Not just heads and tails: The complexity of the sperm epigenome
2018; Elsevier BV; Volume: 293; Issue: 36 Linguagem: Inglês
10.1074/jbc.r117.001561
ISSN1083-351X
AutoresHannah B. Gold, Yoon Hee Jung, Victor G. Corces,
Tópico(s)Reproductive Health and Technologies
ResumoTransgenerational inheritance requires mechanisms by which epigenetic information is transferred via gametes. Canonical thought holds that mammalian sperm chromatin would be incapable of carrying epigenetic information as post-translational modifications of histones because of their replacement with protamine proteins. Furthermore, compaction of the sperm genome would hinder DNA accessibility of proteins involved in transcriptional regulation and genome architecture. In this Minireview, we delineate the paternal chromatin remodeling events during spermatogenesis and fertilization. Sperm chromatin is epigenetically modified at various time points throughout its development. This allows for the addition of environment-specific modifications that can be passed from parents to offspring. Transgenerational inheritance requires mechanisms by which epigenetic information is transferred via gametes. Canonical thought holds that mammalian sperm chromatin would be incapable of carrying epigenetic information as post-translational modifications of histones because of their replacement with protamine proteins. Furthermore, compaction of the sperm genome would hinder DNA accessibility of proteins involved in transcriptional regulation and genome architecture. In this Minireview, we delineate the paternal chromatin remodeling events during spermatogenesis and fertilization. Sperm chromatin is epigenetically modified at various time points throughout its development. This allows for the addition of environment-specific modifications that can be passed from parents to offspring. Sperm chromatin in mammals is thought to be structurally distinct from that of somatic cells. In somatic cells, chromatin contains epigenetic information in the form of DNA methylation and post-translational modifications on histones, information that is thought to influence chromosome architecture and gene expression. Methylation at the 5-position of a cytosine base pair is an epigenetic mark predominantly located at cytosine–phosphate–guanine (CpG) 2The abbreviations used are: CpGcytosine–phosphate–guanineESCembryonic stem cellmESCmouse ESCDNMTDNA methyltransferaseTETten-eleven translocation methylcytosine dioxygenasePGCprimordial germ cellEembryonic day5mC5-methylcytosinemiRNAmicroRNAseqsequencingATACassay for transposase-accessible chromatinDHSDNase I–hypersensitive siteTSStranscription start siteCTCFCCCTC-binding factor. dinucleotides and is associated with gene silencing when at the promoter and active transcription when in the gene body (1Schultz M.D. He Y. Whitaker J.W. Hariharan M. Mukamel E.A. Leung D. Rajagopal N. Nery J.R. Urich M.A. Chen H. Lin S. Lin Y. Jung I. 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Equally important as site-specific methylation in the sperm genome is the absence of this modification from specific sequences. Sites in sperm that are demethylated despite the dense global methylation levels lie mostly in CpG islands, regions of high CpG density, found mostly near promoters (26Gardiner-Garden M. Frommer M. CpG islands in vertebrate genomes.J. Mol. Biol. 1987; 196 (3656447): 261-28210.1016/0022-2836(87)90689-9Crossref PubMed Scopus (2741) Google Scholar). One comparison study between human sperm and embryonic stem cells (ESCs) found very similar distributions of methylation in each cell type. They found an enrichment of hypomethylated regions at promoters and highly methylated repeat elements (27Molaro A. Hodges E. Fang F. Song Q. McCombie W.R. Hannon G.J. Smith A.D. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates.Cell. 2011; 146 (21925323): 1029-104110.1016/j.cell.2011.08.016Abstract Full Text Full Text PDF PubMed Scopus (282) Google Scholar). This group also found that sperm-specific hypomethylated regions are located within genes related to germ cell development. Another group confirmed these findings in a comparison study with oocytes and early embryos. They found hypomethylated sequences enriched at high-density CpG promoters, enhancers, and exons. Sperm exhibits a high density of methylation at intergenic regions (28Guo H. Zhu P. Yan L. Li R. Hu B. Lian Y. Yan J. Ren X. Lin S. Li J. Jin X. Shi X. Liu P. Wang X. Wang W. et al.The DNA methylation landscape of human early embryos.Nature. 2014; 511 (25079557): 606-61010.1038/nature13544Crossref PubMed Scopus (661) Google Scholar). There is evidence of parent-of-origin–specific methylation patterns in the early embryo, with the male sperm contributing primarily differentially methylated sites in intergenic regions (29Smith Z.D. Chan M.M. Mikkelsen T.S. Gu H. Gnirke A. Regev A. Meissner A. A unique regulatory phase of DNA methylation in the early mammalian embryo.Nature. 2012; 484 (22456710): 339-34410.1038/nature10960Crossref PubMed Scopus (769) Google Scholar). DNA methylation is globally erased and re-established both during spermatogenesis and after fertilization, suggesting that 5mC may not be a good candidate, on its own, to carry epigenetic information between generations in mammals. However, evidence of site-specific methylation in mature sperm suggests there must be complementary or alternative pathways by which epigenetic information can be altered and transmitted through the paternal germline. Other candidate mechanisms are discussed below. In 1977, Balhorn et al. (30Balhorn R. Gledhill B.L. Wyrobek A.J. Mouse sperm chromatin proteins: quantitative isolation and partial characterization.Biochemistry. 1977; 16 (911755): 4074-408010.1021/bi00637a021Crossref PubMed Scopus (189) Google Scholar) examined histones retained in human and mouse sperm by electrophoretic analyses of HCl-extracted proteins from sperm chromatin. They determined that only 1% of the mouse sperm genome is associated with histones (Fig. 1A), and these histones were said to be related to developmental and/or housekeeping genes important for embryo development (31Gatewood J.M. Cook G.R. Balhorn R. Bradbury E.M. Schmid C.W. Sequence-specific packaging of DNA in human sperm chromatin.Science. 1987; 236 (3576213): 962-96410.1126/science.3576213Crossref PubMed Scopus (301) Google Scholar). However, more recent studies using micrococcal nuclease DNA digestion and ATAC-seq (assay for transposase-accessible chromatin using sequencing) techniques revealed that 7.5% of histones present in diploid somatic cells are retained in sperm nuclei when taking ploidy into account. The distribution and location of these histones in the paternal genome are actively debated, with some reports suggesting histones are distributed primarily within distal intergenic and intronic regions, and others have identified enrichment in imprinted genes (14Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm.Dev. Cell. 2014; 30 (24998598): 11-2210.1016/j.devcel.2014.05.024Abstract Full Text Full Text PDF PubMed Scopus (173) Google Scholar, 15Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Uniformity of nucleosome preservation pattern in mammalian sperm and its connection to repetitive DNA elements.Dev. Cell. 2014; 30 (24998597): 23-3510.1016/j.devcel.2014.05.023Abstract Full Text Full Text PDF PubMed Scopus (110) Google Scholar). This discrepancy may be explained by differences in methodology (14Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm.Dev. Cell. 2014; 30 (24998598): 11-2210.1016/j.devcel.2014.05.024Abstract Full Text Full Text PDF PubMed Scopus (173) Google Scholar). Results from ATAC-seq and ChIP-seq experiments suggest that sperm histones located in promoter regions possess post-translational modifications that are both a consequence of the transcriptional state of the preceding round spermatid stage as well as a prelude to expression patterns observed in ESCs and adult tissues (Fig. 1B). Modifications on histones at promoters can either be active, repressive, or bivalent. Approximately 60% of sperm promoters are in an active epigenetic state, and the TSSs of these promoters are flanked by three to four nucleosomes upstream and five to six nucleosomes downstream (16Jung Y.H. Sauria M.E.G. Lyu X. Cheema M.S. Ausio J. Taylor J. Corces V.G. Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes.Cell Rep. 2017; 18 (28178516): 1366-138210.1016/j.celrep.2017.01.034Abstract Full Text Full Text PDF PubMed Scopus (178) Google Scholar). It has been shown that 28% of promoters containing H3K27me3 also have H3K4me2, bivalent marks indicative of a poised promoter state (13Brykczynska U. Hisano M. Erkek S. Ramos L. Oakeley E.J. Roloff T.C. Beisel C. Schübeler D. Stadler M.B. Peters A.H. Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa.Nat. Struct. Mol. 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Perhaps these histone modifications contain epigenetic information that affects transcription in the early embryo. Sperm not only have promoters in a primed state that correlates with expression in mESCs, but they also appear to have enhancers in a similar state (Fig. 1B). Sperm enhancers were defined by the presence of ATAC-seq signal and the presence of H3K4me1 and H3K27ac (16Jung Y.H. Sauria M.E.G. Lyu X. Cheema M.S. Ausio J. Taylor J. Corces V.G. Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes.Cell Rep. 2017; 18 (28178516): 1366-138210.1016/j.celrep.2017.01.034Abstract Full Text Full Text PDF PubMed Scopus (178) Google Scholar). Results from ATAC-seq experiments suggest the presence of around 58,000 transposase-hypersensitive sites that may be bound by specific transcription factors, 10,240 of which correspond to enhancers previously identified in embryonic or adult tissues. In addition to typical enhancers, the sperm genome also contains around 645 super-enhancers, most of them in common with mESCs or specific cell lineages found in the adult organism. Interestingly, super-enhancers are present in loops formed by CTCF and cohesin to create insulated neighborhoods as found previously in mESCs (Fig. 1B) (36Dowen J.M. Fan Z.P. Hnisz D. Ren G. Abraham B.J. Zhang L.N. Weintraub A.S. Schujiers J. Lee T.I. Zhao K. Young R.A. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.Cell. 2014; 159 (25303531): 374-38710.1016/j.cell.2014.09.030Abstract Full Text Full Text PDF PubMed Scopus (619) Google Scholar). These results suggest that enhancer elements are already specified in the sperm and may be primed for subsequent function during embryogenesis and in the establishment of specific cell fates during the formation of differentiated tissues (16Jung Y.H. Sauria M.E.G. Lyu X. Cheema M.S. Ausio J. Taylor J. Corces V.G. Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes.Cell Rep. 2017; 18 (28178516): 1366-138210.1016/j.celrep.2017.01.034Abstract Full Text Full Text PDF PubMed Scopus (178) Google Scholar). The dense compaction of sperm chromatin was thought to result in the establishment of a 3D architecture very different from that of somatic cells. However, recent studies suggest that the three-dimensional organization of sperm chromatin is very similar to that of other cells, in particular the ESCs (16Jung Y.H. Sauria M.E.G. Lyu X. Cheema M.S. Ausio J. Taylor J. Corces V.G. Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes.Cell Rep. 2017; 18 (28178516): 1366-138210.1016/j.celrep.2017.01.034Abstract Full Text Full Text PDF PubMed Scopus (178) Google Scholar, 37Battulin N. Fishman V.S. Mazur A.M. Pomaznoy M. Khabarova A.A. Afonnikov D.A. Prokhortchouk E.B. Serov O.L. Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach.Genome Biol. 2015; 16 (25886366): 7710.1186/s13059-015-0642-0Crossref PubMed Scopus (89) Google Scholar). CTCF is an architectural protein responsible, at least in part, for this organization (38Ong C.-T. Corces V.G. CTCF: an architectural protein bridging genome topology and function.Nat. Rev. Genet. 2014; 15 (24614316): 234-24610.1038/nrg3663Crossref PubMed Scopus (706) Google Scholar), and binding motifs for CTCF can be detected at micrococcal nuclease and ATAC-seq sites on sperm DNA, suggesting that this protein may be retained in the sperm nucleus (Fig. 1B) (14Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm.Dev. Cell. 2014; 30 (24998598): 11-2210.1016/j.devcel.2014.05.024Abstract Full Text Full Text PDF PubMed Scopus (173) Google Scholar, 16Jung Y.H. Sauria M.E.G. Lyu X. Cheema M.S. Ausio J. Taylor J. Corces V.G. Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes.Cell Rep. 2017; 18 (28178516): 1366-138210.1016/j.celrep.2017.01.034Abstract Full Text Full Text PDF PubMed Scopus (178) Google Scholar). The presence of CTCF at sequence motifs in accessible sperm DNA was confirmed via ChIP-seq experiments (16Jung Y.H. Sauria M.E.G. Lyu X. Cheema M.S. Ausio J. Taylor J. Corces V.G. Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes.Cell Rep. 2017; 18 (28178516): 1366-138210.1016/j.celrep.2017.01.034Abstract Full Text Full Text PDF PubMed Scopus (178) Google Scholar). CTCF has been found to be essential for normal spermiogenesis, sperm fertility, and histone retention in mature sperm (39Hernández-Hernández A. Lilienthal I. Fukuda N. Galjart N. Höög C. CTCF contributes in a critical way to spermatogenesis and male fertility.Sci. 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Recent single-nucleus Hi-C experiments have shown that a similar higher-order chromatin organization also exists in the female gamete at the germinal vesicle stage but not in the MII stage, at which time the oocyte is arrested in metaphase (40Flyamer I.M. Gassler J. Imakaev M. Brandão H.B. Ulianov S.V. Abdennur N. Razin S.V. Mirny L.A. Tachibana-Konwalski K. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.Nature. 2017; 544 (28355183): 110-11410.1038/nature21711Crossref PubMed Scopus (463) Google Scholar). It is now understood that mature sperm DNA is both highly methylated and bound by protamines, modified histones, and transcription factors when it first encounters an oocyte. Fertilization begins with the binding of the sperm head to the oocyte zona pellucida. Sperm fusion with the membrane activates the oocyte and initiates completion of meiosis II. The sperm head and its contents are then engulfed by the oocyte. While the oocyte completes meiosis II, the sperm nucleus undergoes several changes. Its chromatin is primed for later nuclear syngamy and transcription in two ways: the first is through the replacement of protamines with histones, and the second is through active demethylation. Decondensation of the sperm nucleus occurs ∼45–60 min after fertilization. Disulfide bonds, which allow protamines to attach to sperm DNA, are broken upon exposure to oocyte-produced chemicals such as GSH (41Perreault S.D. Chromatin remodeling in mammalian zygotes.Mutat. Res. 1992; 296 (1279407): 43-5510.1016/0165-1110(92)90031-4Crossref PubMed Scopus (122) Google Scholar); however, it is unclear whether chromatin decondensation is initiated by protamine detachment. Experiments showing a depletion of radiolabeled protamines occurring after chromatin decondensation (41Perreault S.D. Chromatin remodeling in mammalian zygotes.Mutat. 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Differential H4 acetylation of paternal and maternal chromatin precedes DNA replication and differential transcriptional activity in pronuclei of 1-cell mouse embryos.Development. 1997; 124 (9409678): 4615-4625Crossref PubMed Google Scholar). Therefore, any demethylation occurring prior to the start of replication must be active. One proposed mechanism for this demethylation is the oxidation of 5-methylcytosine by TET proteins present in the oocyte cytoplasm (52Iqbal K. Jin S.-G. Pfeifer G.P. Szabó P.E. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine.Proc. Natl. Acad. Sci. U.S.A. 2011; 108 (21321204): 3642-364710.1073/pnas.1014033108Crossref PubMed Scopus (563) Google Scholar, 53Wossidlo M. Arand J. Sebastiano V. Lepikhov K. Boiani M. Reinhardt R. Schöler H. Walter J. Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes.EMBO J. 2010; 29 (20442707): 1877-188810.1038/emboj.2010.80Crossref PubMed Scopus (204) Google Scholar54Guo F. Li X. Liang D. Li T. Zhu P. Guo H. Wu X. Wen L. Gu T.-P. Hu B. Walsh C.P. Li J. Tang F. Xu G.-L. Active and passive demethylation of male and female pronuclear DNA in the mammalian zygote.Cell Stem Cell. 2014; 15 (25220291): 447-45910.1016/j.stem.2014.08.003Abstract Full Text Full Text PDF PubMed Scopus (281) Google Scholar). One study confirmed the presence of 5-hydroxymethylcytosine (5hmC) in the mouse male pronucleus using antibody staining and the specific expression of TET protein in the early embryo (52Iqbal K. Jin S.-G. Pfeifer G.P. Szabó P.E. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine.Proc. Natl. Acad. Sci. U.S.A. 2011; 108 (21321204): 3642-364710.1073/pnas.1014033108Crossref PubMed Scopus (563) Google Scholar). The 5hmC signal increases significantly between stage PN0 and PN5, and a deficiency of Tet3 prevents the oxidation of 5mC into 5hmC and results in developmental abnormalities (55Gu T.-P. Guo F. Yang H. Wu H.-P. Xu G.-F. Liu W. Xie Z.-G. Shi L. He X. Jin S.-G. Iqbal K. Shi Y.G. Deng Z. Szabó P.E. Pfeifer G.P. Li J. Xu G.-L. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes.Nature. 2011; 477 (21892189): 606-61010.1038/nature10443Crossref PubMed Scopus (898) Google Scholar). Another model suggests the presence of sperm chromatin-specific demethylases in the oocyte mediating pronuclear demethylation (42Morgan H.D. Santos F. Green K. Dean W. Reik W. Epigenetic reprogramming in mammals.Hum. Mol. Genet. 2005; 14 (Spec. No. 1, 15809273): R47-R5810.1093/hmg/ddi114Crossref PubMed Scopus (1082) Google Scholar). Enrichment of 5hmC in sperm highlights the differences in the methylation state of male and female pronuclear chromatin before the start of nuclear syngamy. Recent studies explore the apparent asymmetry in the epigenetic states of male and female pronuclei and its implications in the later stages of embryonic development. Inoue et al. (56Inoue A. Jiang L. Lu F. Suzuki T. Zhang Y. Maternal H3K27me3 controls DNA methylation-independent imprinting.Nature. 2017; 547 (28723896): 419-42410.1038/nature23262Crossref PubMed Scopus (277) Google Scholar) used DNase-sequencing techniques to compare DNase I–hypersensitive sites (DHSs) in the maternal and paternal mature gametes, pronuclei, morula, and blastula stage embryos. In searching for allele specificity and proof of parent-specific inheritance of epigenetic marks, they discovered that most DHSs in the early embryo are maternally derived and prime differential gene expression at the time of zygotic genome activation (56Inoue A. Jiang L. Lu F. Suzuki T. Zhang Y. Maternal H3K27me3 controls DNA methylation-independent imprinting.Nature. 2017; 547 (28723896): 419-42410.1038/nature23262Crossref PubMed Scopus (277) Google Scholar). Certain aspects of the epigenetic state of sperm and oocyte chromatin are maintained throughout early stages of embryonic development, suggesting a role for the transfer of information from the gamete to the embryo. Current research reveals that sperm chromatin contains far more complex epigenetic information than was previously recognized. The sperm nucleus contains sex-specific methylation patterns, nucleosomes at promoters carrying both active and silencing histone modifications, putative enhancer and super-enhancer elements flanked by nucleosomes and possibly bound by transcription factors, and CTCF/cohesin bound at specific sites to establish highly-organized chromatin interactions within the three-dimensional nuclear space. It is difficult to imagine that the presence of this wealth of information in the sperm is not used during early embryonic development to guide the initial steps controlling gene expression after fertilization. DNA methylation, an obvious candidate to explain the inheritance of epigenetic information through generations, is erased and re-established during spermatogenesis and after fertilization and thus has been discounted as a plausible mechanism underlying transgenerational effects (57Heard E. Martienssen R.A. Transgenerational epigenetic inheritance: myths and mechanisms.Cell. 2014; 157 (24679529): 95-10910.1016/j.cell.2014.02.045Abstract Full Text Full Text PDF PubMed Scopus (1131) Google Scholar). However, the erasure of 5mC in the paternal genome is only partial, suggesting the existence of mechanisms that maintain some of the epigenetic information established by DNA methylation. It is possible that the presence of DNA-bound transcription factors and histone modifications in specific regions of the genome may serve to guide re-methylation of the DNA after the demethylation of the paternal chromosomes that takes place immediately after fertilization. Under this model, although part of the epigenetic information specified by DNA methylation of the paternal chromosomes may be erased after fertilization, some information may be maintained by the interaction of specific DNA-bound transcription factors that preserve a memory of critical regulatory functions encoded by enhancers, super-enhancers, and 3D organization (16Jung Y.H. Sauria M.E.G. Lyu X. Cheema M.S. Ausio J. Taylor J. Corces V.G. Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes.Cell Rep. 2017; 18 (28178516): 1366-138210.1016/j.celrep.2017.01.034Abstract Full Text Full Text PDF PubMed Scopus (178) Google Scholar).
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