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Epigenetic modifications in sex heterochromatin of vole rodents

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Abstract

The genome of some vole rodents contains large blocks of heterochromatin coupled to the sex chromosomes. While the DNA content of these heterochromatic blocks has been extensively analyzed, little is known about the epigenetic modifications controlling their structure and dynamics. To better understand its organization and functions within the nucleus, we have compared the distribution pattern of several epigenetic marks in cells from two species, Microtus agrestis and Microtus cabrerae. We first could show that the heterochromatic blocks are identifiable within the nuclei due to their AT enrichment detectable by DAPI staining. By immunostaining analyses, we demonstrated that enrichment in H3K9me3 and HP1, depletion of DNA methylation as well as H4K8ac and H3K4me2, are major conserved epigenetic features of this heterochromatin in both sex chromosomes. Furthermore, we provide evidence of transcriptional activity for some repeated DNAs in cultivated cells. These transcripts are partially polyadenylated and their levels are not altered during mitotic arrest. In summary, we show here that enrichment in H3K9me3 and HP1, DNA demethylation, and transcriptional activity are major epigenetic features of sex heterochromatin in vole rodents.

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References

  • Aagaard L, Laible G, Selenko P, Schmid M, Dorn R, Schotta G, Kuhfittig S, Wolf A, Lebersorger A, Singh PB, Reuter G, Jenuwein T (1999) Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J 18:1923–1938

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Acosta MJ, Marchal JA, Fernández-Espartero CH, Bullejos M, Sánchez A (2008) Retroelements (LINEs and SINEs) in vole genomes: differential distribution in the constitutive heterochromatin. Chromosome Res 167:949–959

    Article  Google Scholar 

  • Acosta MJ, Marchal JA, Mitsainas GP, Rovatsos MT, Fernández-Espartero CH, Giagia-Athanasopoulou EB, Sánchez A (2009) A new pericentromeric repeated DNA sequence in Microtus thomasi. Cytogenet Genome Res 124:27–36

    Article  CAS  PubMed  Google Scholar 

  • Acosta MJ, Romero-Fernández I, Sánchez A, Marchal JA (2011) Comparative analysis by chromosome painting of the sex chromosomes in arvicolid rodents. Cytogenet Genome Res 132:47–54

    Article  CAS  PubMed  Google Scholar 

  • Agarwal N, Hardt T, Brero A, Nowak D, Rothbauer U, Becker A, Leonhardt H, Cardoso MC (2007) MeCP2 interacts with HP1 and modulates its heterochromatin association during myogenic differentiation. Nucleic Acids Res 35:5402–5408

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bártová E, Krejcí J, Harnicarová A, Galiová G, Kozubek S (2008) Histone modifications and nuclear architecture: a review. J Histochem Cytochem 56:711–721. doi:10.1369/jhc.2008.951251

    Article  PubMed Central  PubMed  Google Scholar 

  • Barbin A, Montpellier C, Kokalj-Vokac N, Gibaud A, Niveleau A, Malfoy B, Dutrillaux B, Buorgeois CA (1994) New sites of methylcytosine-rich DNA detected on metaphase chromosomes. Hum Genet 94:684–692

    Article  CAS  PubMed  Google Scholar 

  • Bouzinba-Segard H, Guais A, Francastel C (2006) Accumulation of small murine minor satellite transcripts leads to impaired centromeric architecture and function. Proc Natl Sci USA 103:8709–8714

    Article  CAS  Google Scholar 

  • Brero A, Easwaran HP, Nowak D, Grunewald I, Cremer T, Leonhardt H, Cardoso MC (2005) Methyl CpG-binding proteins induce large-scale chromatin reorganization during terminal differentiation. J Cell Biol 169:733–743

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Brero A, Leonhardt H, Cardoso MC (2006) Replication and translation of epigenetic information. Curr Top Microbiol Immunol 301:21–44

    CAS  PubMed  Google Scholar 

  • Brown SW (1966) Heterochromatin. Science 151:417–425

    Article  CAS  PubMed  Google Scholar 

  • Bulynko YA, Hsing LC, Mason RW, Tremethick DJ, Grigoryev SA (2006) Cathepsin L stabilizes the histone modification landscape on the Y chromosome and pericentromeric heterochromatin. Mol Cell Biol 26:4172–4184

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Casas-Delucchi CS, Becker A, Bolius JJ, Cardoso MC (2012) Targeted manipulation of heterochromatin rescues MeCP2 Rett mutants and re-establishes higher order chromatin organization. Nucleic Acids Res 40:e176. doi:10.1093/nar/gks784

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cowell IG, Aucott R, Mahadevaiah SK, Burgoyne PS, Huskisson N, Bongiorni S, Prantera G, Fanti L, Pimpinelli S, Wu R, Gilbert DM, Shi W, Fundele R, Morrison H, Jeppesen P, Singh PB (2002) Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals. Chromosoma 111:22–36

    Article  CAS  PubMed  Google Scholar 

  • Fernández R, Barragán MJ, Bullejos M, Marchal JA, Martínez S, Díaz de la Guardia R, Sánchez A (2001) Molecular and cytogenetic characterization of highly repeated DNA sequences in the vole Microtus cabrerae. Heredity 87:637–646

    Article  PubMed  Google Scholar 

  • Francastel C, Schübeler D, Martin DI, Groudine M (2000) Nuclear compartmentalization and gene activity. Nat Rev Mol Cell Biol 1:137–143

    Article  CAS  PubMed  Google Scholar 

  • Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481–514

    Article  CAS  PubMed  Google Scholar 

  • Grewal SI, Elgin SC (2007) Transcription and RNA interference in the formation of heterochromatin. Nature 447:399–406

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Grewal SI, Jia S (2007) Heterochromatin revisited. Nat Rev Genet 8:35–46

    Article  CAS  PubMed  Google Scholar 

  • Henikoff S, Dalal Y (2005) Centromeric chromatin: what makes it unique? Curr Opin Genet Dev 15:177–184

    Article  CAS  PubMed  Google Scholar 

  • Jost KL, Rottach A, Milden M, Bertulat B, Becker A, Wolf P, Sandoval J, Petazzi P, Huertas D, Esteller M, Kremmer E, Leonhardt H, Cardoso MC (2011) Generation and characterization of rat and mouse monoclonal antibodies specific for MeCP2 and their use in X-inactivation studies. PLoS ONE 6:e26499. doi:10.1371/journal.pone.0026499

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jost KL, Bertulat B, Cardoso MC (2012) Chromosoma 121:555–563

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kalscheuer V, Singh AP, Nanda I, Sperling K, Neitzel H (1996) Evolution of the gonosomal heterochromatin of Microtus agrestis: rapid amplification of a large, multimeric, repeat unit containing a 3.0-kb (GATA)11-positive, middle repetitive element. Cytogenet Cell Genet 73:171–178

    Article  CAS  PubMed  Google Scholar 

  • Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM, Rajewsky K (2005) Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19:489–501

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705

    Article  CAS  PubMed  Google Scholar 

  • Kwon SH, Workman JL (2008) The heterochromatin protein 1 (HP1) family: put away a bias toward HP1. Mol Cells 26:217–227

    CAS  PubMed  Google Scholar 

  • Lee JC, Yunis JJ (1970) Constitutive heterochromatin during early embryogenesis of Microtus agrestis. Exp Cell Res 59:339–341

    Article  CAS  PubMed  Google Scholar 

  • Lee JC, Yunis JJ (1971) A developmental study of constitutive heterochromatin in Microtus agrestis. Chromosoma 32:237–250

    Article  CAS  PubMed  Google Scholar 

  • Lehnertz B, Ueda Y, Derijck AA, Braunschweig U, Perez-Burgos J, Kubicek S, Chen T, Li E, Jenuwein T, Peters AH (2003) Suv39hmediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol 13:1192–1200

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Kirschmann DA, Wallrath LL (2002) Does heterochromatin protein 1 always follow code? Proc Natl Acad Sci U S A 99:16462–16469

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lu J, Gilbert DM (2007) Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin. Cell Biol 179:411–421

    Article  CAS  Google Scholar 

  • Lu J, Gilbert DM (2008) Cell cycle regulated transcription of heterochromatin in mammals vs. fission yeast: functional conservation or coincidence. Cell Cycle 7:1907–1910

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lyon MF (1961) Gene Action in the X-chromosome of the Mouse (Mus musculus L. Nature 190:372–373. doi:10.1038/190372a0

    Article  CAS  PubMed  Google Scholar 

  • Maison C, Bailly D, Peters AH, Quivy JP, Roche D, Taddei A, Lachner M, Jenuwein T, Almouzni G (2002) Higher order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat Genet 30:329–334

    Article  PubMed  Google Scholar 

  • Marchal JA, Acosta MJ, Bullejos M, Díaz de la Guardia R, Sánchez A (2003) Sex chromosomes, sex determination, and sex-linked sequences in Microtidae. Cytogenet Genome Res 101:266–273

    Article  CAS  PubMed  Google Scholar 

  • Marchal JA, Acosta MJ, Bullejos M, Díaz de la Guardia R, Sánchez A (2004a) A repeat DNA sequence from the Y chromosome in species of the genus Microtus. Chromosome Res 12:757–765

    Article  CAS  PubMed  Google Scholar 

  • Marchal JA, Acosta MJ, Nietzel H, Sperling K, Bullejos M, Díaz de la Guardia R, Sánchez A (2004b) X chromosome painting in Microtus: origin and evolution of the giant sex chromosomes. Chromosome Res 12:767–776

    Article  CAS  PubMed  Google Scholar 

  • Marchal JA, Acosta MJ, Bullejos M, Puerma E, Díaz de la Guardia R, Sánchez A (2006) Distribution of L1-retroposons on the giant sex chromosomes of Microtus cabrerae (Arvicolidae, Rodentia): functional and evolutionary implications. Chromosome Res 14:177–186

    Article  CAS  PubMed  Google Scholar 

  • Marchal JA, Acosta MJ, Bullejos M, Díaz de la Guardia R, Sánchez A (2008) Origin and spread of the SRY gene on the X and Y chromosomes of the rodent Microtus cabrerae: role of L1 elements. Genomics 91:142–151

    Article  CAS  PubMed  Google Scholar 

  • Minc E, Allory Y, Worman HJ, Courvalin JC, Buendia B (1999) Localization and phosphorylation of HP1 proteins during the cell cycle in mammalian cells. Chromosoma 108:220–234

    Article  CAS  PubMed  Google Scholar 

  • Miniou P, Jeanpierre M, Blanquet V, Sibella V, Bonneau D, Herbelin C, Fischer A, Niveleau A, Viegas-Péquignot E (1994) Abnormal methylation pattern in constitutive and facultative (X inactive chromosome) heterochromatin of ICF patients. Hum Mol Genet 3:2093–2102

    Article  CAS  PubMed  Google Scholar 

  • Modi WS (1992) Nucleotide sequence and genomic organization of a tandem satellite array from the rock vole Microtus chrotorrhinus (Rodentia). Mamm Genome 3:226–232

    Article  CAS  PubMed  Google Scholar 

  • Modi WS, Serdyukova NA, Vorobieva NV, Graphodatsky AS (2003) Chromosomal localization of six repeated DNA sequences among species of Microtus (Rodentia). Chromosome Res 11:705–713

    Article  CAS  PubMed  Google Scholar 

  • Montpellier C, Burgeois CA, Kokalj-Vokac N, Muleris M, Niveleau A, Reynaud C, Gibaud A et al (1994) Detection of methylcytosine rich heterochromatin on banded chromosomes. Application to cells with various status of DNA methylation. Cancer Genet Cytogenet 78:87–93

    Article  CAS  PubMed  Google Scholar 

  • Muchardt C, Guilleme M, Seeler JS, Trouche D, Dejean A, Yaniv M (2002) Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1alpha. EMBO Rep 3:975–981

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nan X, Meehan RR, Bird A (1993) Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 21:4886–4892

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Neitzel H, Kalscheuer V, Henschel S, Digweed M, Sperling K (1998) Beta-heterochromatin in mammals: evidence from studies in Microtus agrestis based on the extensive accumulation of L1 and non-L1 retroposons in the heterochromatin. Cytogenet Cell Genet 80:165–172

    Article  CAS  PubMed  Google Scholar 

  • Neitzel H, Kalscheuer V, Singh AP, Henschel S, Sperling K (2002) Copy and paste: the impact of a new non-L1 retroposon on the gonosomal heterochromatin of Microtus agrestis. Cytogenet Genome Res 96:179–185

    Article  CAS  PubMed  Google Scholar 

  • Neumann P, Yan H, Jiang J (2007) The centromeric retrotransposons of rice are transcribed and differentially processed by RNA interference. Genetics 176:749–761

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pezer Z, Ugarkovic D (2008) Transcription of pericentromeric heterochromatin in beetles—satellite DNAs as active regulatory elements. PLoS ONE 3:1594

    Article  Google Scholar 

  • Pezer Z, Ugarkovic D (2012) Satellite DNA-associated siRNAs as mediators of heat shock response in insects. RNA Biol 9:587–595

    Article  CAS  PubMed  Google Scholar 

  • Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y (2003) Role of histone H3 lysine 27 methylation in Xinactivation. Science 300:131–135

    Article  CAS  PubMed  Google Scholar 

  • Prasanth SG, Shen Z, Prasanth KV, Stillman B (2010) Human origin recognition complex is essential for HP1 binding to chromatin and heterochromatin organization. Proc Natl Acad Sci U S A 107:15093–15098. doi:10.1073/pnas.1009945107

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Probst AV, Okamoto I, Casanova M, El Marjou F, Le Baccon P, Almouzni G (2010) A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development. Dev Cell 19:625–638

    Article  CAS  PubMed  Google Scholar 

  • Rea S, Eisenhaber F, O’Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, Jenuwein T (2000) Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406:593–599

    Article  CAS  PubMed  Google Scholar 

  • Rens W, Wallduck MS, Lovell FL, Ferguson-Smith MA, Ferguson-Smith AC (2010) Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation. Proc Natl Acad Sci U S A 107(41):17657–62. doi:10.1073/pnas.0910322107

  • Richards EJ, Elgin SC (2002) Epigenetic codes for heterochromatin formation andsilencing: rounding up the usual suspects. Cell 108:489–500

    Article  CAS  PubMed  Google Scholar 

  • Rizzi N, Denegri M, Chiodi I, Corioni M, Valgardsdottir R, Cobianchi F, Riva S, Biamonti G (2004) Transcriptional activation of a constitutive heterochromatic domain of the human genome in response to heat shock. Mol Biol Cell 15:543–551

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rovatsos MT, Marchal JA, Romero-Fernández I, Fernández FJ, Giagia-Athanosopoulou EB, Sánchez A (2011) Rapid, independent, and extensive amplification of telomeric repeats in pericentromeric regions in karyotypes of arvicoline rodents. Chromosome Res 19:869–882

    Article  CAS  PubMed  Google Scholar 

  • Serrano A, Rodríguez-Corsino M, Losada A (2009) Heterochromatin protein 1 (HP1) proteins do not drive pericentromeric cohesin enrichment in human cells. PLoS ONE 4:e5118. doi:10.1371/journal.pone.0005118

    Article  PubMed Central  PubMed  Google Scholar 

  • Shi X, Seluanov A, Gorbunova V (2007) Cell divisions are required for L1 retrotransposition. Mol Cell Biol 27:1264–1270

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sieger M, Pera F, Schwarzacher HG (1970) Genetic inactivity of heterochromatin and heteropycnosis in Microtus agrestis. Chromosoma 29:349–364

    Article  CAS  PubMed  Google Scholar 

  • Sitnikova NA, Romanenko SA, O'Brien PC, Perelman PL, Fu B, Rubtsova NV, Serdukova NA, Golenishchev FN, Trifonov VA, Ferguson-Smith MA, Yang F, Graphodatsky AS (2007) Chromosomal evolution of Arvicolinae (Cricetidae, Rodentia). I. The genome homology of tundra vole, field vole, mouse and golden hamster revealed by comparative chromosome painting. Chromosome Res 15:447–456

    Article  CAS  PubMed  Google Scholar 

  • Shevchenko AI, Pavlova SV, Dementyeva EV, Zakian SM (2009) Mosaic heterochromatin of the inactive X chromosome in vole Microtus rossiaemeridionalis. Mamm Genome 20:644–653. doi:10.1007/s00335-009-9201-x

    Article  PubMed  Google Scholar 

  • Schwarzacher (1976) Chromosomes in mitosis and interphase. Springer Publ, Berlin

    Google Scholar 

  • Sperling K, Kerem BS, Goitein R, Kottsuch V, Cedar H, Marcus M (1985) DNase I sensitivity in facultative and constitutive heterochromatin. Chromosoma 93:38–42

    Article  CAS  PubMed  Google Scholar 

  • Sperling K, Kalscheuer V, Neitzel H (1987) Transcriptional activity of constitutive heterochromatin in the mammal Microtus agrestis (Rodentia, Cricetidae). Exp Cell Res 73:463–472

    Article  Google Scholar 

  • Sperling K, Henschel S, Schulze I, Neitzel H (2004) Constitutive heterochromatin of Microtus agrestis: molecular organization and genetic activity in mitotic and meiotic cells. In: Schmid M, Nanda I (eds) Chromosomes today, vol 14. Springer Publ, Berlin, pp 235–246

    Chapter  Google Scholar 

  • Usakin L, Abad J, Vagin VV, de Pablos B, Villasante A, Gvozdev VA (2007) Transcription of the 1.688 satellite DNA family is under the control of RNA interference machinery in Drosophila melanogaster ovaries. Genetics 176:1343–1349

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Valgardsdottir R, Chiodi I, Giordano M, Rossi A, Bazzini S, Ghigna C, Riva S, Biamonti G (2007) Transcription of Satellite III non-coding RNAs is a general stress response in human cells. Nucleic Acid Res 36:423–434

    Article  PubMed Central  PubMed  Google Scholar 

  • Wang F, Koyama N, Nishida H, Haraguchi T, Reith W, Tsukamoto T (2006) The assembly and maintenance of heterochromatin initiated by transgene repeats are independent of the RNA interference pathway in mammalian cells. Mol Cell Biol 26:4028–4040

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wong LH, Brettingham-Moore KH, Chan L, Quach JM, Anderson MA, Northrop EL, Hannan R, Saffery R, Shaw ML, Williams E, Choo KH (2007) Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere. Genome Res 17:1146–1160

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yan H, Jiang J (2007) Rice as a model for centromere and heterochromatin research. Chromosome Res 15:77–84

    Article  CAS  PubMed  Google Scholar 

  • Zhu Q, Pao GM, Huynh AM, Suh H, Tonnu N, Nederlof PM, Gage FH, Verma IM (2011) BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. Nature 477:179–184

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by Ministerio de Ciencia y Tecnología of Spain (grant CGL2009-07754, cofunded by European Regional Development Fund), by Junta de Andalucía (Funding program “Ayudas a grupos de investigación,” reference BIO 220) and by the Deustche Forschungsgemeinschaft grants Ca 198/7-2 and Ca 198/9-1. The authors express their gratitude to K. Sperling and H. Neitzel for providing the cell line of M. agrestis and to Junta de Castilla y Leon for capture permits of M. agrestis. We thank Anne Lehmkuhl for excellent help with cell culture. Technical and human support provided by CICT of Universidad de Jaén (UJA, MINECO, Junta de Andalucía, FEDER) is gratefully acknowledged.

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The authors declare no conflict of interests.

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Authors and Affiliations

  1. Department of Experimental Biology, University of Jaén, Jaén, E-23071, Spain

    I. Romero-Fernández, M. Cano-Linares, M. Arroyo, A. Sánchez & J. A. Marchal

  2. Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany

    C. S. Casas-Delucchi & M. C. Cardoso

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  1. I. Romero-Fernández
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  2. C. S. Casas-Delucchi
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Romero-Fernández, I., Casas-Delucchi, C.S., Cano-Linares, M. et al. Epigenetic modifications in sex heterochromatin of vole rodents. Chromosoma 124, 341–351 (2015). https://doi.org/10.1007/s00412-014-0502-9

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