Convergent evolution of a vertebrate-like methylome in a marine sponge

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Abstract

Vertebrates have highly methylated genomes at CpG positions, whereas invertebrates have sparsely methylated genomes. This increase in methylation content is considered a major regulatory innovation of vertebrate genomes. However, here we report that a sponge, proposed as the potential sister group to the rest of animals, has a highly methylated genome. Despite major differences in genome size and architecture, we find similarities between the independent acquisitions of the hypermethylated state. Both lineages show genome-wide CpG depletion, conserved strong transcription factor methyl-sensitivity and developmental methylation dynamics at 5-hydroxymethylcytosine enriched regions. Together, our findings trace back patterns associated with DNA methylation in vertebrates to the early steps of animal evolution. Thus, the sponge methylome challenges previous hypotheses concerning the uniqueness of vertebrate genome hypermethylation and its implications for regulatory complexity.

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Fig. 1: Amphimedon has a vertebrate-like methylome.
Fig. 2: Methyl-sensitive transcription factors are enriched at unmethylated Amphimedon promoters.
Fig. 3: Methylation dynamics during Amphimedon development.
Fig. 4: Genomic DNA hydroxymethylation is enriched at transcription factor binding sites in Amphimedon.

Data availability

Sequencing data have been deposited in Gene Expression Omnibus under the following accession number GSE124016.

Code availability

The code used to generate the analysis can be accessed at https://github.com/AlexdeMendoza/SpongeMethylation.

References

  1. 1.

    Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).

  2. 2.

    Schübeler, D. Function and information content of DNA methylation. Nature 517, 321–326 (2015).

  3. 3.

    Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010).

  4. 4.

    Feng, S. et al. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl Acad. Sci. USA 107, 8689–8694 (2010).

  5. 5.

    Jones, Pa Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484–492 (2012).

  6. 6.

    Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011).

  7. 7.

    Bogdanović, O. et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat. Genet. 48, 417–426 (2016).

  8. 8.

    Suzuki, M. M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9, 465–476 (2008).

  9. 9.

    Lyko, F. The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat. Rev. Genet. 19, 81–92 (2018).

  10. 10.

    Wu, X. & Zhang, Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat. Rev. Genet. 18, 517–534 (2017).

  11. 11.

    Iyer, L. M., Abhiman, S. & Aravind, L. Natural history of eukaryotic DNA methylation systems. Prog. Mol. Biol. Transl. Sci. 101, 25–104 (2011).

  12. 12.

    Srivastava, M. et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466, 720–726 (2010).

  13. 13.

    Fortunato, S. A. V. et al. Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Nature 514, 620–623 (2014).

  14. 14.

    Ryan, J. F. et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592–1242592 (2013).

  15. 15.

    Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007).

  16. 16.

    Fernandez-Valverde, S. L. & Degnan, B. M. Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome. Sci. Rep. 6, 22496 (2016).

  17. 17.

    Suzuki, M. M., Kerr, A. R. W., De Sousa, D. & Bird, A. CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res. 17, 625–631 (2007).

  18. 18.

    Francis, W. R. et al. The genome of the contractile demosponge Tethya wilhelma and the evolution of metazoan neural signalling pathways. Preprint at bioRxiv https://doi.org/10.1101/120998 (2017).

  19. 19.

    Cohen, N. M., Kenigsberg, E. & Tanay, A. Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell 145, 773–786 (2011).

  20. 20.

    Boulard, M., Edwards, J. R. & Bestor, T. H. FBXL10 protects polycomb-bound genes from hypermethylation. Nat. Genet. 47, 479–485 (2015).

  21. 21.

    Domcke, S. et al. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528, 575–579 (2015).

  22. 22.

    Yin, Y. et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 356, eaaj2239 (2017).

  23. 23.

    Brandeis, M. et al. Sp1 elements protect a CpG island from de novo methylation. Nature 371, 435–438 (1994).

  24. 24.

    Macleod, D., Charlton, J., Mullins, J. & Bird, A. P. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 8, 2282–2292 (1994).

  25. 25.

    Bartlett, A. et al. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat. Protoc. 12, 1659–1672 (2017).

  26. 26.

    Nitta, K. R. et al. Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. eLife 4, 1–20 (2015).

  27. 27.

    Krebs, A. R., Dessus-Babus, S., Burger, L. & Schübeler, D. High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions. eLife 3, e04094 (2014).

  28. 28.

    Gaiti, F. et al. Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity. eLife 6, e22194 (2017).

  29. 29.

    Schwaiger, M. et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 24, 639–650 (2014).

  30. 30.

    Hontelez, S. et al. Embryonic transcription is controlled by maternally defined chromatin state. Nat. Commun. 6, 10148 (2015).

  31. 31.

    Yu, M. et al. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat. Protoc. 7, 2159–2170 (2012).

  32. 32.

    Sardina, J. L. et al. Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate. Cell Stem Cell 23, 727–741.e9 (2018).

  33. 33.

    Marlétaz, F. et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 564, 64–70 (2018).

  34. 34.

    Delatte, B. et al. RNA biochemistry. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 351, 282–285 (2016).

  35. 35.

    Zhang, Z. et al. Genome-wide and single-base resolution DNA methylomes of the sea lamprey (Petromyzon marinus) reveal gradual transition of the genomic methylation pattern in early vertebrates. Preprint at bioRxiv https://doi.org/10.1101/033233 (2015).

  36. 36.

    Bewick, A. J., Vogel, K. J., Moore, A. J. & Schmitz, R. J. Evolution of DNA methylation across insects. Mol. Biol. Evol. 34, 654–665 (2017).

  37. 37.

    Rošić, S. et al. Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity. Nat. Genet. 50, 452–459 (2018).

  38. 38.

    Mugal, C. F., Arndt, P. F., Holm, L. & Ellegren, H. Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes. G3 5, 441–447 (2015).

  39. 39.

    Bewick, A. J. et al. On the origin and evolutionary consequences of gene body DNA methylation. Proc. Natl Acad. Sci. USA 113, 9111–9116 (2016).

  40. 40.

    Wang, X. et al. Function and evolution of DNA methylation in Nasonia vitripennis. PLoS Genet. 9, e1003872–e1003872 (2013).

  41. 41.

    Bewick, A. J. et al. Diversity of cytosine methylation across the fungal tree of life. Nat. Ecol. Evol. 3, 479–490 (2019).

  42. 42.

    Takuno, S., Ran, J.-H. & Gaut, B. S. Evolutionary patterns of genic DNA methylation vary across land plants. Nat. Plants 2, 15222 (2016).

  43. 43.

    Niederhuth, C. E. et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 17, 194 (2016).

  44. 44.

    Baubec, T. et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 520, 243–247 (2015).

  45. 45.

    Bewick, A. J. et al. Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics Chromatin 12, 6 (2019).

  46. 46.

    Schulz, N. K. E. et al. Dnmt1 has an essential function despite the absence of CpG DNA methylation in the red flour beetle Tribolium castaneum. Sci. Rep. 8, 16462 (2018).

  47. 47.

    Lechner, M. et al. The correlation of genome size and DNA methylation rate in metazoans. Theory Biosci. 132, 47–60 (2013).

  48. 48.

    Regev, A., Lamb, M. J. & Jablonka, E. The role of DNA methylation in invertebrates: developmental regulation/ror genome defense? Mol. Biol. Evol. 15, 880–891 (1998).

  49. 49.

    Sebé-Pedrós, A. et al. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat. Ecol. Evol. 2, 1176–1188 (2018).

  50. 50.

    Wang, X. et al. Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation. BMC Genom. 15, 1119 (2014).

  51. 51.

    Zhang, G. G. et al. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490, 49–54 (2012).

  52. 52.

    Dunn, C. W., Leys, S. P. & Haddock, S. H. D. The hidden biology of sponges and ctenophores. Trends Ecol. Evol. 30, 282–291 (2015).

  53. 53.

    Leys, S. P. et al. Isolation of Amphimedon developmental material. CSH Protoc. 2008, db.prot5095 (2008).

  54. 54.

    Leys, S. P. & Degnan, B. M. Embryogenesis and metamorphosis in a haplosclerid demosponge: gastrulation and transdifferentiation of larval ciliated cells to choanocytes. Invertebr. Biol. 121, 171–189 (2005).

  55. 55.

    Pang, K. & Martindale, M. Q. Comb jellies (ctenophora): a model for Basal metazoan evolution and development. CSH Protoc. 2008, db.emo106 (2008).

  56. 56.

    Guo, W. et al. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genom. 14, 774–774 (2013).

  57. 57.

    Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014).

  58. 58.

    Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).

  59. 59.

    Burger, L., Gaidatzis, D., Schübeler, D. & Stadler, M. B. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155–e155 (2013).

  60. 60.

    Sebé-Pedrós, A. et al. The dynamic regulatory genome of capsaspora and the origin of animal multicellularity. Cell 165, 1224–1237 (2016).

  61. 61.

    Wu, H. et al. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res. 43, e141–e141 (2015).

  62. 62.

    Fernandez-Valverde, S. L., Calcino, A. D. & Degnan, B. M. Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica. BMC Genom. 16, 1–11 (2015).

  63. 63.

    Leininger, S. et al. Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nat. Commun. 5, 3905–3905 (2014).

  64. 64.

    Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

  65. 65.

    Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).

  66. 66.

    Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637–644 (2008).

  67. 67.

    Smit, A. F. A. & Hubley, R. RepeatModeler Open-1.0 (RepeatMasker, 2008); http://www.repeatmasker.org.

  68. 68.

    Bogdanovic, O. et al. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res. 22, 2043–2053 (2012).

  69. 69.

    Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).

  70. 70.

    Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

  71. 71.

    Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195–e1002195 (2011).

  72. 72.

    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

  73. 73.

    Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

  74. 74.

    Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

  75. 75.

    Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).

  76. 76.

    Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25–R25 (2009).

  77. 77.

    Simion, P. et al. A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals. Curr. Biol. 27, 958–967 (2017).

  78. 78.

    Whelan, N. V. et al. Ctenophore relationships and their placement as the sister group to all other animals. Nat. Ecol. Evol. 1, 1737–1746 (2017).

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Acknowledgements

We thank J. M. Polo for critical reading of this manuscript. This work was supported by the Australian Research Council (ARC) Centre of Excellence programme in Plant Energy Biology (grant no. CE140100008). R.L. was supported by a Sylvia and Charles Viertel Senior Medical Research Fellowship, ARC Future Fellowship (no. FT120100862) and Howard Hughes Medical Institute International Research Scholarship. S.M.D. and B.M.D. were supported by grants from the ARC (grant nos. DP160100573 and DP170102353). Research in A.H.’s group was supported by the European Research Council Community’s Framework Program Horizon 2020 (2014–2020) ERC grant agreement (no. 648861) and an NSF IRFP Postdoctoral Fellowship (no. 1158629) to K.P. A.d.M. was funded by an EMBO long-term fellowship (no. ALTF 144-2014). U.T. was funded by a grant from the Austrian Science Fund FWF (grant no. P27353).

Author information

A.d.M. and R.L. designed the study. A.d.M. prepared methylC-seq, TAB-seq and DAP–seq libraries, with the help of O.B. and J.P. The data were analysed by A.d.M., with help from S.B. Amphimedon materials were provided by S.M.D., B.M.D. and W.L.H. Mnemiopsis materials were provided by K.P. and A.H. Sycon material was provided by S.L. and M.A. Nematostella material was provided by U.T. The manuscript was written by A.d.M. and R.L. All authors commented on the final manuscript.

Correspondence to Alex de Mendoza or Ryan Lister.

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