Skip to main content
SpringerLink
Log in

High histone variant H3.3 content in mouse prospermatogonia suggests a role in epigenetic reformatting

  • Research Article
  • Published:
Chromosoma Aims and scope Submit manuscript

Abstract

Histone variants can incorporate into the nucleosome outside of S-phase. Some are known to play important roles in mammalian germ cell development, this cell lineage being characterized by long phases of quiescence, a protracted meiotic phase, and genome-wide epigenetic reformatting events. The best known example of such an event is the global-scale erasure of DNA methylation in sexually indifferent primordial germ cells, then its re-establishment in fetal prospermatogonia and growing oocytes. Histone H3 and its post-translationally modified forms provide important waypoints in the establishment of epigenetic states. Using mass spectrometry and immunoblotting, we show that the H3.3 replacement variant is present at an unusually high amount in mouse prospermatogonia at the peak stage of global DNA methylation re-establishment. We speculate that H3.3 facilitates this process through achieving a greater level of accessibility of chromatin modifiers to DNA.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Abe M, Tsai SY, Jin SG, Pfeifer GP, Szabó PE (2011) Sex-specific dynamics of global chromatin changes in fetal mouse germ cells. PLoS One 6e23848

  • Ahmad K, Henikoff S (2002) The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 9:1191–1200

    Article  CAS  PubMed  Google Scholar 

  • Akiyama T, Suzuki O, Matsuda J, Aoki F (2011) Dynamic replacement of histone H3 variants reprograms epigenetic marks in early mouse embryos. PLoS Genet 7e1002279

  • Aravin AA, Sachidanandam R, Bourc’his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31:785–799

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bonner WM, West MH, Stedman JD (1980) Two-dimensional gel analysis of histones in acid extracts of nuclei, cells, and tissues. Eur J Biochem 109:17–23

    Article  CAS  PubMed  Google Scholar 

  • Bourc’his D, Bestor TH (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431:96–99

    Article  PubMed  Google Scholar 

  • Bourc’his D, Xu GL, Lin CS, Bollman B, Bestor TH (2001) Dnmt3L and the establishment of maternal genomic imprints. Science 294:2536–2539

    Article  PubMed  Google Scholar 

  • Bowles J, Koopman P (2010) Sex determination in mammalian germ cells: Extrinsic versus intrinsic factors. Reproduction 139:943–958

    Article  CAS  PubMed  Google Scholar 

  • Brandeis M, Kafri T, Ariel M, Chaillet JR, McCarrey J, Razin A, Cedar H (1993) The ontogeny of allele-specific methylation associated with imprinted genes in the mouse. EMBO J 12:3669–3677

    CAS  PubMed Central  PubMed  Google Scholar 

  • Carmell MA, Girard A, van de Kant HJ, Bourc’his D, Bestor TH, de Rooij DG, Hannon GJ (2007) MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell 12:503–514

    Article  CAS  PubMed  Google Scholar 

  • Chakraborty A, Regnier FE (2002) Global internal standard technology for comparative proteomics. J Chromatogr A 949:173–184

    Article  CAS  PubMed  Google Scholar 

  • Chen P, Zhao J, Wang Y, Wang M, Long H, Liang D, Huang L, Wen Z, Li W et al (2013) H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev 27:2109–2124

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chow CM, Georgiou A, Szutorisz H, Maia Silva A, Pombo A, Barahona I, Dargelos E, Canzonetta C, Dillon N (2005) Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division. EMBO Rep 6:354–360

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Davis TL, Yang GJ, McCarrey JR, Bartolomei MS (2000) The H19 methylation imprint is erased and re-established differentially on the parental alleles during male germ cell development. Hum Mol Genet 9:2885–2894

    Article  CAS  PubMed  Google Scholar 

  • Drané P, Ouararhni K, Depaux A, Shuaib M, Hamiche A (2010) The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev 24:1253–1265

    Article  PubMed Central  PubMed  Google Scholar 

  • Greaves IK, Rangasamy D, Devoy M, Marshall Graves JA, Tremethick DJ (2006) The X and Y chromosomes assemble into H2A.Z-containing facultative heterochromatin following meiosis. Mol Cell Biol 26:5394–5405

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Grove GW, Zweidler A (1984) Regulation of nucleosomal core histone variant levels in differentiating murine erythroleukemia cells. Biochemistry 23:4436–4443

    Article  CAS  PubMed  Google Scholar 

  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999

    Article  CAS  PubMed  Google Scholar 

  • Hake SB, Allis CD (2006) Histone H3 variants and their potential role in indexing mammalian genomes: the “H3 barcode hypothesis”. Proc Natl Acad Sci U S A 103:6428–6435

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hendzel MJ, Davie JR (1990) Nucleosomal histones of transcriptionally active/competent chromatin preferentially exchange with newly synthesized histones in quiescent chicken erythrocytes. Biochem J 271:67–73

    CAS  PubMed Central  PubMed  Google Scholar 

  • Hoyer-Fender S, Costanzi C, Pehrson JR (2000) Histone macroH2A1.2 is concentrated in the XY-body by the early pachytene stage of spermatogenesis. Exp Cell Res 258:254–260

    Article  CAS  PubMed  Google Scholar 

  • Jin C, Felsenfeld G (2007) Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev 21:1519–1529

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kafri T, Ariel M, Brandeis M, Shemer R, Urven L, McCarrey J, Cedar H, Razin A (1992) Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev 6:705–714

    Article  CAS  PubMed  Google Scholar 

  • Kang ER, Iqbal K, Tran DA, Rivas GE, Singh P, Pfeifer GP, Szabó PE (2011) Effects of endocrine disruptors on imprinted gene expression in the mouse embryo. Epigenetics 6:937–950

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kato Y, Kaneda M, Hata K, Kumaki K, Hisano M, Kohara Y, Okano M, Li E, Nozaki M, Sasaki H (2007) Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. Hum Mol Genet 16:2272–2280

    Article  CAS  PubMed  Google Scholar 

  • Kipping M, Pollack L, Langridge J (2005) Label free quantitative proteomics: High resolution electrospray LC-MS for functional proteome analysis. BIOspektrum 11:780–781

    CAS  Google Scholar 

  • Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Totoki Y, Toyoda A, Ikawa M, Asada N, Kojima K, Yamaguchi Y et al (2008) DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev 22:908–917

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • La Salle S, Oakes CC, Neaga OR, Bourc’his D, Bestor TH, Trasler JM (2007) Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L. BMC Dev Biol 7104

  • Lee J, Inoue K, Ono R, Ogonuki N, Kohda T, Kaneko-Ishino T, Ogura A, Ishino F (2002) Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells. Development 129:1807–1817

    Article  CAS  PubMed  Google Scholar 

  • Lees-Murdock DJ, De Felici M, Walsh CP (2003) Methylation dynamics of repetitive DNA elements in the mouse germ cell lineage. Genomics 82:230–237

    Article  CAS  PubMed  Google Scholar 

  • Lefevre C, Mann JR (2008) RNA expression microarray analysis in mouse prospermatogonia: identification of candidate epigenetic modifiers. Dev Dyn 237:1082–1089

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lewis PW, Elsaesser SJ, Noh KM, Stadler SC, Allis CD (2010) Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres. Proc Natl Acad Sci U S A 107:14075–14080

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lucifero D, Mann MR, Bartolomei MS, Trasler JM (2004) Gene-specific timing and epigenetic memory in oocyte imprinting. Hum Mol Genet 13:839–849

    Article  CAS  PubMed  Google Scholar 

  • Lucifero D, Mertineit C, Clarke HJ, Bestor TH, Trasler JM (2002) Methylation dynamics of imprinted genes in mouse germ cells. Genomics 79:530–538

    Article  CAS  PubMed  Google Scholar 

  • Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260

    Article  CAS  PubMed  Google Scholar 

  • Mahadevaiah SK, Turner JM, Baudat F, Rogakou EP, de Boer P, Blanco-Rodríguez J, Jasin M, Keeney S, Bonner WM, Burgoyne PS (2001) Recombinational DNA double-strand breaks in mice precede synapsis. Nat Genet 27:271–276

    Article  CAS  PubMed  Google Scholar 

  • Marzluff WF, Gongidi P, Woods KR, Jin J, Maltais LJ (2002) The human and mouse replication-dependent histone genes. Genomics 80:487–498

    Article  CAS  PubMed  Google Scholar 

  • Marzluff WF, Wagner EJ, Duronio RJ (2008) Metabolism and regulation of canonical histone mRNAs: Life without a poly (A) tail. Nat Rev Genet 9:843–854

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mirzaei H, McBee JK, Watts J, Aebersold R (2008) Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol Cell Proteomics 7:813–823

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mito Y, Henikoff JG, Henikoff S (2005) Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet 37:1090–1097

    Article  CAS  PubMed  Google Scholar 

  • Monk M, Boubelik M, Lehnert S (1987) Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99:371–382

    CAS  PubMed  Google Scholar 

  • Obata Y, Kono T (2002) Maternal primary imprinting is established at a specific time for each gene throughout oocyte growth. J Biol Chem 277:5285–5289

    Article  CAS  PubMed  Google Scholar 

  • Richler C, Dhara SK, Wahrman J (2000) Histone macroH2A1.2 is concentrated in the XY compartment of mammalian male meiotic nuclei. Cytogenet Cell Genet 89:118–120

    Article  CAS  PubMed  Google Scholar 

  • Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154–1169

    Article  CAS  PubMed  Google Scholar 

  • Sanford JP, Clark HJ, Chapman VM, Rossant J (1987) Differences in DNA methylation during oogenesis and spermatogenesis and their persistence during early embryogenesis in the mouse. Genes Dev 1:1039–1046

    Article  CAS  PubMed  Google Scholar 

  • Santenard A, Ziegler-Birling C, Koch M, Tora L, Bannister AJ, Torres-Padilla ME (2010) Heterochromatin formation in the mouse embryo requires critical residues of the histone variant H3.3. Nat Cell Biol 12:853–862

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Schwartz BE, Ahmad K (2005) Transcriptional activation triggers deposition and removal of the histone variant H3.3. Genes Dev 19:804–814

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Shechter D, Dormann HL, Allis CD, Hake SB (2007) Extraction, purification and analysis of histones. Nat Protoc 2:1445–1457

    Article  CAS  PubMed  Google Scholar 

  • Siedlecki P, Zielenkiewicz P (2006) Mammalian DNA methyltransferases. Acta Biochim Pol 53:245–256

    CAS  PubMed  Google Scholar 

  • Singer-Sam J, LeBon JM, Dai A, Riggs AD (1992) A sensitive, quantitative assay for measurement of allele-specific transcripts differing by a single nucleotide. PCR Methods Appl 1:160–163

    Article  CAS  PubMed  Google Scholar 

  • Singh P, Li AX, Tran DA, Oates N, Kang ER, Wu X, Szabó PE (2013) De novo DNA methylation in the male germ line occurs by default but is excluded at sites of H3K4 methylation. Cell Rep 4:205–219

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Soboleva TA, Nekrasov M, Pahwa A, Williams R, Huttley GA, Tremethick DJ (2012) A unique H2A histone variant occupies the transcriptional start site of active genes. Nat Struct Mol Biol 19:25–30

    Article  CAS  Google Scholar 

  • Szabó PE, Hübner K, Schöler H, Mann JR (2002) Allele-specific expression of imprinted genes in mouse migratory primordial germ cells. Mech Dev 115:157–160

    Article  PubMed  Google Scholar 

  • Szabó PE, Mann JR (1995) Biallelic expression of imprinted genes in the mouse germ line: implications for erasure, establishment, and mechanisms of genomic imprinting. Genes Dev 9:1857–1868

    Article  PubMed  Google Scholar 

  • Ueda T, Abe K, Miura A, Yuzuriha M, Zubair M, Noguchi M, Niwa K, Kawase Y, Kono T et al (2000) The paternal methylation imprint of the mouse H19 locus is acquired in the gonocyte stage during foetal testis development. Genes Cells 5:649–659

    Article  CAS  PubMed  Google Scholar 

  • Urban MK, Zweidler A (1983) Changes in nucleosomal core histone variants during chicken development and maturation. Dev Biol 95:421–428

    Article  CAS  PubMed  Google Scholar 

  • van der Heijden GW, Derijck AA, Pósfai E, Giele M, Pelczar P, Ramos L, Wansink DG, van der Vlag J, Peters AH, de Boer P (2007) Chromosome-wide nucleosome replacement and H3.3 incorporation during mammalian meiotic sex chromosome inactivation. Nat Genet 39:251–258

    Article  PubMed  Google Scholar 

  • Walsh CP, Bestor TH (1999) Cytosine methylation and mammalian development. Genes Dev 13:26–34

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Walsh CP, Chaillet JR, Bestor TH (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20:116–117

    Article  CAS  PubMed  Google Scholar 

  • Wang G, Wu WW, Zeng W, Chou CL, Shen RF (2006) Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes. J Proteome Res 5:1214–1223

    Article  CAS  PubMed  Google Scholar 

  • Waterborg JH, Robertson AJ (1996) Common features of analogous replacement histone H3 genes in animals and plants. J Mol Evol 43:194–206

    Article  CAS  PubMed  Google Scholar 

  • Webster KE, O’Bryan MK, Fletcher S, Crewther PE, Aapola U, Craig J, Harrison DK, Aung H, Phutikanit N et al (2005) Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc Natl Acad Sci U S A 102:4068–4073

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Western PS, Miles DC, van den Bergen JA, Burton M, Sinclair AH (2008) Dynamic regulation of mitotic arrest in fetal male germ cells. Stem Cells 26:339–347

    Article  CAS  PubMed  Google Scholar 

  • Wong LH, McGhie JD, Sim M, Anderson MA, Ahn S, Hannan RD, George AJ, Morgan KA, Mann JR, Choo KH (2010) ATRX interacts with H3.3 in maintaining telomere structural integrity in pluripotent embryonic stem cells. Genome Res 20:351–360

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wood MJ, Whittingham DG, Rall WF (1987) The low temperature storage of mouse oocytes and embryos. In: Monk M (ed) Mammalian development: a practical approach. IRL Press, Oxford, pp 255–280

    Google Scholar 

  • Wu RS, Tsai S, Bonner WM (1982) Patterns of histone variant synthesis can distinguish G0 from G1 cells. Cell 31:367–374

    Article  CAS  PubMed  Google Scholar 

  • Wu RS, Tsai S, Bonner WM (1983) Changes in histone H3 composition and synthesis pattern during lymphocyte activation. Biochemistry 22:3868–3873

    Article  CAS  PubMed  Google Scholar 

  • Yoshioka H, McCarrey JR, Yamazaki Y (2009) Dynamic nuclear organization of constitutive heterochromatin during fetal male germ cell development in mice. Biol Reprod 80:804–812

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by a Melbourne Research Scholarship awarded to MCT by The University of Melbourne and by the National Health and Medical Research Council, Australia.

Author information

Authors and Affiliations

  1. Department of Zoology, The University of Melbourne, Gate 12 Royal Parade, Parkville, VIC, 3010, Australia

    Michelle C. W. Tang

  2. Genetics Theme, Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, VIC, 3052, Australia

    Michelle C. W. Tang & Jeffrey R. Mann

  3. Department of Primary Industries, Biosciences Research Division, 1 Park Drive, Bundoora, VIC, 3083, Australia

    Steve Binos

  4. Scientific Services, Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, VIC, 3052, Australia

    Eng K. Ong

  5. Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia

    Lee H. Wong

Authors
  1. Michelle C. W. Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Steve Binos
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eng K. Ong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lee H. Wong
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jeffrey R. Mann
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jeffrey R. Mann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 403 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tang, M.C.W., Binos, S., Ong, E.K. et al. High histone variant H3.3 content in mouse prospermatogonia suggests a role in epigenetic reformatting. Chromosoma 123, 587–595 (2014). https://doi.org/10.1007/s00412-014-0475-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00412-014-0475-8

Keywords

Search

Navigation