151
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Wu C, Ding X, Li H, Zhu C, Xiong C. Genome-wide promoter methylation profile of human testis and epididymis: identified from cell-free seminal DNA. BMC Genomics 2013; 14:288. [PMID: 23622456 PMCID: PMC3653781 DOI: 10.1186/1471-2164-14-288] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 04/24/2013] [Indexed: 01/05/2023] Open
Abstract
Background DNA methylation analysis is useful for investigation of male fertility in mammals, whereas the reliance on tissues limits the research on human. We have previously found the presence of high concentration of cell-free seminal DNA (cfsDNA) in human semen. We proposed that some testis and epididymis-specific methylated promoters could be detected in human cfsDNA, and thus hold promise as noninvasive epigenetic biomarkers for male infertility, of which most cases are caused by defects in testicular sperm production or epididymal sperm maturation. Results The ejaculate of successfully vasectomized men does not contain any secretion from testis and epididymis. Here we compared genome-wide promoter methylation profiles in cfsDNA between health donors and post-vasectomy men. Promoters of 367 testis and epididymis-specific hypomethylated genes and 134 hypermethylated genes were identified. Subsequent validation by Methyl-DNA immunoprecipitation and MethyLight analysis confirmed the result of promoter microarray. Gene Ontology analysis revealed many genes involved in male reproduction. Conclusion We detected the testis and epididymis-specific methylated promoters in human cfsDNA, which may be used for noninvasive epigenetic biomarkers for the study and diagnosis of male infertility.
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Affiliation(s)
- Chunlin Wu
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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152
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Shufaro Y, Laufer N. Epigenetic concerns in assisted reproduction: update and critical review of the current literature. Fertil Steril 2013; 99:605-6. [DOI: 10.1016/j.fertnstert.2013.01.126] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 01/06/2023]
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153
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Boissonnas CC, Jouannet P, Jammes H. Epigenetic disorders and male subfertility. Fertil Steril 2013; 99:624-31. [DOI: 10.1016/j.fertnstert.2013.01.124] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/18/2013] [Accepted: 01/21/2013] [Indexed: 11/24/2022]
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154
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Humm KC, Sakkas D. Role of increased male age in IVF and egg donation: is sperm DNA fragmentation responsible? Fertil Steril 2013; 99:30-36. [DOI: 10.1016/j.fertnstert.2012.11.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/14/2012] [Accepted: 11/14/2012] [Indexed: 01/10/2023]
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155
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Barzideh J, Scott RJ, Aitken RJ. Analysis of the global methylation status of human spermatozoa and its association with the tendency of these cells to enter apoptosis. Andrologia 2012; 45:424-9. [DOI: 10.1111/and.12033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2012] [Indexed: 12/13/2022] Open
Affiliation(s)
- J. Barzideh
- Discipline of Biological Sciences; Faculty of Science and IT; University of Newcastle; Callaghan NSW Australia
- Discipline of Medical Genetics; Faculty of Health; University of Newcastle; Callaghan NSW Australia
- Hunter Medical Research Institute, John Hunter Hospital, New Lambton; NSW Australia
| | - R. J. Scott
- Discipline of Medical Genetics; Faculty of Health; University of Newcastle; Callaghan NSW Australia
- Hunter Medical Research Institute, John Hunter Hospital, New Lambton; NSW Australia
| | - R. J. Aitken
- Discipline of Biological Sciences; Faculty of Science and IT; University of Newcastle; Callaghan NSW Australia
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156
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Heyn H, Ferreira HJ, Bassas L, Bonache S, Sayols S, Sandoval J, Esteller M, Larriba S. Epigenetic disruption of the PIWI pathway in human spermatogenic disorders. PLoS One 2012; 7:e47892. [PMID: 23112866 PMCID: PMC3480440 DOI: 10.1371/journal.pone.0047892] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/17/2012] [Indexed: 11/24/2022] Open
Abstract
Epigenetic changes are involved in a wide range of common human diseases. Although DNA methylation defects are known to be associated with male infertility in mice, their impact on human deficiency of sperm production has yet to be determined. We have assessed the global genomic DNA methylation profiles in human infertile male patients with spermatogenic disorders by using the Infinium Human Methylation27 BeadChip. Three populations were studied: conserved spermatogenesis, spermatogenic failure due to germ cell maturation defects, and Sertoli cell-only syndrome samples. A disease-associated DNA methylation profile, characterized by targeting members of the PIWI-associated RNA (piRNA) processing machinery, was obtained. Bisulfite genomic sequencing and pyrosequencing in a large cohort (n = 46) of samples validated the altered DNA methylation patterns observed in piRNA-processing genes. In particular, male infertility was associated with the promoter hypermethylation-associated silencing of PIWIL2 and TDRD1. The downstream effects mediated by the epigenetic inactivation of the PIWI pathway genes were a defective production of piRNAs and a hypomethylation of the LINE-1 repetitive sequence in the affected patients. Overall, our data suggest that DNA methylation, at least that affecting PIWIL2/TDRD1, has a role in the control of gene expression in spermatogenesis and its imbalance contributes to an unsuccessful germ cell development that might explain a group of male infertility disorders.
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Affiliation(s)
- Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Humberto J. Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- PhD Programme in Experimental Biology and Biomedicine, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Lluís Bassas
- Laboratory of Seminology and Embryology, Andrology Service-Fundació Puigvert, Barcelona, Catalonia, Spain
| | - Sandra Bonache
- Human Molecular Genetics Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- * E-mail:
| | - Sara Larriba
- Human Molecular Genetics Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
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157
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Schagdarsurengin U, Paradowska A, Steger K. Analysing the sperm epigenome: roles in early embryogenesis and assisted reproduction. Nat Rev Urol 2012; 9:609-19. [PMID: 23045264 DOI: 10.1038/nrurol.2012.183] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An understanding of the epigenetic mechanisms involved in sperm production and their impact on the differentiating embryo is essential if we are to optimize fertilization and assisted reproduction techniques in the future. Male germ cells are unique in terms of size, robustness, and chromatin structure, which is highly condensed owing to the replacement of most histones by protamines. Analysis of sperm epigenetics requires specific techniques that enable the isolation of high quality chromatin and associated nucleic acids. Histone modification, DNA methylation and noncoding RNAs have important, but so far underestimated, roles in the production of fertile sperm. Aberrations in these epigenetic processes have detrimental consequences for both early embryo development and assisted reproductive technology. Emerging computational techniques are likely to improve our understanding of chromatin dynamics in the future.
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Affiliation(s)
- Undraga Schagdarsurengin
- Justus Liebig University, Department of Urology, Pediatric Urology and Andrology, Section Molecular Andrology, Giessen, Germany
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158
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Novel insights into DNA methylation features in spermatozoa: stability and peculiarities. PLoS One 2012; 7:e44479. [PMID: 23071498 PMCID: PMC3467000 DOI: 10.1371/journal.pone.0044479] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/07/2012] [Indexed: 02/08/2023] Open
Abstract
Data about the entire sperm DNA methylome are limited to two sperm donors whereas
studies dealing with a greater number of subjects focused only on a few genes or
were based on low resolution arrays. This implies that information about what we
can consider as a normal sperm DNA methylome and whether it is stable among
different normozoospermic individuals is still missing. The definition of the
DNA methylation profile of normozoospermic men, the entity of inter-individual
variability and the epigenetic characterization of quality-fractioned sperm
subpopulations in the same subject (intra-individual variability) are relevant
for a better understanding of pathological conditions. We addressed these
questions by using the high resolution Infinium 450K methylation array and
compared normal sperm DNA methylomes against somatic and cancer cells. Our
study, based on the largest number of subjects (n = 8) ever
considered for such a large number of CpGs (n = 487,517),
provided clear evidence for i) a highly conserved DNA methylation profile among
normozoospermic subjects; ii) a stable sperm DNA methylation pattern in
different quality-fractioned sperm populations of the same individual. The
latter finding is particularly relevant if we consider that different quality
fractioned sperm subpopulations show differences in their structural features,
metabolic and genomic profiles. We demonstrate, for the first time, that DNA
methylation in normozoospermic men remains highly uniform regardless the quality
of sperm subpopulations. In addition, our analysis provided both confirmatory
and novel data concerning the sperm DNA methylome, including its peculiar
features in respect to somatic and cancer cells. Our description about a highly
polarized sperm DNA methylation profile, the clearly distinct genomic and
functional organization of hypo- versus hypermethylated loci as well as the
association of histone-enriched hypomethylated loci with embryonic development,
which we now extended also to hypomethylated piRNAs-linked genes, provides solid
basis for future basic and clinical research.
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159
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Denomme MM, Mann MRW. Genomic imprints as a model for the analysis of epigenetic stability during assisted reproductive technologies. Reproduction 2012; 144:393-409. [DOI: 10.1530/rep-12-0237] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Gamete and early embryo development are important stages when genome-scale epigenetic transitions are orchestrated. The apparent lack of remodeling of differential imprinted DNA methylation during preimplantation development has lead to the argument that epigenetic disruption by assisted reproductive technologies (ARTs) is restricted to imprinted genes. We contend that aberrant imprinted methylation arising from assisted reproduction or infertility may be an indicator of more global epigenetic instability. Here, we review the current literature on the effects of ARTs, including ovarian stimulation,in vitrooocyte maturation, oocyte cryopreservation, IVF, ICSI, embryo culture, and infertility on genomic imprinting as a model for evaluating epigenetic stability. Undoubtedly, the relationship between impaired fertility, ARTs, and epigenetic stability is unquestionably complex. What is clear is that future studies need to be directed at determining the molecular and cellular mechanisms giving rise to epigenetic errors.
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160
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Rotondo JC, Bosi S, Bazzan E, Di Domenico M, De Mattei M, Selvatici R, Patella A, Marci R, Tognon M, Martini F. Methylenetetrahydrofolate reductase gene promoter hypermethylation in semen samples of infertile couples correlates with recurrent spontaneous abortion. Hum Reprod 2012; 27:3632-8. [PMID: 23010533 DOI: 10.1093/humrep/des319] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
STUDY QUESTION Is the methylation status of the methylenetetrahydrofolate reductase (MTHFR) promoter region in semen samples associated with 'recurrent spontaneous abortion' (RSA)? SUMMARY ANSWER MTHFR promoter hypermethylation is more frequent in semen samples from RSA couples than in semen samples from infertile couples with no history of RSA (NRSA) and affects the whole sperm population significantly more often. WHAT IS KNOWN ALREADY Modifications to the MTHFR gene such as polymorphisms and promoter methylations are associated with male infertility. STUDY DESIGN, SIZE AND DURATION Retrospective cohort study of semen samples from 20 RSA couples, 147 NRSA couples and 20 fertile men between 2011 and 2012. MATERIALS, SETTING AND METHODS DNA from the semen samples of RSA, NRSA and fertile men were analyzed by methylation-specific PCR amplification using primers which anneal to the methylated or unmethylated cytosine-phosphodiester bond guanine (CpG) islands within the promoter region of MTHFR. The specificity of the PCR products was assessed by DNA sequencing. MAIN RESULTS AND THE ROLE OF CHANCE The methylated MTHFR epigenotype (including samples where it co-existed with unmethylated MTHFR epigenotypes) was detected in 75% of RSA men, 54% of NRSA men and 15% of fertile men. MTHFR methylation was observed in the whole sperm population in semen samples from 55% of RSA men compared with 8% in NRSA men (P < 0.05) and 0% in fertile men (P < 0.05). DNA sequencing analysis was fully concordant with the PCR results and revealed that when MTHFR methylation occurred, CpG islands within the promoter region were 100% methylated (hypermethylation of MTHFR promoter). LIMITATIONS, REASONS FOR CAUTION The relatively small sample size of RSA infertile couples. WIDER IMPLICATIONS OF THE FINDINGS The hypermethylation of the MTHFR gene promoter should be taken into consideration as a novel putative risk factor in RSA etiology. STUDY FUNDING/COMPETING INTEREST(S) Our institution has received an FAR research grant from the University of Ferrara, Ferrara, Italy. No competing interests declared.
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Affiliation(s)
- J C Rotondo
- Department of Morphology and Embryology, University of Ferrara, Ferrara 44121, Italy
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161
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Dallol A, Al-Maghrabi J, Buhmeida A, Gari MA, Chaudhary AG, Schulten HJ, Abuzenadah AM, Al-Ahwal MS, Sibiany A, Al-Qahtani MH. Methylation of the polycomb group target genes is a possible biomarker for favorable prognosis in colorectal cancer. Cancer Epidemiol Biomarkers Prev 2012; 21:2069-75. [PMID: 23010642 DOI: 10.1158/1055-9965.epi-12-0755] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the second most common cancer in the Kingdom of Saudi Arabia with ever increasing incidence rates. DNA methylation is a common event in CRC where it is now considered an important phenomenon in CRC carcinogenesis and useful for the classification and prognosis of CRC. METHODS To gain insight into the molecular mechanisms underpinning CRC in Saudi Arabian patients, we profiled the DNA methylation frequency of key genes (MLH1, MSH2, RASSF1A, SLIT2, HIC1, MGMT, SFRP1, MYOD1, APC, CDKN2A, as well as five CIMP markers) in 120 sporadic CRC cases. CRC tumors originating from the rectum, left, and right colons are represented in this cohort of formalin-fixed paraffin-embedded tissues. RESULTS The most common methylation frequency was detected in the polycomb group target genes (PCGT) including SFRP1 (70%), MYOD1 (60.8%), HIC1 (61.7%), and SLIT2 (56.7%). In addition, MGMT methylation was detected at a high frequency (68.3%). RASSF1A, APC, and CDKN2A methylation frequencies were 42.5%, 25%, and 32.8%, respectively. K-means clustering analysis of the methylation events results in the clustering of the CRC samples into three groups depending on the level of methylation detected. CONCLUSION Group II (PCGT methylation and CIMP-negative) methylation signature carried a favorable prognosis for male patients, whereas older patients with group I rare methylation signature have a potentially poorer clinical outcome. IMPACT Methylation of the PCGT genes along with RASSF1A, APC, and MGMT can be potentially used as a new biomarker for the classification and prognosis of CRC tumors and independently of where the tumor has originated.
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Affiliation(s)
- Ashraf Dallol
- Center of Excellence in Genomic Medicine Research, King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, 21589 Jeddah, Kingdom of Saudi Arabia.
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162
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Abstract
There is evidence that expression and methylation of the imprinted paternally expressed gene 1/mesoderm-specific transcript homologue (PEG1/MEST) gene may be affected by assisted reproductive technologies (ARTs) and infertility. In this study, we sought to assess the imprinting status of the MEST gene in a large cohort of in vitro-derived human preimplantation embryos, in order to characterise potentially adverse effects of ART and infertility on this locus in early human development. Embryonic genomic DNA from morula or blastocyst stage embryos was screened for a transcribed AflIII polymorphism in MEST and imprinting analysis was then performed in cDNA libraries derived from these embryos. In 10 heterozygous embryos, MEST expression was monoallelic in seven embryos, predominantly monoallelic in two embryos, and biallelic in one embryo. Screening of cDNA derived from 61 additional human preimplantation embryos, for which DNA for genotyping was unavailable, identified eight embryos with expression originating from both alleles (biallelic or predominantly monoallelic). In some embryos, therefore, the onset of imprinted MEST expression occurs during late preimplantation development. Variability in MEST imprinting was observed in both in vitro fertilization and intracytoplasmic sperm injection-derived embryos. Biallelic or predominantly monoallelic MEST expression was not associated with any one cause of infertility. Characterisation of the main MEST isoforms revealed that isoform 2 was detected in early development and was itself variably imprinted between embryos. To our knowledge, this report constitutes the largest expression study to date of genomic imprinting in human preimplantation embryos and reveals that for some imprinted genes, contrasting imprinting states exist between embryos.
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163
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Cortessis VK, Thomas DC, Levine AJ, Breton CV, Mack TM, Siegmund KD, Haile RW, Laird PW. Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet 2012; 131:1565-89. [PMID: 22740325 PMCID: PMC3432200 DOI: 10.1007/s00439-012-1189-8] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/07/2012] [Indexed: 12/15/2022]
Abstract
Changes in epigenetic marks such as DNA methylation and histone acetylation are associated with a broad range of disease traits, including cancer, asthma, metabolic disorders, and various reproductive conditions. It seems plausible that changes in epigenetic state may be induced by environmental exposures such as malnutrition, tobacco smoke, air pollutants, metals, organic chemicals, other sources of oxidative stress, and the microbiome, particularly if the exposure occurs during key periods of development. Thus, epigenetic changes could represent an important pathway by which environmental factors influence disease risks, both within individuals and across generations. We discuss some of the challenges in studying epigenetic mediation of pathogenesis and describe some unique opportunities for exploring these phenomena.
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Affiliation(s)
- Victoria K. Cortessis
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 USA
| | - Duncan C. Thomas
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2001 N. Soto St., SSB-202F, Los Angeles, CA 90089-9234 USA
| | - A. Joan Levine
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 USA
| | - Carrie V. Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2001 N. Soto St., Los Angeles, CA 90089-9234 USA
| | - Thomas M. Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 USA
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2001 N. Soto St., Los Angeles, CA 90089-9234 USA
| | - Robert W. Haile
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 USA
| | - Peter W. Laird
- Departments of Surgery, Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, Epigenome Center, 1441 Eastlake Avenue, Los Angeles, CA 90089-9601 USA
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164
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Aston KI, Punj V, Liu L, Carrell DT. Genome-wide sperm deoxyribonucleic acid methylation is altered in some men with abnormal chromatin packaging or poor in vitro fertilization embryogenesis. Fertil Steril 2012; 97:285-92. [DOI: 10.1016/j.fertnstert.2011.11.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/15/2011] [Accepted: 11/14/2011] [Indexed: 12/15/2022]
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165
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van Montfoort APA, Hanssen LLP, de Sutter P, Viville S, Geraedts JPM, de Boer P. Assisted reproduction treatment and epigenetic inheritance. Hum Reprod Update 2012; 18:171-97. [PMID: 22267841 PMCID: PMC3282574 DOI: 10.1093/humupd/dmr047] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The subject of epigenetic risk of assisted reproduction treatment (ART), initiated by reports on an increase of children with the Beckwith–Wiedemann imprinting disorder, is very topical. Hence, there is a growing literature, including mouse studies. METHODS In order to gain information on transgenerational epigenetic inheritance and epigenetic effects induced by ART, literature databases were searched for papers on this topic using relevant keywords. RESULTS At the level of genomic imprinting involving CpG methylation, ART-induced epigenetic defects are convincingly observed in mice, especially for placenta, and seem more frequent than in humans. Data generally provide a warning as to the use of ovulation induction and in vitro culture. In human sperm from compromised spermatogenesis, sequence-specific DNA hypomethylation is observed repeatedly. Transmittance of sperm and oocyte DNA methylation defects is possible but, as deduced from the limited data available, largely prevented by selection of gametes for ART and/or non-viability of the resulting embryos. Some evidence indicates that subfertility itself is a risk factor for imprinting diseases. As in mouse, physiological effects from ART are observed in humans. In the human, indications for a broader target for changes in CpG methylation than imprinted DNA sequences alone have been found. In the mouse, a broader range of CpG sequences has not yet been studied. Also, a multigeneration study of systematic ART on epigenetic parameters is lacking. CONCLUSIONS The field of epigenetic inheritance within the lifespan of an individual and between generations (via mitosis and meiosis, respectively) is growing, driven by the expansion of chromatin research. ART can induce epigenetic variation that might be transmitted to the next generation.
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Affiliation(s)
- A P A van Montfoort
- Department of Obstetrics & Gynaecology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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166
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Anton E, Krawetz SA. Spermatozoa as biomarkers for the assessment of human male infertility and genotoxicity. Syst Biol Reprod Med 2012; 58:41-50. [DOI: 10.3109/19396368.2011.637152] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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167
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Campion S, Catlin N, Heger N, McDonnell EV, Pacheco SE, Saffarini C, Sandrof MA, Boekelheide K. Male reprotoxicity and endocrine disruption. EXPERIENTIA SUPPLEMENTUM (2012) 2012; 101:315-60. [PMID: 22945574 DOI: 10.1007/978-3-7643-8340-4_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mammalian reproductive tract development is a tightly regulated process that can be disrupted following exposure to drugs, toxicants, endocrine-disrupting chemicals (EDCs), or other compounds via alterations to gene and protein expression or epigenetic regulation. Indeed, the impacts of developmental exposure to certain toxicants may not be fully realized until puberty or adulthood when the reproductive tract becomes sexually mature and altered functionality is manifested. Exposures that occur later in life, once development is complete, can also disrupt the intricate hormonal and paracrine interactions responsible for adult functions, such as spermatogenesis. In this chapter, the biology and toxicology of the male reproductive tract is explored, proceeding through the various life stages including in utero development, puberty, adulthood, and senescence. Special attention is given to the discussion of EDCs, chemical mixtures, low-dose effects, transgenerational effects, and potential exposure-related causes of male reproductive tract cancers.
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Affiliation(s)
- Sarah Campion
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
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168
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Aston KI, Carrell DT. Emerging evidence for the role of genomic instability in male factor infertility. Syst Biol Reprod Med 2011; 58:71-80. [PMID: 22142145 DOI: 10.3109/19396368.2011.635751] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Male infertility is a common and complex pathology affecting about 7% of men of reproductive age. Given its complexity, the underlying etiology for male infertility is often unknown. A growing amount of evidence suggests genomic instability may be an important factor in some cases of male factor infertility. While some specific manifestations of genomic instability, such as increased sperm aneuploidy rates and increased somatic translocations and inversions in infertile men, are well established, other facets of genomic instability associated with male infertility have not been thoroughly investigated. A limited body of recent work has identified a potential association between microsatellite instability and spermatogenic failure. In addition, mutations in mismatch repair and tumor suppressor genes, which could potentially lead to genomic instability, have been identified in some infertile men and animal models. In addition, results of two epidemiologic studies suggest spermatogenic defects might be just one aspect of a more systemic problem, possibly due to increased genomic instability. In this review we discuss well-established links between genomic instability and male infertility, as well as some of the emerging but less established data to support this relationship. We also propose some important areas of future research toward a more complete understanding of the underlying mechanisms for male infertility.
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Affiliation(s)
- Kenneth I Aston
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
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169
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Repeated assessment by high-throughput assay demonstrates that sperm DNA methylation levels are highly reproducible. Fertil Steril 2011; 96:1325-30. [PMID: 22035967 DOI: 10.1016/j.fertnstert.2011.09.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 09/01/2011] [Accepted: 09/20/2011] [Indexed: 01/18/2023]
Abstract
OBJECTIVE To assess reliability of a high-throughput assay of sperm DNA methylation. DESIGN Observational study comparing DNA methylation of sperm isolated from 3 divided and 12 longitudinally collected semen samples. SETTING Academic medical center. PATIENT(S) One man undergoing screening semen analysis during evaluation of an infertile couple and 2 healthy fertile male volunteers. INTERVENTION(S) Spermatozoa were separated from seminal plasma and somatic cells using gradient separation. DNA was extracted from spermatozoa, and DNA methylation was assessed at 1,505 DNA sequence-specific sites. MAIN OUTCOME MEASURE(S) Repeatability of sperm DNA methylation measures, estimated by correlation coefficients. RESULT(S) DNA methylation levels were highly correlated within matched sets of divided samples (all r ≥ 0.97) and longitudinal samples (average r = 0.97). CONCLUSION(S) The described methodology reliably assessed methylation of sperm DNA at large numbers of sites. Methylation profiles were consistent over time. High-throughput assessment of sperm DNA methylation is a promising tool for studying the role of epigenetic state in male fertility.
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170
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Díaz-García C, Estella C, Perales-Puchalt A, Simón C. Reproductive medicine and inheritance of infertility by offspring: the role of fetal programming. Fertil Steril 2011; 96:536-45. [PMID: 21794856 DOI: 10.1016/j.fertnstert.2011.06.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Revised: 06/22/2011] [Accepted: 06/23/2011] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To summarize the molecular processes involved in fetal programming, to describe how assisted reproduction technologies (ART) may affect the epigenetic pattern of the embryo, and to highlight the current knowledge of the role of perinatal events in the subsequent development of reproductive pathology affecting infertile patients. DESIGN A literature review of fetal programming of adulthood gynecologic diseases and ART. A Medline search was performed with the following keywords: (fetal programming OR epigenetics OR methylation OR acetylation) AND (IVF OR ART) AND (gynecology). Articles up to October 2010 were selected. Articles and recent reviews were classified by human and animals studies and also according to their experimental or observational design. SETTING University hospital research center. PATIENT(S) None. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) None. RESULT(S) Data from experimental animal models and case-control studies support the potential effect of ART in changing methylation patterns in gametes and embryos. However, these findings are not supported by population studies or experimental studies performed in human gametes/embryos. Experimental and epidemiologic studies support the hypothesis that some adult gynecologic diseases causing infertility may have a fetal origin. CONCLUSION(S) Although it seems clear that some adult gynecologic diseases causing infertility may have a fetal origin, there is insufficient evidence to confirm that ART is the origin of later onset, adulthood diseases. Further research in this field must be conducted.
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Affiliation(s)
- César Díaz-García
- Department of Gynecology and Obstetrics, La Fe University Hospital, University of Valencia, Valencia, Spain.
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171
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Chorbov VM, Todorov AA, Lynskey MT, Cicero TJ. Elevated levels of DNA methylation at the OPRM1 promoter in blood and sperm from male opioid addicts. J Opioid Manag 2011; 7:258-264. [PMID: 21957825 PMCID: PMC4142589 DOI: 10.5055/jom.2011.0067] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVE The OPRM1 gene was studied for DNA methylation in opioid dependence and possible paternal contribution to epigenetic inheritance of altered methylation profiles. PARTICIPANTS AND METHODS DNA was extracted from blood and sperm from 13 male opioid addicts and 21 male control subjects. DNA methylation was determined by pyrosequencing in 24 CpG sites at the OPRM1 promoter region. RESULTS The authors found significantly increased overall methylation in blood DNA from addicted subjects (Kruskal-Wallis [K-W] p = 0.013). Seven CpG sites showed significantly hypermethylated blood DNA from cases when compared with blood DNA from controls (p < 0.05 at CpGs 5, 9, 10, 11, 18, 23, and 24). In sperm-derived DNA from addicts, the methylation was significantly increased at CpG 2 (p = 0.012), and overall methylation did not reach significant difference (K-W p = 0.523). CONCLUSIONS Increased DNA methylation in the OPRM1 gene is associated with opioid dependence. Hypermethylated CpG sites located in OPRM1 promoter may potentially block the binding of Sp1 and other transcription activators, thus leading to OPRM1 silencing. The increased DNA methylation in sperm may suggest a way of epigenetic heritability of opioid abuse or dependence phenotypes.
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Affiliation(s)
- Vesselin M Chorbov
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouti, USA
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172
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Pacheco SE, Houseman EA, Christensen BC, Marsit CJ, Kelsey KT, Sigman M, Boekelheide K. Integrative DNA methylation and gene expression analyses identify DNA packaging and epigenetic regulatory genes associated with low motility sperm. PLoS One 2011; 6:e20280. [PMID: 21674046 PMCID: PMC3107223 DOI: 10.1371/journal.pone.0020280] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 04/23/2011] [Indexed: 12/17/2022] Open
Abstract
Background In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function. Methods and Results Sperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic. DNA methylation was measured with the Illumina Infinium array at 27,578 CpG loci. Unsupervised clustering of methylation data differentiated the 21 sperm samples by their motility values. Recursively partitioned mixture modeling (RPMM) of methylation data resulted in four distinct methylation profiles that were significantly associated with sperm motility (P = 0.01). Linear models of microarray analysis (LIMMA) was performed based on motility and identified 9,189 CpG loci with significantly altered methylation (Q<0.05) in the low motility samples. In addition, the majority of these disrupted CpG loci (80%) were hypomethylated. Of the aberrantly methylated CpGs, 194 were associated with imprinted genes and were almost equally distributed into hypermethylated (predominantly paternally expressed) and hypomethylated (predominantly maternally expressed) groups. Sperm mRNA was measured with the Human Gene 1.0 ST Affymetrix GeneChip Array. LIMMA analysis identified 20 candidate transcripts as differentially present in low motility sperm, including HDAC1 (NCBI 3065), SIRT3 (NCBI 23410), and DNMT3A (NCBI 1788). There was a trend among altered expression of these epigenetic regulatory genes and RPMM DNA methylation class. Conclusions Using integrative genome-wide approaches we identified CpG methylation profiles and mRNA alterations associated with low sperm motility.
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Affiliation(s)
- Sara E. Pacheco
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
| | - E. Andres Houseman
- Department of Community Health, Brown University, Providence, Rhode Island, United States of America
| | - Brock C. Christensen
- Department of Community Health, Brown University, Providence, Rhode Island, United States of America
| | - Carmen J. Marsit
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Karl T. Kelsey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Department of Community Health, Brown University, Providence, Rhode Island, United States of America
| | - Mark Sigman
- Division of Urology, Brown University, Providence, Rhode Island, United States of America
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- * E-mail:
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173
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Nanassy L, Carrell DT. Abnormal methylation of the promoter of CREM is broadly associated with male factor infertility and poor sperm quality but is improved in sperm selected by density gradient centrifugation. Fertil Steril 2011; 95:2310-4. [DOI: 10.1016/j.fertnstert.2011.03.096] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/25/2011] [Accepted: 03/26/2011] [Indexed: 11/26/2022]
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174
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Rajender S, Avery K, Agarwal A. Epigenetics, spermatogenesis and male infertility. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2011; 727:62-71. [DOI: 10.1016/j.mrrev.2011.04.002] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 04/07/2011] [Accepted: 04/08/2011] [Indexed: 12/31/2022]
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175
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Jammes H, Junien C, Chavatte-Palmer P. Epigenetic control of development and expression of quantitative traits. Reprod Fertil Dev 2011; 23:64-74. [PMID: 21366982 DOI: 10.1071/rd10259] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In recent years, it has become increasingly clear that epigenetic regulation of gene expression is critical during embryo development and subsequently during pre- and post-natal life. The phenotype of an individual is the result of complex interactions between genotype and current, past and ancestral environment leading to a lifelong remodelling of its epigenome. Practically, if the genome was compared with the hardware in a computer, the epigenome would be the software that directs the computer's operation. This review points to the importance of epigenetic processes for genome function in various biological processes, such as embryo development and the expression of quantitative traits.
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Affiliation(s)
- Hélène Jammes
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78352 Jouy-en-Josas, France.
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176
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Wang X, Suo Y, Yin R, Shen H, Wang H. Ultra-performance liquid chromatography/tandem mass spectrometry for accurate quantification of global DNA methylation in human sperms. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:1647-52. [PMID: 21536504 DOI: 10.1016/j.jchromb.2011.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 03/29/2011] [Accepted: 04/03/2011] [Indexed: 11/26/2022]
Abstract
Aberrant DNA methylation in human sperms has been proposed to be a possible mechanism associated with male infertility. We developed an ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) method for rapid, sensitive, and specific detection of global DNA methylation level in human sperms. Multiple-reaction monitoring (MRM) mode was used in MS/MS detection for accurate quantification of DNA methylation. The intra-day and inter-day precision values of this method were within 1.50-5.70%. By using 2-deoxyguanosine as an internal standard, UPLC-MS/MS method was applied for the detection of global DNA methylation levels in three cultured cell lines. DNA methyltransferases inhibitor 5-aza-2'-deoxycytidine can significantly reduce global DNA methylation levels in treated cell lines, showing the reliability of our method. We further examined global DNA methylation levels in human sperms, and found that global methylation values varied from 3.79% to 4.65%. The average global DNA methylation level of sperm samples washed only by PBS (4.03%) was relatively lower than that of sperm samples in which abnormal and dead sperm cells were removed by density gradient centrifugation (4.25%), indicating the possible aberrant DNA methylation level in abnormal sperm cells. Clinical application of UPLC-MS/MS method in global DNA methylation detection of human sperms will be useful in human sperm quality evaluation and the study of epigenetic mechanisms responsible for male infertility.
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Affiliation(s)
- Xiaoli Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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177
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Zamudio NM, Scott HS, Wolski K, Lo CY, Law C, Leong D, Kinkel SA, Chong S, Jolley D, Smyth GK, de Kretser D, Whitelaw E, O'Bryan MK. DNMT3L is a regulator of X chromosome compaction and post-meiotic gene transcription. PLoS One 2011; 6:e18276. [PMID: 21483837 PMCID: PMC3069080 DOI: 10.1371/journal.pone.0018276] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Accepted: 03/01/2011] [Indexed: 01/14/2023] Open
Abstract
Previous studies on the epigenetic regulator DNA methyltransferase 3-Like (DNMT3L), have demonstrated it is an essential regulator of paternal imprinting and early male meiosis. Dnmt3L is also a paternal effect gene, i.e., wild type offspring of heterozygous mutant sires display abnormal phenotypes suggesting the inheritance of aberrant epigenetic marks on the paternal chromosomes. In order to reveal the mechanisms underlying these paternal effects, we have assessed X chromosome meiotic compaction, XY chromosome aneuploidy rates and global transcription in meiotic and haploid germ cells from male mice heterozygous for Dnmt3L. XY bodies from Dnmt3L heterozygous males were significantly longer than those from wild types, and were associated with a three-fold increase in XY bearing sperm. Loss of a Dnmt3L allele resulted in deregulated expression of a large number of both X-linked and autosomal genes within meiotic cells, but more prominently in haploid germ cells. Data demonstrate that similar to embryonic stem cells, DNMT3L is involved in an auto-regulatory loop in germ cells wherein the loss of a Dnmt3L allele resulted in increased transcription from the remaining wild type allele. In contrast, however, within round spermatids, this auto-regulatory loop incorporated the alternative non-coding alternative transcripts. Consistent with the mRNA data, we have localized DNMT3L within spermatids and sperm and shown that the loss of a Dnmt3L allele results in a decreased DNMT3L content within sperm. These data demonstrate previously unrecognised roles for DNMT3L in late meiosis and in the transcriptional regulation of meiotic and post-meiotic germ cells. These data provide a potential mechanism for some cases of human Klinefelter's and Turner's syndromes.
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Affiliation(s)
- Natasha M. Zamudio
- The Department of Anatomy and Developmental Biology, Monash University, Victoria, Australia
- The Australian Research Council Centre of Excellence in Biotechnology and Development, Monash University, Victoria, Australia
| | - Hamish S. Scott
- The Institute of Medical and Veterinary Science, University of Adelaide, Adelaide, Australia
| | - Katja Wolski
- The Department of Anatomy and Developmental Biology, Monash University, Victoria, Australia
| | - Chi-Yi Lo
- The Department of Anatomy and Developmental Biology, Monash University, Victoria, Australia
| | - Charity Law
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Dillon Leong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Sarah A. Kinkel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Victoria, Australia
| | - Suyinn Chong
- Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Damien Jolley
- The Monash Institute of Health Services Research, Monash University, Victoria, Australia
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - David de Kretser
- The Department of Anatomy and Developmental Biology, Monash University, Victoria, Australia
| | - Emma Whitelaw
- Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Moira K. O'Bryan
- The Department of Anatomy and Developmental Biology, Monash University, Victoria, Australia
- The Australian Research Council Centre of Excellence in Biotechnology and Development, Monash University, Victoria, Australia
- * E-mail: Moira.O'
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178
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Zhu H, Li K, Liang J, Zhang J, Wu Q. Changes in the levels of DNA methylation in testis and liver of SD rats neonatally exposed to 5-aza-2′-deoxycytidine and cadmium. J Appl Toxicol 2011; 31:484-95. [DOI: 10.1002/jat.1673] [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: 01/21/2011] [Accepted: 01/21/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Hongyan Zhu
- School of Public Health; Fudan University and Key Laboratory of Public Health Safety, Ministry of Education; 130 DongAn Road; Shanghai; 200032; China
| | - Keyong Li
- School of Public Health; Fudan University and Key Laboratory of Public Health Safety, Ministry of Education; 130 DongAn Road; Shanghai; 200032; China
| | - Jiren Liang
- School of Public Health; Fudan University and Key Laboratory of Public Health Safety, Ministry of Education; 130 DongAn Road; Shanghai; 200032; China
| | - Jie Zhang
- School of Public Health; Fudan University and Key Laboratory of Public Health Safety, Ministry of Education; 130 DongAn Road; Shanghai; 200032; China
| | - Qing Wu
- School of Public Health; Fudan University and Key Laboratory of Public Health Safety, Ministry of Education; 130 DongAn Road; Shanghai; 200032; China
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179
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Abstract
Although genetics determines endocrine phenotypes, it cannot fully explain the great variability and reversibility of the system in response to environmental changes. Evidence now suggests that epigenetics, i.e. heritable but reversible changes in gene function without changes in nucleotide sequence, links genetics and environment in shaping endocrine function. Epigenetic mechanisms, including DNA methylation, histone modification, and microRNA, partition the genome into active and inactive domains based on endogenous and exogenous environmental changes and developmental stages, creating phenotype plasticity that can explain interindividual and population endocrine variability. We will review the current understanding of epigenetics in endocrinology, specifically, the regulation by epigenetics of the three levels of hormone action (synthesis and release, circulating and target tissue levels, and target-organ responsiveness) and the epigenetic action of endocrine disruptors. We will also discuss the impacts of hormones on epigenetics. We propose a three-dimensional model (genetics, environment, and developmental stage) to explain the phenomena related to progressive changes in endocrine functions with age, the early origin of endocrine disorders, phenotype discordance between monozygotic twins, rapid shifts in disease patterns among populations experiencing major lifestyle changes such as immigration, and the many endocrine disruptions in contemporary life. We emphasize that the key for understanding epigenetics in endocrinology is the identification, through advanced high-throughput screening technologies, of plasticity genes or loci that respond directly to a specific environmental stimulus. Investigations to determine whether epigenetic changes induced by today's lifestyles or environmental 'exposures' can be inherited and are reversible should open doors for applying epigenetics to the prevention and treatment of endocrine disorders.
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Affiliation(s)
- Xiang Zhang
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati College of Medicine, 3223 Eden Avenue, Kettering Complex Suite 130, Cincinnati, Ohio 45267, USA
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180
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Carrell DT, Aston KI. The search for SNPs, CNVs, and epigenetic variants associated with the complex disease of male infertility. Syst Biol Reprod Med 2011; 57:17-26. [PMID: 21208142 DOI: 10.3109/19396368.2010.521615] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Understanding the genetic basis of idiopathic male infertility has long been the focus of many researchers. Numerous recent studies have attempted to identify relevant single nucleotide polymorphisms (SNPs) through medical re-sequencing studies in which candidate genes are sequenced in large numbers of cases and controls in the search for risk or causative polymorphisms. Two major characteristics have limited the utility of the re-sequencing studies. First, reported SNPs have only accounted for a small percentage of idiopathic male infertility. Second, SNPs reported to have an association with male infertility based on gene re-sequencing studies often fail validation in follow-up studies. Recent advances in the tools available for genetic studies have enabled interrogation of the entire genome in search of common, and more recently, rare variants. In this review, we discuss the progress of studies on genetic and epigenetic variants of male infertility as well as future directions that we predict will be the most productive in identifying the genetic basis for male factor infertility based on our current state of knowledge in this field as well as lessons learned about the genetic basis for complex diseases from other disease models.
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Affiliation(s)
- Douglas T Carrell
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA.
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181
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Choi SH, Heo K, Byun HM, An W, Lu W, Yang AS. Identification of preferential target sites for human DNA methyltransferases. Nucleic Acids Res 2011; 39:104-18. [PMID: 20841325 PMCID: PMC3017615 DOI: 10.1093/nar/gkq774] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 08/01/2010] [Accepted: 08/14/2010] [Indexed: 12/14/2022] Open
Abstract
DNA methyltransferases (DNMTs) play an important role in establishing and maintaining DNA methylation. Aberrant expression of DNMTs and their isoforms has been found in many types of cancer, and their contribution to aberrant DNA methylation has been proposed. Here, we generated HEK 293T cells stably transfected with each of 13 different DNMTs (DNMT1, two DNMT3A isoforms, nine DNMT3B isoforms and DNMT3L) and assessed the DNA methylation changes induced by each DNMT. We obtained DNA methylation profiles of DNA repetitive elements and 1505 CpG sites from 808 cancer-related genes. We found that DNMTs have specific and overlapping target sites and their DNA methylation target profiles are a reflection of the DNMT domains. By examining H3K4me3 and H3K27me3 modifications in the 808 gene promoter regions using promoter ChIP-on-chip analysis, we found that specific de novo DNA methylation target sites of DNMT3A1 are associated with H3K4me3 modification that are transcriptionally active, whereas the specific target sites of DNMT3B1 are associated with H3K27me3 modification that are transcriptionally inactive. Our data suggest that different DNMT domains are responsible for targeting DNA methylation to specific regions of the genome, and this targeting might be associated with histone modifications.
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Affiliation(s)
- Si Ho Choi
- Jane Anne Nohl Division of Hematology, Norris Cancer Center, Department of Biochemistry and Molecular Biology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA and Research Center, Dongnam Institute of Radiological and Medical Science, Busan 619–753, R.O.K
| | - Kyu Heo
- Jane Anne Nohl Division of Hematology, Norris Cancer Center, Department of Biochemistry and Molecular Biology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA and Research Center, Dongnam Institute of Radiological and Medical Science, Busan 619–753, R.O.K
| | - Hyang-Min Byun
- Jane Anne Nohl Division of Hematology, Norris Cancer Center, Department of Biochemistry and Molecular Biology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA and Research Center, Dongnam Institute of Radiological and Medical Science, Busan 619–753, R.O.K
| | - Woojin An
- Jane Anne Nohl Division of Hematology, Norris Cancer Center, Department of Biochemistry and Molecular Biology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA and Research Center, Dongnam Institute of Radiological and Medical Science, Busan 619–753, R.O.K
| | - Wange Lu
- Jane Anne Nohl Division of Hematology, Norris Cancer Center, Department of Biochemistry and Molecular Biology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA and Research Center, Dongnam Institute of Radiological and Medical Science, Busan 619–753, R.O.K
| | - Allen S. Yang
- Jane Anne Nohl Division of Hematology, Norris Cancer Center, Department of Biochemistry and Molecular Biology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA and Research Center, Dongnam Institute of Radiological and Medical Science, Busan 619–753, R.O.K
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182
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Germ Cell Cancer, Testicular Dysgenesis Syndrome and Epigenetics. EPIGENETICS AND HUMAN REPRODUCTION 2011. [DOI: 10.1007/978-3-642-14773-9_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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183
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El Hajj N, Zechner U, Schneider E, Tresch A, Gromoll J, Hahn T, Schorsch M, Haaf T. Methylation Status of Imprinted Genes and Repetitive Elements in Sperm DNA from Infertile Males. Sex Dev 2011; 5:60-9. [DOI: 10.1159/000323806] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2010] [Indexed: 01/19/2023] Open
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184
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Wu W, Shen O, Qin Y, Niu X, Lu C, Xia Y, Song L, Wang S, Wang X. Idiopathic male infertility is strongly associated with aberrant promoter methylation of methylenetetrahydrofolate reductase (MTHFR). PLoS One 2010; 5:e13884. [PMID: 21085488 PMCID: PMC2976703 DOI: 10.1371/journal.pone.0013884] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 10/21/2010] [Indexed: 01/31/2023] Open
Abstract
Background Abnormal germline DNA methylation in males has been proposed as a possible mechanism compromising spermatogenesis of some men currently diagnosed with idiopathic infertility. Previous studies have been focused on imprinted genes with DNA methylation in poor quality human sperms. However, recent but limited data have revealed that sperm methylation abnormalities may involve large numbers of genes or shown that genes that are not imprinted are also affected. Methodology/Principal Findings Using the methylation-specific polymerase chain reaction and bisulfite sequencing method, we examined methylation patterns of the promoter of methylenetetrahydrofolate reductase (MTHFR) gene (NG_013351: 1538–1719) in sperm DNA obtained from 94 idiopathic infertile men and 54 normal fertile controls. Subjects with idiopathic infertility were further divided into groups of normozoospermia and oligozoospermia. Overall, 45% (41/94) of idiopathic infertile males had MTHFR hypermethylation (both hemimethylation and full methylation), compared with 15% of fertile controls (P<0.05). Subjects with higher methylation level of MTHFR were more likely to have idiopathic male infertility (P-value for trend = 0.0007). Comparing the two groups of idiopathic infertile subjects with different sperm concentrations, a higher methylation pattern was found in the group with oligozoospermia. Conclusions Hypermethylation of the promoter of MTHFR gene in sperms is associated with idiopathic male infertility. The functional relevance of hypermathylation of MTHFR to male fertility warrants further investigation.
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Affiliation(s)
- Wei Wu
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
| | - Ouxi Shen
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
| | - Xiaobing Niu
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chuncheng Lu
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
| | - Ling Song
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
| | - Shoulin Wang
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
| | - Xinru Wang
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
- * E-mail:
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185
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Epigenetic regulatory mechanisms associated with infertility. Obstet Gynecol Int 2010; 2010. [PMID: 20814440 PMCID: PMC2929612 DOI: 10.1155/2010/198709] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 06/29/2010] [Indexed: 11/21/2022] Open
Abstract
Infertility is a complex human condition and is known to be caused by numerous factors including genetic alterations and abnormalities. Increasing evidence from studies has associated perturbed epigenetic mechanisms with spermatogenesis and infertility. However, there has been no consensus on whether one or a collective of these altered states is responsible for the onset of infertility. Epigenetic alterations involve changes in factors that regulate gene expression without altering the physical sequence of DNA. Understanding these altered epigenetic states at the genomic level along with higher order organisation of chromatin in genes associated with infertility and pericentromeric regions of chromosomes, particularly 9 and Y, could further identify causes of idiopathic infertility. Determining the association between DNA methylation, chromatin state, and noncoding RNAs with the phenotype could further determine what possible mechanisms are involved. This paper reviews certain mechanisms of epigenetic regulation with particular emphasis on their possible role in infertility.
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186
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Navarro-Costa P, Nogueira P, Carvalho M, Leal F, Cordeiro I, Calhaz-Jorge C, Gonçalves J, Plancha CE. Incorrect DNA methylation of the DAZL promoter CpG island associates with defective human sperm. Hum Reprod 2010; 25:2647-54. [PMID: 20685756 PMCID: PMC2939755 DOI: 10.1093/humrep/deq200] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Successful gametogenesis requires the establishment of an appropriate epigenetic state in developing germ cells. Nevertheless, an association between abnormal spermatogenesis and epigenetic disturbances in germline-specific genes remains to be demonstrated. METHODS In this study, the DNA methylation pattern of the promoter CpG island (CGI) of two germline regulator genes--DAZL and DAZ, was characterized by bisulphite genomic sequencing in quality-fractioned ejaculated sperm populations from normozoospermic (NZ) and oligoasthenoteratozoospermic (OAT) men. RESULTS OAT patients display increased methylation defects in the DAZL promoter CGI when compared with NZ controls. Such differences are recorded when analyzing sperm fractions enriched either in normal or defective germ cells (P< 0.001 in both cases). Significant differences in DNA methylation profiles are also observable when comparing the qualitatively distinct germ cell fractions inside the NZ and OAT groups (P= 0.003 and P= 0.007, respectively). Contrastingly, the unmethylation pattern of the DAZ promoter CGI remains correctly established in all experimental groups. CONCLUSIONS An association between disrupted DNA methylation of a key spermatogenesis gene and abnormal human sperm is described here for the first time. These results suggest that incorrect epigenetic marks in germline genes may be correlated with male gametogenic defects.
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Affiliation(s)
- Paulo Navarro-Costa
- Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, 1649-028 Lisboa, Portugal.
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187
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Aitken RJ. Whither must spermatozoa wander? The future of laboratory seminology. Asian J Androl 2010; 12:99-103. [PMID: 20111089 DOI: 10.1038/aja.2008.42] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This commentary celebrates the publication of the 5th edition of the World Health Organization Laboratory Manual for the Examination and Processing of Human Semen. This is the most complete text to date on the creation of a conventional semen profile and includes invaluable reference limits for specific aspects of semen quality based on the analysis of over 1 900 recent fathers. The new edition of the manual also includes detailed protocols for monitoring different aspects of sperm function and new chapters on the preparation of spermatozoa for assisted conception and cryopreservation. Given that this publication is the definitive statement on how to perform a descriptive semen analysis, we might speculate on the future of this field and the sorts of tests that might feature in future editions of the manual. Cell biologists are currently being empowered by the 'omics revolution, which is placing at their disposal technologies of unprecedented power to examine the biochemical composition of cells such as spermatozoa. Indeed, spermatozoa are perfect vehicles for this kind of analysis because they can be obtained as extremely pure suspensions, exist naturally in isolation and can be induced to express their capacity for fertilization and the initiation of embryonic development in vitro. The application of 'omics technologies to these cells, in concert with detailed assessments of their functional competence, should provide insights into the biochemical basis of defective semen quality. This information will then help us understand the causes of male infertility and to develop rational methods for its treatment and possible prevention.
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Affiliation(s)
- R John Aitken
- ARC Centre of Excellence in Biotechnology and Development, University of Newcastle, Callaghan NSW, Australia
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188
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Chari R, Thu KL, Wilson IM, Lockwood WW, Lonergan KM, Coe BP, Malloff CA, Gazdar AF, Lam S, Garnis C, MacAulay CE, Alvarez CE, Lam WL. Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. Cancer Metastasis Rev 2010; 29:73-93. [PMID: 20108112 DOI: 10.1007/s10555-010-9199-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Advances in high-throughput, genome-wide profiling technologies have allowed for an unprecedented view of the cancer genome landscape. Specifically, high-density microarrays and sequencing-based strategies have been widely utilized to identify genetic (such as gene dosage, allelic status, and mutations in gene sequence) and epigenetic (such as DNA methylation, histone modification, and microRNA) aberrations in cancer. Although the application of these profiling technologies in unidimensional analyses has been instrumental in cancer gene discovery, genes affected by low-frequency events are often overlooked. The integrative approach of analyzing parallel dimensions has enabled the identification of (a) genes that are often disrupted by multiple mechanisms but at low frequencies by any one mechanism and (b) pathways that are often disrupted at multiple components but at low frequencies at individual components. These benefits of using an integrative approach illustrate the concept that the whole is greater than the sum of its parts. As efforts have now turned toward parallel and integrative multidimensional approaches for studying the cancer genome landscape in hopes of obtaining a more insightful understanding of the key genes and pathways driving cancer cells, this review describes key findings disseminating from such high-throughput, integrative analyses, including contributions to our understanding of causative genetic events in cancer cell biology.
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Affiliation(s)
- Raj Chari
- Genetics Unit - Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
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189
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Wu W, Lu C, Xia Y, Shen O, Ji G, Gu A, Song L, Wang X. Lack of association between DAZ gene methylation patterns and spermatogenic failure. Clin Chem Lab Med 2010; 48:355-360. [PMID: 20170395 DOI: 10.1515/cclm.2010.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
BACKGROUND Abnormal DNA methylation of the male germ line is proposed as a possible mechanism causing compromised spermatogenesis in some men diagnosed with idiopathic infertility. Previous studies suggested that aberrant DNA methylation of several genes is associated with disruptions in spermatogenesis. However, little information is available on DNA methylation patterns of testis-specific genes in idiopathic male infertility. METHODS To investigate the association between DAZ gene methylation patterns and spermatogenic failure, we performed an analysis of methylation patterns in 174 idiopathic infertile patients and 58 fertile controls using bisulfite-modified sequencing. RESULTS We found that the methylation patterns of CpG island (CGI) in the DAZ gene promoter region were different between somatic cells and spermatic cells in the control group. DAZ gene methylation patterns among groups with different spermatogenic status were the same in somatic cells, completely methylated, and in spermatic cells. The results were concordant, except for the group with azoospermia (AZ) which were completely unmethylated. CONCLUSIONS Our data indicate that the methylation patterns of the DAZ gene are not associated with spermatogenic failure. This suggests that epigenetic modification of DAZ is unlikely to be involved in the etiology of spermatogenic failure.
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Affiliation(s)
- Wei Wu
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China
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190
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Boissonnas CC, Abdalaoui HE, Haelewyn V, Fauque P, Dupont JM, Gut I, Vaiman D, Jouannet P, Tost J, Jammes H. Specific epigenetic alterations of IGF2-H19 locus in spermatozoa from infertile men. Eur J Hum Genet 2010; 18:73-80. [PMID: 19584898 DOI: 10.1038/ejhg.2009.117] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
DNA methylation marks, a key modification of imprinting, are erased in primordial germ cells and sex specifically re-established during gametogenesis. Abnormal epigenetic programming has been proposed as a possible mechanism compromising male fertility. We analysed by pyrosequencing the DNA methylation status of 47 CpGs located in differentially methylated regions (DMRs), the DMR0 and DMR2 of the IGF2 gene and in the 3rd and 6th CTCF-binding sites of the H19 DMR in human sperm from men with normal semen and patients with teratozoospermia (T) and/or oligo-astheno-teratozoospermia (OAT). All normal semen samples presented the expected high global methylation level for all CpGs analysed. In the teratozoospermia group, 11 of 19 patients presented a loss of methylation at variable CpG positions either in the IGF2 DMR2 or in both the IGF2 DMR2 and the 6th CTCF of the H19 DMR. In the OAT group, 16 of 22 patients presented a severe loss of methylation of the 6th CTCF, closely correlated with sperm concentration. The methylation state of DMR0 and of the 3rd CTCF was never affected by the pathological status of sperm samples. This study demonstrates that epigenetic perturbations of the 6th CTCF site of the H19 DMR might be a relevant biomarker for quantitative defects of spermatogenesis in humans. Moreover, we defined a methylation threshold sustaining the classification of patients in two groups, unmethylated and methylated. Using this new classification of patients, the observed intrinsic imprinting defects of spermatozoa appear not to impair significantly the outcome of assisted reproductive technologies.
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Affiliation(s)
- Céline Chalas Boissonnas
- Biology of Reproduction-CECOS, Cochin-Saint Vincent de Paul Hospital, AP-HP, Department of Genetics and Development, Cochin Institute, University Paris-Descartes, Paris, France
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191
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Houshdaran S, Hawley S, Palmer C, Campan M, Olsen MN, Ventura AP, Knudsen BS, Drescher CW, Urban ND, Brown PO, Laird PW. DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines. PLoS One 2010; 5:e9359. [PMID: 20179752 PMCID: PMC2825254 DOI: 10.1371/journal.pone.0009359] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 10/26/2009] [Indexed: 12/31/2022] Open
Abstract
Background Epithelial ovarian carcinoma is a significant cause of cancer mortality in women worldwide and in the United States. Epithelial ovarian cancer comprises several histological subtypes, each with distinct clinical and molecular characteristics. The natural history of this heterogeneous disease, including the cell types of origin, is poorly understood. This study applied recently developed methods for high-throughput DNA methylation profiling to characterize ovarian cancer cell lines and tumors, including representatives of three major histologies. Methodology/Principal Findings We obtained DNA methylation profiles of 1,505 CpG sites (808 genes) in 27 primary epithelial ovarian tumors and 15 ovarian cancer cell lines. We found that the DNA methylation profiles of ovarian cancer cell lines were markedly different from those of primary ovarian tumors. Aggregate DNA methylation levels of the assayed CpG sites tended to be higher in ovarian cancer cell lines relative to ovarian tumors. Within the primary tumors, those of the same histological type were more alike in their methylation profiles than those of different subtypes. Supervised analyses identified 90 CpG sites (68 genes) that exhibited ‘subtype-specific’ DNA methylation patterns (FDR<1%) among the tumors. In ovarian cancer cell lines, we estimated that for at least 27% of analyzed autosomal CpG sites, increases in methylation were accompanied by decreases in transcription of the associated gene. Significance The significant difference in DNA methylation profiles between ovarian cancer cell lines and tumors underscores the need to be cautious in using cell lines as tumor models for molecular studies of ovarian cancer and other cancers. Similarly, the distinct methylation profiles of the different histological types of ovarian tumors reinforces the need to treat the different histologies of ovarian cancer as different diseases, both clinically and in biomarker studies. These data provide a useful resource for future studies, including those of potential tumor progenitor cells, which may help illuminate the etiology and natural history of these cancers.
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Affiliation(s)
- Sahar Houshdaran
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California, United States of America
| | - Sarah Hawley
- Canary Foundation, Palo Alto, California, United States of America
| | - Chana Palmer
- Canary Foundation, Palo Alto, California, United States of America
| | - Mihaela Campan
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California, United States of America
- Department of Surgery, University of Southern California, Los Angeles, California, United States of America
| | - Mari N. Olsen
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Aviva P. Ventura
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Beatrice S. Knudsen
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Charles W. Drescher
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Nicole D. Urban
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Peter W. Laird
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California, United States of America
- Department of Surgery, University of Southern California, Los Angeles, California, United States of America
- University of Southern California Epigenome Center, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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192
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Miller D, Brinkworth M, Iles D. Paternal DNA packaging in spermatozoa: more than the sum of its parts? DNA, histones, protamines and epigenetics. Reproduction 2010; 139:287-301. [PMID: 19759174 DOI: 10.1530/rep-09-0281] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Haploid male germ cells package their DNA into a volume that is typically 10% or less that of a somatic cell nucleus. To achieve this remarkable level of compaction, spermatozoa replace most of their histones with smaller, highly basic arginine and (in eutherians) cysteine rich protamines. One reason for such a high level of compaction is that it may help optimise nuclear shape and hence support the gametes' swimming ability for the long journey across the female reproductive tract to the oocyte. Super-compaction of the genome may confer additional protection from the effects of genotoxic factors. However, many species including the human retain a fraction of their chromatin in the more relaxed nucleosomal configuration that appears to run counter to the ergonomic, toroidal and repackaging of sperm DNA. Recent research suggests that the composition of this 'residual' nucleosomal compartment, a generally overlooked feature of the male gamete, is far more significant and important than previously thought. In this respect, the transport and incorporation of modified paternal histones by the spermatozoon to the zygote has been demonstrated and indicates another potential paternal effect in the epigenetic reprogramming of the zygote following fertilisation that is independent of imprinting status. In this review, the most recent research into mammalian spermatozoal chromatin composition is discussed alongside evidence for conserved, non-randomly located nucleosomal domains in spermatozoal nuclei, all supporting the hypothesis that the spermatozoon delivers a novel epigenetic signature to the egg that may be crucial for normal development. We also provide some thoughts on why this signature may be required in early embryogenesis.
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Affiliation(s)
- David Miller
- Division of Reproduction and Early Development, Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Clarendon Way, Leeds LS2 9JT, UK.
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193
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Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer. Br J Cancer 2010; 102:419-27. [PMID: 20051947 PMCID: PMC2816664 DOI: 10.1038/sj.bjc.6605505] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Testicular germ cell tumour (TGCT) is the most common malignant tumour in young males. Although aberrant DNA methylation is implicated in the pathophysiology of many cancers, only a limited number of genes are known to be epigenetically changed in TGCT. This report documents the genome-wide analysis of differential methylation in an in vitro model culture system. Interesting genes were validated in TGCT patient samples. Methods: In this study, we used methylated DNA immunoprecipitation (MeDIP) and whole-genome tiling arrays to identify differentially methylated regions (DMRs). Results: We identified 35 208 DMRs. However, only a small number of DMRs mapped to promoters. A genome-wide analysis of gene expression revealed a group of differentially expressed genes that were regulated by DNA methylation. We identified several candidate genes, including APOLD1, PCDH10 and RGAG1, which were dysregulated in TGCT patient samples. Surprisingly, APOLD1 had previously been mapped to the TGCT susceptibility locus at 12p13.1, suggesting that it may be important in TGCT pathogenesis. We also observed aberrant methylation in the loci of some non-coding RNAs (ncRNAs). One of the ncRNAs, hsa-mir-199a, was downregulated in TGCT patient samples, and also in our in vitro model culture system. Conclusion: This report is the first application of MeDIP-chip for identifying epigenetically regulated genes and ncRNAs in TGCT. We also demonstrated the function of intergenic and intronic DMRs in the regulation of ncRNAs.
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194
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Carrell DT, Hammoud SS. The human sperm epigenome and its potential role in embryonic development. Mol Hum Reprod 2009; 16:37-47. [PMID: 19906823 DOI: 10.1093/molehr/gap090] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Along with many of the genome-wide transitions in chromatin composition throughout spermatogenesis, epigenetic modifications on histone tails and DNA are continuously modified to ensure stage specific gene expression in the maturing spermatid. Recent findings have suggested that the repertoire of epigenetic modifications in the mature sperm may have a potential role in the developing embryo and alterations in the epigenetic profile have been associated with infertility. These changes include DNA demethylation and the retention of modified histones at important developmental, signaling and micro-RNA genes, which resemble the epigenetic state of an embryonic stem cell. This review assesses the significance of epigenetic changes during spermatogenesis, and provides insight on recent associations made between altered epigenetic profiles in the mature sperm and its relationship to infertility.
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Affiliation(s)
- Douglas T Carrell
- IVF and Andrology Laboratories, Departments of Surgery (Urology), Obstetrics and Gynecology, and Physiology, 675 S. Arapeen Dr, Suite #205, University of Utah School of Medicine, Salt Lake City, UT 84108, USA.
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195
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Epigenetic side-effects of common pharmaceuticals: A potential new field in medicine and pharmacology. Med Hypotheses 2009; 73:770-80. [DOI: 10.1016/j.mehy.2008.10.039] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 09/29/2008] [Accepted: 10/01/2008] [Indexed: 11/22/2022]
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196
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Tunc O, Tremellen K. Oxidative DNA damage impairs global sperm DNA methylation in infertile men. J Assist Reprod Genet 2009; 26:537-44. [PMID: 19876730 DOI: 10.1007/s10815-009-9346-2] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 09/16/2009] [Indexed: 01/07/2023] Open
Abstract
PURPOSE Methylation of sperm DNA is impaired in many infertile men potentially adversely effecting reproductive outcomes. In somatic cells oxidative damage to DNA and hyperhomocysteinaemia are linked with DNA hypomethylation. The objective of this study was to investigate if these pathologies also impair sperm DNA methylation. METHODS The relationship between sperm DNA quality, oxidative stress and serum homocysteine was analysed at study entry and after 3 months of antioxidant treatment. RESULTS Overall a significant negative correlation was observed between sperm DNA methylation and sperm DNA fragmentation, as well as seminal reactive oxygen species (ROS) production. Sperm DNA methylation was not significantly related to serum homocysteine concentrations. Administration of an antioxidant supplement produced a significant fall in seminal ROS levels and sperm DNA fragmentation, while increasing sperm DNA methylation. CONCLUSIONS These results suggest that oxidative stress related damage to sperm DNA impedes the process of methylation, while antioxidant supplementation appears to have the potential to reduce DNA damage and normalize sperm DNA methylation.
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Affiliation(s)
- Ozlem Tunc
- Research Centre for Reproductive Health, Discipline of Obstetrics and Gynaecology, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia
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197
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Abstract
Quantitative methylation profiling was performed using the Illumina GoldenGate Assay in untreated Follicular Lymphoma (FL) (164), paired pre- and post-transformation FL (20), benign haematopoietic (24) samples and purified B & T cells from two FL cases. Methylation values allowed separation of untreated FL samples from controls with one exception based primarily on tumour-specific gains of methylation typically occurring within CpG islands. Genes which are targets for epigenetic repression in stem cells by Polycomb Repressor Complex 2 were significantly overrepresented among hypermethylated genes. Methylation profiles were conserved in sequential FL and t-FL biopsies suggesting that widespread methylation represents an early event in lymphomagenesis and may not contribute substantially to transformation. Significant (p<0.05) correlation between FL methylation values and reduced gene expression was demonstrated for up to 28% of loci. Methylation changes occurred predominantly in B cells with variability in the amount of non-malignant tissue between samples preventing conclusive correlation with survival. This represents an important caveat in attributing prognostic relevance to methylation and future studies in cancer will optimally require purified tumour populations to address the impact of methylation on clinical outcome.
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198
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Arpanahi A, Brinkworth M, Iles D, Krawetz SA, Paradowska A, Platts AE, Saida M, Steger K, Tedder P, Miller D. Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. Genome Res 2009; 19:1338-49. [PMID: 19584098 DOI: 10.1101/gr.094953.109] [Citation(s) in RCA: 202] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
During the haploid phase of mammalian spermatogenesis, nucleosomal chromatin is ultimately repackaged by small, highly basic protamines to generate an extremely compact, toroidal chromatin architecture that is critical to normal spermatozoal function. In common with several species, however, the human spermatozoon retains a small proportion of its chromatin packaged in nucleosomes. As nucleosomal chromatin in spermatozoa is structurally more open than protamine-packaged chromatin, we considered it likely to be more accessible to exogenously applied endonucleases. Accordingly, we have used this premise to identify a population of endonuclease-sensitive DNA sequences in human and murine spermatozoa. Our results show unequivocally that, in contrast to the endonuclease-resistant sperm chromatin packaged by protamines, regions of increased endonuclease sensitivity are closely associated with gene regulatory regions, including many promoter sequences and sequences recognized by CCCTC-binding factor (CTCF). Similar differential packaging of promoters is observed in the spermatozoal chromatin of both mouse and man. These observations imply the existence of epigenetic marks that distinguish gene regulatory regions in male germ cells and prevent their repackaging by protamines during spermiogenesis. The ontology of genes under the control of endonuclease-sensitive regulatory regions implies a role for this phenomenon in subsequent embryonic development.
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Affiliation(s)
- Ali Arpanahi
- Reproduction and Early Development Unit, Leeds Institute of Genetics and Health Therapeutics, University of Leeds, Leeds, United Kingdom
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199
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El-Maarri O, Kareta MS, Mikeska T, Becker T, Diaz-Lacava A, Junen J, Nüsgen N, Behne F, Wienker T, Waha A, Oldenburg J, Chédin F. A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation. Hum Mol Genet 2009; 18:1755-68. [PMID: 19246518 DOI: 10.1093/hmg/ddp088] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Causes underlying inter-individual variations in DNA methylation profiles among normal healthy populations are not thoroughly understood. To investigate the contribution of genetic variation in DNA methyltransferase (DNMT) genes to such epigenetic variation, we performed a systematic search for polymorphisms in all known human DNMT genes [DNMT1, DNMT3A, DNMT3B, DNMT3L and DNMT2 (TRDMT1)] in 192 healthy males and females. One hundred and eleven different polymorphisms were detected. Of these, 24 were located in coding regions and 10 resulted in an amino acid change that may affect the corresponding DNMT protein structure or function. Association analysis between all major polymorphisms (frequency > 1%) and quantitative DNA methylation profiles did not return significant results after correction for multiple testing. Polymorphisms leading to an amino acid change were further investigated for changes in global DNA methylation by differential methylation hybridization. This analysis revealed that a rare change at DNMT3L (R271Q) was associated with significant DNA hypomethylation. Biochemical characterization confirmed that DNMT3L(R271Q) is impaired in its ability to stimulate de novo DNA methylation by DNMT3A. Methylated DNA immunoprecipitation based analysis using CpG island microarrays revealed that the hypomethylation in this sample preferentially clustered to subtelomeric genomic regions with affected loci corresponding to a subset of repetitive CpG islands with low predicted promoter potential located outside of genes.
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Affiliation(s)
- Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany.
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