somatic cells and the sperm of other mammals, and raise questions regarding the dynamics of DNA methylation in bovine male germline. Whether sperm undermethylation has potential interactions with structural variation in the cattle genome may deserve further attention.
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Affiliation(s)
- Jean-Philippe Perrier
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
- Present Address: Laboratory of Animal Reproduction, Department of Biological Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
| | - Eli Sellem
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
- ALLICE, 149 rue de Bercy, 75012 Paris, France
| | - Audrey Prézelin
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Maxime Gasselin
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Luc Jouneau
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - François Piumi
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
- Present Address: Institut Curie, PSL Research University, CNRS, UMR3664, 75005 Paris, France
- Present Address: Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Hala Al Adhami
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
- CNRS, Université de Strasbourg, UMR7242 Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, 67412 Illkirch cedex, France
| | - Michaël Weber
- CNRS, Université de Strasbourg, UMR7242 Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, 67412 Illkirch cedex, France
| | - Sébastien Fritz
- ALLICE, 149 rue de Bercy, 75012 Paris, France
- UMR GABI, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Didier Boichard
- UMR GABI, INRA, AgroParisTech, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Chrystelle Le Danvic
- ALLICE, 149 rue de Bercy, 75012 Paris, France
- UMR CNRS/USTL 8576, UGSF, Villeneuve D’Ascq, France
| | | | - Hélène Jammes
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Hélène Kiefer
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
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Tian M, Bao H, Martin FL, Zhang J, Liu L, Huang Q, Shen H. Association of DNA Methylation and Mitochondrial DNA Copy Number with Human Semen Quality1. Biol Reprod 2014; 91:101. [DOI: 10.1095/biolreprod.114.122465] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Hales BF, Grenier L, Lalancette C, Robaire B. Epigenetic programming: From gametes to blastocyst. ACTA ACUST UNITED AC 2011; 91:652-65. [DOI: 10.1002/bdra.20781] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/01/2010] [Accepted: 12/07/2010] [Indexed: 01/16/2023]
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Benchaib M, Ajina M, Lornage J, Niveleau A, Durand P, Guérin JF. Quantitation by image analysis of global DNA methylation in human spermatozoa and its prognostic value in in vitro fertilization: a preliminary study. Fertil Steril 2003; 80:947-53. [PMID: 14556817 DOI: 10.1016/s0015-0282(03)01151-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To determine the relationship between sperm DNA methylation level and sperm characteristics and pregnancy rates. DESIGN Prospective study. Quantitation by image analysis of DNA methylation in sperm nucleus. SETTING Department of Reproduction Biology, Edouard Herriot Hospital, Lyon, France. PATIENT(S) Infertile couples undergoing IVF-ET. INTERVENTION(S) The immunostaining of 5 methyl-cytosine was performed on the spare sperm suspension that was used for an assisted reproduction technology procedure. MAIN OUTCOME MEASURE(S) Sperm characteristics according to World Health Organization criteria, sperm motility parameters with computer-assisted semen analysis, sperm DNA methylation level, and heterogeneity index (HI). RESULT(S) Sperm DNA methylation level and HI are correlated with sperm DNA characteristics. HI is negatively correlated with fertilization rate; sperm DNA methylation level is correlated with pregnancy rate. CONCLUSION(S) The DNA methylation level in human spermatozoa could be a new approach to evaluating the ability of spermatozoa to fertilize and lead to normal embryo development.
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Affiliation(s)
- Mehdi Benchaib
- Laboratoire de Biologie de la Reproduction, Lyon, France.
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Schmits R, Kubuschok B, Schuster S, Preuss KD, Pfreundschuh M. Analysis of the B cell repertoire against autoantigens in patients with giant cell arteritis and polymyalgia rheumatica. Clin Exp Immunol 2002; 127:379-85. [PMID: 11876765 PMCID: PMC1906335 DOI: 10.1046/j.1365-2249.2002.01751.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The analysis of the antibody repertoire of patients with giant cell arteritis (GCA) and polymyalgia rheumatica (PMR) might identify target antigens of the autoimmune response with potential relevance to our understanding of the pathogenesis of the disease and to the development of serodiagnostic tests. To detect such antigens, we screened a cDNA library derived from normal human testis for antigens reacting with IgG antibodies in the 1 : 250 diluted sera of three patients with untreated GCA using SEREX, the serological identification of antigens by recombinant cDNA expression cloning. Of 100 000 clones screened with each serum, six, 28 and six clones, respectively, were positive, representing a total of 33 different antigens. Most of the antigens reacted only with the serum used for identification and/or at a similar frequency with normal control sera. However, lamin C and the nuclear antigen of 14 kD reacted specifically with 32% of GCA/PMR, but with none of the control sera, while human cytokeratin 15, mitochondrial cytochrome oxidase subunit II, and a new gene product were detected preferentially, but not exclusively by sera from GCA/PMR patients. We conclude that patients with GCA/PMR develop antibodies against a broad spectrum of human autoantigens. Antibodies against human lamin C, the nuclear autoantigen of 14 kD as well as human cytokeratin 15, mitochondrial cytochrome oxidase subunit II and the product of a new gene should be investigated further to determine their value as tools for the diagnosis and/or the definition of clinical subgroups of patients with GCA/PMR.
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Affiliation(s)
- R Schmits
- Department of Medicine, Saarland University Medical School, Homburg, Germany
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Hornsby PJ, Yang L, Gunter LE. Demethylation of satellite I DNA during senescence of bovine adrenocortical cells in culture. ACTA ACUST UNITED AC 1992; 275:13-9. [PMID: 1372683 DOI: 10.1016/0921-8734(92)90004-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the finite proliferative life span of cultured bovine adrenocortical cells, satellite I DNA shows a progressive and extensive loss of methylation at CCGG sites. This was shown by Southern blotting after digestion with the methylation-sensitive enzyme HpaII alone, which provides a sensitive indicator of methylation loss, or digestion with the combination of EcoRI and HpaII, which provides a quantitative indication of loss of methylation. Bovine tissues, including adrenal cortex, all showed a much higher level of satellite methylation than cultured adrenocortical cells. After adrenocortical cells are placed in culture, some demethylation of satellite I is seen as early as 10 population doublings. By 80 population doublings, loss of satellite DNA methylation is extensive. The loss does not appear to prevent continued cell division, since an extended life span clone of bovine adrenocortical cells transfected with SV40 T antigen showed a similar pattern of extensive demethylation. Satellite demethylation has been reported in aging in vivo and the present cell culture system may provide an in vitro model for this form of genetic instability.
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Affiliation(s)
- P J Hornsby
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta 30912
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Hornsby PJ, Yang LQ, Raju SG, Cheng CY. Changes in gene expression and DNA methylation in adrenocortical cells senescing in culture. Mutat Res 1991; 256:105-13. [PMID: 1722003 DOI: 10.1016/0921-8734(91)90004-u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent experiments in cultured bovine adrenocortical cells show that the previously observed phenotypic switching of CYP17 (steroid 17 alpha-hydroxylase) expression is preceded at a much earlier time by changes in methylation in the CYP17 5' flanking region. Two CpG sites that are methylated in the adrenal cortex in vivo were observed to undergo rapid demethylation when adrenocortical cells were placed in culture. Two adjacent CpG sites that are also methylated in vivo did not demethylate; these two sites are completely nonmethylated in fibroblasts. All CpG sites downstream, in the promoter or coding region, are always methylated in all tissues and in bovine adrenocortical cells even after many population doublings in culture. In contrast to the specific and rapid demethylation of sites in CYP17, satellite I shows a slower and apparently random loss of methylation that extends over the entire replicative life span. These changes in methylation provide examples of genetic instability in cells that undergo senescence in culture. Future experiments will focus on the relationship of these events to the phenotypic switching process.
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Affiliation(s)
- P J Hornsby
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta 30912
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Abstract
DNA methylation is found almost ubiquitously in nature and the methyltransferases show evidence of a common evolutionary origin. It will be a fascinating study in protein evolution to follow the ways in which the structures of the various enzymes have developed. Although methylation may have a direct effect on DNA structure the evidence for the importance of this in vivo is accumulating only slowly. In contrast, there is now abundant evidence that methylation of DNA affects DNA-protein interactions and so may have a function in all processes in which such interactions occur. The binding of nucleases is affected in the processes of mismatch repair, DNA restriction and possibly demethylation during differentiation in vertebrates. The binding of transcription factors is affected by DNA methylation and the association of DNA with packaging and segregation proteins may play a part in the control of transcription and replication. The interplay of these effects makes DNA methylation a complex but rewarding area for study. Perhaps we should no longer refer to methylcytosine and methyladenine as minor bases, but rather as key bases which help regulate the functions of DNA.
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Mays-Hoopes LL. Age-related changes in DNA methylation: do they represent continued developmental changes? INTERNATIONAL REVIEW OF CYTOLOGY 1989; 114:181-220. [PMID: 2472365 DOI: 10.1016/s0074-7696(08)60861-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- L L Mays-Hoopes
- Department of Biology, Occidental College, Los Angeles, California 90041
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Abstract
To study whether changes in methylation of DNA are related to the structural and functional changes that chromatin undergoes throughout rooster spermatogenenis, we analyzed, by high-performance liquid chromatography, the 5-methylcytosine content of DNA purified from rooster testis cell nuclei at successive stages of the cell differentiation process. The DNA of meiotic and postmeiotic cells appears partially under-methylated, containing approximately 30% less methylcytosines than the DNA obtained from premeiotic and somatic cells.
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Jaenisch R, Jähner D. Methylation, expression and chromosomal position of genes in mammals. BIOCHIMICA ET BIOPHYSICA ACTA 1984; 782:1-9. [PMID: 6372865 DOI: 10.1016/0167-4781(84)90099-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Ponzetto-Zimmerman C, Wolgemuth DJ. Methylation of satellite sequences in mouse spermatogenic and somatic DNAs. Nucleic Acids Res 1984; 12:2807-22. [PMID: 6324127 PMCID: PMC318707 DOI: 10.1093/nar/12.6.2807] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The distribution of 5-methyl cytosine (5-MeC) residues in a highly repetitive sequence, mouse major satellite, was examined in germinal versus somatic DNAs by digestion with the methylation sensitive isoschizomers Msp I and Hpa II and Southern blot analysis, using a cloned satellite probe. DNA from liver, brain, and a mouse fibroblast cell line, C3H 10T1/2, yielded a multimeric hybridization pattern after digestion with Msp I (and control Eco RI) but were resistant to digestion with Hpa II, reflecting a high level of methylation of the satellite sequences. In contrast, DNA from mature sperm was undermethylated at these same sequences as indicated by the ability of Hpa II to generate a multimeric pattern. DNAs from purified populations of testis cells in different stages of spermatogenesis were examined to determine when during germ cell differentiation the undermethylation was established. As early as in primitive type A, type A, and type B spermatogonia, an undermethylation of satellite sequences was observed. This suggest that this highly specific undermethylation of germ cell satellite DNA occurs very early in the germ cell lineage, prior to entry into meiosis.
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Abstract
Eukaryotic genomes contain 5-methylcytosine (5mC) as a rare base.5mC arises by postsynthetic modification of cytosine and occurs, at least in animals, predominantly in the dinucleotide CpG. The base is not distributed randomly in these genomes but conforms to a pattern. This pattern varies between taxa but appears to be inherited in a semi-conservative fashion. At the level of the genome, gross changes in the level of DNA methylation have been noted. This has encouraged speculation that the modification may play a role in cellular differentiation. Tissue-specific patterns of DNA methylation, predicted by various models of differentiation, have been found for most vertebrate genes so far examined. A correlation has emerged between the undermethylation of these regions and their transcription, but this is not always the case. While data for eukaryotic viral sequences are less equivocal, studies of this kind cannot in isolation distinguish between undermethylation being a cause or a consequence of gene activity. If it were a cause, it is probable that the demethylation of specific CpG sites would be a necessary yet not a sufficient condition for transcription to occur. The introduction of artificially methylated DNA sequences into individual eukaryotic cells by microinjection or transformation may provide the means to elucidate these questions in the future. In the meantime, the study of eukaryotic DNA methylation promises to contribute much to our understanding of the regulation of gene expression in these organisms.
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