BACKGROUND: S. latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed. The regions tend to expand over time resulting in the formation of evolutionary strata. Non-recombination and later accumulation of repetitive sequences is a putative cause of the size increase in the Y chromosome. Gene decay and accumulation of repetitive DNA are identified as key evolutionary events. Transposons in the X and Y chromosomes are distributed differently and there is a regulation of transposon insertion by DNA methylation of the target sequences, this points to an important role of DNA methylation during sex chromosome evolution in Silene latifolia. The aim of this study was to elucidate whether the reduced expression of the Y allele in S. latifolia is caused by genetic degeneration or if the cause is methylation triggered by transposons and repetitive sequences. RESULTS: Gene expression analysis in S. latifolia males has shown expression bias in both X and Y alleles. To determine whether these differences are caused by genetic degeneration or methylation spread by transposons and repetitive sequences, we selected several sex-linked genes with varying degrees of degeneration and from different evolutionary strata. Immunoprecipitation of methylated DNA (MeDIP) from promoter, exon and intron regions was used and validated through bisulfite sequencing. We found DNA methylation in males, and only in the promoter of genes of stratum I (older). The Y alleles in genes of stratum I were methylation enriched compared to X alleles. There was also abundant and high percentage methylation in the CHH context in most sequences, indicating de novo methylation through the RdDM pathway. CONCLUSIONS: We speculate that TE accumulation and not gene decay is the cause of DNA methylation in the S. latifolia Y sex chromosome with influence on the process of heterochromatinization.

Plant Developmental Genetics Institute of Biophysics v v i Academy of Sciences of the Czech Republic Královopolská 135 612 65 Brno Czech Republic

Zobrazit více v PubMed

Hobza R, Vyskot B. Sex chromosomes in plants. In: Teixeira da Silva J, editor. Floriculture, ornamental and plant biotechnology (Advances and Topical Issues) Middlesex, UK: Global Science Books; 2006. p. 646.

Hobza R, Kejnovsky E, Vyskot B, Widmer A. The role of chromosomal rearrangements in the evolution of Silene latifolia sex chromosomes. Mol Gen Genomics. 2007;278(6):633–638. doi: 10.1007/s00438-007-0279-0. PubMed DOI

Bergero R, Forrest A, Kamau E, Charlesworth D. Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: evidence from new sex-linked genes. Genetics. 2007;175(4):1945–1954. doi: 10.1534/genetics.106.070110. PubMed DOI PMC

Marais GA, Nicolas M, Bergero R, Chambrier P, Kejnovsky E, Moneger F, Hobza R, Widmer A, Charlesworth D. Evidence for degeneration of the Y chromosome in the dioecious plant Silene latifolia. Curr Biol. 2008;18(7):545–549. doi: 10.1016/j.cub.2008.03.023. PubMed DOI

Kazama Y, Ishii K, Aonuma W, Ikeda T, Kawamoto H, Koizumi A, Filatov DA, Chibalina M, Bergero R, Charlesworth D et al: A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome. Sci Rep 2016, 6:18917. PubMed PMC

Zluvova J, Janousek B, Negrutiu I, Vyskot B. Comparison of the X and Y chromosome organization in Silene latifolia. Genetics. 2005;170(3):1431–1434. doi: 10.1534/genetics.105.040444. PubMed DOI PMC

Charlesworth D. Plant sex chromosome evolution. J Exp Bot. 2013;64(2):405–420. doi: 10.1093/jxb/ers322. PubMed DOI

Cermak T, Kubat Z, Hobza R, Koblizkova A, Widmer A, Macas J, Vyskot B, Kejnovsky E. Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes. Chromosom Res. 2008;16(7):961–976. doi: 10.1007/s10577-008-1254-2. PubMed DOI

Kubat Z, Zluvova J, Vogel I, Kovacova V, Cermak T, Cegan R, Hobza R, Vyskot B, Kejnovsky E. Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome. New Phytol. 2014;202(2):662–678. doi: 10.1111/nph.12669. PubMed DOI

Li SF, Zhang GJ, Yuan JH, Deng CL, Gao WJ. Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes. Planta. 2016;243(5):1083–1095. doi: 10.1007/s00425-016-2485-7. PubMed DOI

Sigman MJ, Slotkin RK. The first rule of plant transposable element silencing: location, location, location. Plant Cell. 2016;28(2):304–313. doi: 10.1105/tpc.15.00869. PubMed DOI PMC

Livernois AM, Waters SA, Deakin JE, Graves JAM, Waters PD. Independent evolution of transcriptional inactivation on sex chromosomes in birds and mammals. PLoS Genet. 2013;9(7):e1003635. doi: 10.1371/journal.pgen.1003635. PubMed DOI PMC

Waddington CH. Towards a theoretical biology. Nature. 1968;218:525–527. doi: 10.1038/218525a0. PubMed DOI

Takuno S, Ran J-H, Gaut BS. Evolutionary patterns of genic DNA methylation vary across land plants. Nature Plants. 2016;2(2):15222. doi: 10.1038/nplants.2015.222. PubMed DOI

Niederhuth C, Schmitz R. Putting DNA methylation in context: from genomes to gene expression in plants. Biochim Biophys Acta. 2017;1860(1):149. doi: 10.1016/j.bbagrm.2016.08.009. PubMed DOI PMC

Bewick AJ, Niederhuth CE, Ji L, Rohr NA, Griffin PT, Leebens-Mack J, Schmitz RJ. The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. Genome Biol. 2017;18(1):65. doi: 10.1186/s13059-017-1195-1. PubMed DOI PMC

Pikaard C, Haag J, Pontes O, Blevins T, Cocklin R. A transcription fork model for pol IV and pol v–dependent RNA-directed DNA methylation. In: Cold spring Harb Symp quant biol: 2012: Cold Spring Harbor Laboratory Press NY USA; 2012. p. 205–12. PubMed

Zhang W, Wang X, Yu Q, Ming R, Jiang J. DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Res. 2008;18(12):1938–1943. doi: 10.1101/gr.078808.108. PubMed DOI PMC

Gorelick R. Evolution of dioecy and sex chromosomes via methylation driving Muller's ratchet. Biol J Linn Soc. 2003;80(2):353–368. doi: 10.1046/j.1095-8312.2003.00244.x. DOI

Janoušek B, Široký J, Vyskot B. Epigenetic control of sexual phenotype in a dioecious plant, Melandrium album. Mol Gen Genet. 1996;250(4):483–490. doi: 10.1007/BF02174037. PubMed DOI

Hobza R, Cegan R, Jesionek W, Kejnovsky E, Vyskot B, Kubat Z. Impact of repetitive elements on the Y chromosome formation in plants. Genes. 2017;8(11):302. doi: 10.3390/genes8110302. PubMed DOI PMC

Li SF, Su T, Cheng GQ, Wang BX, Li X, Deng CL, Gao WJ. Chromosome evolution in connection with repetitive sequences and epigenetics in plants. Genes. 2017;8(10):290. doi: 10.3390/genes8100290. PubMed DOI PMC

Farbos I, Oliveira M, Negrutiu I, Mouras A. Sex organ determination and differentiation in the dioecious plant Melandrium album (Silene latifolia): a cytological and histological analysis. Sexual Plant Reprod. 1997;10(3):155–167. doi: 10.1007/s004970050083. DOI

Blavet N, Blavet H, Muyle A, Käfer J, Cegan R, Deschamps C, Zemp N, Mousset S, Aubourg S, Bergero R. Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia. BMC Genomics. 2015;16(1):546. doi: 10.1186/s12864-015-1698-7. PubMed DOI PMC

Čegan R, Marais GA, Kubekova H, Blavet N, Widmer A, Vyskot B, Dolezel J, Safar J, Hobza R. Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia. BMC Plant Biol. 2010;10:180. doi: 10.1186/1471-2229-10-180. PubMed DOI PMC

Papadopulos AS, Chester M, Ridout K, Filatov DA. Rapid Y degeneration and dosage compensation in plant sex chromosomes. Proc Natl Acad Sci U S A. 2015; PubMed PMC

Filatov DA. Evolutionary history of Silene latifolia sex chromosomes revealed by genetic mapping of four genes. Genetics. 2005;170(2):975–979. doi: 10.1534/genetics.104.037069. PubMed DOI PMC

Hobza R, Kubat Z, Čegan R, Jesionek W, Vyskot B, Kejnovsky E. Impact of repetitive DNA on sex chromosome evolution in plants. Chromosom Res. 2015;23(3):561–570. doi: 10.1007/s10577-015-9496-2. PubMed DOI

Bräutigam K, Soolanayakanahally R, Champigny M, Mansfield S, Douglas C, Campbell MM, Cronk Q. Sexual epigenetics: gender-specific methylation of a gene in the sex determining region of Populus balsamifera. Sci Rep. 2017;7:45388. doi: 10.1038/srep45388. PubMed DOI PMC

Susan JC, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 1994;22(15):2990–2997. doi: 10.1093/nar/22.15.2990. PubMed DOI PMC

Gehring M. Prodigious plant methylomes. Genome Biol. 2016;17(1):197. doi: 10.1186/s13059-016-1065-2. PubMed DOI PMC

Feng S, Cokus SJ, Zhang X, Chen P-Y, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A. 2010;107(19):8689–8694. doi: 10.1073/pnas.1002720107. PubMed DOI PMC

Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 2010;328(5980):916–919. doi: 10.1126/science.1186366. PubMed DOI

Zakrzewski F, Schmidt M, Van Lijsebettens M, Schmidt T. DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.) Plant J. 2017;90(6):1156–1175. doi: 10.1111/tpj.13526. PubMed DOI

Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM. RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc Natl Acad Sci. 2015;112(47):14728–14733. doi: 10.1073/pnas.1514680112. PubMed DOI PMC

Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, Dawe RK. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res. 2013;23(4):628–637. doi: 10.1101/gr.146985.112. PubMed DOI PMC

Huang J, Lynn J, Schulte L, Vendramin S, McGinnis K. Chapter two-epigenetic control of gene expression in maize. Int Rev Cell Mol Biol. 2017;328:25–48. doi: 10.1016/bs.ircmb.2016.08.002. PubMed DOI

Hsu FM, Yen MR, Wang CT, Lin CY, Wang CR, Chen PY. Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics Chromatin. 2017;10(1):42. doi: 10.1186/s13072-017-0148-y. PubMed DOI PMC

Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452(7184):215–219. doi: 10.1038/nature06745. PubMed DOI PMC

Blavet N, Blavet H, Čegan R, Zemp N, Zdanska J, Janousek B, Hobza R, Widmer A. Comparative analysis of a plant pseudoautosomal region (PAR) in Silene latifolia with the corresponding S. vulgaris autosome. BMC Genomics. 2012;13:226. doi: 10.1186/1471-2164-13-226. PubMed DOI PMC

Chibalina MV, Filatov DA. Plant Y chromosome degeneration is retarded by haploid purifying selection. Curr Biol. 2011;21(17):1475–1479. doi: 10.1016/j.cub.2011.07.045. PubMed DOI

Ruijter J, Ramakers C, Hoogaars W, Karlen Y, Bakker O, Van den Hoff M, Moorman A. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009;37(6):e45. doi: 10.1093/nar/gkp045. PubMed DOI PMC

Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3(7):research0034. 0031. doi: 10.1186/gb-2002-3-7-research0034. PubMed DOI PMC

Kovacova V, Janousek B. Bisprimer—a program for the design of primers for bisulfite-based genomic sequencing of both plant and mammalian DNA samples. J Hered. 2012;103(2):308–312. doi: 10.1093/jhered/esr137. PubMed DOI

Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R. Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC bioinformatics. 2008;9(1):371. doi: 10.1186/1471-2105-9-371. PubMed DOI PMC

Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia

The Formation of Sex Chromosomes in Silene latifolia and S. dioica Was Accompanied by Multiple Chromosomal Rearrangements