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Early metazoan cell type diversity and the evolution of multicellular gene regulation

Nature Ecology & Evolution volume 2, pages 1176–1188 (2018)Cite this article

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Abstract

A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement cell-type-specific functions. However, the evolution of metazoan cell types and their underlying gene regulatory programmes remains largely uncharacterized. Here, we use whole-organism single-cell RNA sequencing to map cell-type-specific transcription in Porifera (sponges), Ctenophora (comb jellies) and Placozoa species. We describe the repertoires of cell types in these non-bilaterian animals, uncovering diverse instances of previously unknown molecular signatures, such as multiple types of peptidergic cells in Placozoa. Analysis of the regulatory programmes of these cell types reveals variable levels of complexity. In placozoans and poriferans, sequence motifs in the promoters are predictive of cell-type-specific programmes. By contrast, the generation of a higher diversity of cell types in ctenophores is associated with lower specificity of promoter sequences and the existence of distal regulatory elements. Our findings demonstrate that metazoan cell types can be defined by networks of transcription factors and proximal promoters, and indicate that further genome regulatory complexity may be required for more diverse cell type repertoires.

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Fig. 1: Comparison of genomic features of early metazoans and phylogenetically related species.
Fig. 2: A. queenslandica adult and larval cell type atlases.
Fig. 3: M. leidyi and T. adhaerens cell type atlases.
Fig. 4: Phylogenetic patterns of cell-type-specific gene repertoires.
Fig. 5: Transcription factor regulatory programmes in A. queenslandica, M. leidyi and T. adhaerens.
Fig. 6: Regulatory sequence analysis in A. queenslandica, M. leidyi and T. adhaerens.

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References

  1. Arendt, D. et al. The origin and evolution of cell types. Nat. Rev. Genet. 17, 744–757 (2016).

    CAS  PubMed  Google Scholar 

  2. Sebé-Pedrós, A., Degnan, B. M. & Ruiz-Trillo, I. The origin of Metazoa: a unicellular perspective. Nat. Rev. Genet. 18, 498–512 (2017).

    PubMed  Google Scholar 

  3. 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).

    PubMed  PubMed Central  Google Scholar 

  4. 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).

    CAS  PubMed  Google Scholar 

  5. Hejnol, A. et al. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. B 276, 4261–4270 (2009).

    PubMed  PubMed Central  Google Scholar 

  6. Dunn, C. W. et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745–749 (2008).

    CAS  PubMed  Google Scholar 

  7. Valentine, J. W. in Keywords and Concepts in Evolutionary Developmental Biology (eds. Hall, B. & Olson, W.) 35–53 (Harvard Univ. Press, Cambridge, MA, 2003).

  8. Cunningham, J. A., Liu, A. G., Bengtson, S. & Donoghue, P. C. J. The origin of animals: can molecular clocks and the fossil record be reconciled? BioEssays 39, e201600120 (2017).

    Google Scholar 

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

    PubMed  Google Scholar 

  10. Jager, M. & Manuel, M. Ctenophores: an evolutionary-developmental perspective. Curr. Opin. Genet. Dev. 39, 85–92 (2016).

    CAS  PubMed  Google Scholar 

  11. Jékely, G., Paps, J. & Nielsen, C. The phylogenetic position of ctenophores and the origin(s) of nervous systems. EvoDevo 6, 1 (2015).

    PubMed  PubMed Central  Google Scholar 

  12. Moroz, L. L. et al. The ctenophore genome and the evolutionary origins of neural systems. Nature 510, 109–114 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Simpson, T. L. The Cell Biology of Sponges (Springer, New York, NY, 1984).

  14. Schierwater, B. & DeSalle, R. Placozoa. Curr. Biol. 28, R97–R98 (2018).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 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, 387 (2015).

    Google Scholar 

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

    PubMed  PubMed Central  Google Scholar 

  18. Srivastava, M. et al. The Trichoplax genome and the nature of placozoans. Nature 454, 955–960 (2008).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  20. Cao, J. et al. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 357, 661–667 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Sebé-Pedrós, A. et al. Cnidarian cell type diversity and regulation revealed by whole-organism single-cell RNA-Seq. Cell 173, 1520–1534 (2018).

    PubMed  Google Scholar 

  22. Jaitin, D. A. et al. Massively parallel single-cell RNA-Seq for marker-free decomposition of tissues into cell types. Science 343, 776–779 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Gonobobleva, E. & Maldonado, M. Choanocyte ultrastructure in Halisarca dujardini (Demospongiae, Halisarcida). J. Morphol. 270, 615–627 (2009).

    PubMed  Google Scholar 

  24. Funayama, N., Nakatsukasa, M., Hayashi, T. & Agata, K. Isolation of the choanocyte in the fresh water sponge, Ephydatia fluviatilis and its lineage marker, Ef annexin. Dev. Growth Differ. 47, 243–253 (2005).

    CAS  PubMed  Google Scholar 

  25. Nickel, M., Scheer, C., Hammel, J. U., Herzen, J. & Beckmann, F. The contractile sponge epithelium sensu lato—body contraction of the demosponge Tethya wilhelma is mediated by the pinacoderm. J. Exp. Biol. 214, 1692–1698 (2011).

    PubMed  Google Scholar 

  26. Nichols, S. A., Roberts, B. W., Richter, D. J., Fairclough, S. R. & King, N. Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex. Proc. Natl Acad. Sci. USA 109, 13046–13051 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Adamska, M. et al. The evolutionary origin of hedgehog proteins. Curr. Biol. 17, 836–837 (2007).

    Google Scholar 

  28. Nakanishi, N., Sogabe, S. & Degnan, B. M. Evolutionary origin of gastrulation: insights from sponge development. BMC Biol. 12, 26 (2014).

    PubMed  PubMed Central  Google Scholar 

  29. Müller, W. E. G. The stem cell concept in sponges (Porifera): metazoan traits. Semin. Cell Dev. Biol. 17, 481–491 (2006).

    PubMed  Google Scholar 

  30. Alié, A. et al. The ancestral gene repertoire of animal stem cells. Proc. Natl Acad. Sci. USA 112, E7093–E7100 (2015).

    PubMed  PubMed Central  Google Scholar 

  31. Rieger, R. M. The biphasic life cycle—a central theme of metazoan evolution. Am. Zool. 34, 484–491 (1994).

    Google Scholar 

  32. Degnan, S. M. & Degnan, B. M. The origin of the pelagobenthic metazoan life cycle: what’s sex got to do with it? Integr. Comp. Biol. 46, 683–690 (2006).

    PubMed  Google Scholar 

  33. Nakanishi, N., Stoupin, D., Degnan, S. M. & Degnan, B. M. Sensory flask cells in sponge larvae regulate metamorphosis via calcium signaling. Integr. Comp. Biol. 55, 1018–1027 (2015).

    CAS  PubMed  Google Scholar 

  34. Adamska, M. et al. Wnt and TGF-β expression in the sponge Amphimedon queenslandica and the origin of metazoan embryonic patterning. PLoS ONE 2, e1031 (2007).

    PubMed  PubMed Central  Google Scholar 

  35. Philippe, H. et al. Phylogenomics revives traditional views on deep animal relationships. Curr. Biol. 19, 706–712 (2009).

    CAS  PubMed  Google Scholar 

  36. Liebeskind, B. J., Hofmann, H. A., Hillis, D. M. & Zakon, H. H. Evolution of animal neural systems. Annu. Rev. Ecol. Evol. Syst. 48, 377–398 (2017).

    Google Scholar 

  37. Schnitzler, C. E. et al. Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. BMC Biol. 10, 107 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Satterlie, R. & Case, J. Gap junctions suggest epithelial conduction within the comb plates of the ctenophore Pleurobrachia bachei. Cell Tissue Res. 193, 87–91 (1978).

    CAS  PubMed  Google Scholar 

  39. Steinmetz, P. R. H. et al. Independent evolution of striated muscles in cnidarians and bilaterians. Nature 487, 231–234 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Sebé-Pedrós, A. et al. Insights into the origin of metazoan filopodia and microvilli. Mol. Biol. Evol. 30, 2013–2023 (2013).

    PubMed  PubMed Central  Google Scholar 

  41. Tudor, J. E., Pallaghy, P. K., Pennington, M. W. & Norton, R. S. Solution structure of ShK toxin, a novel potassium channel inhibitor from a sea anemone. Nat. Struct. Biol. 3, 317–320 (1996).

    CAS  PubMed  Google Scholar 

  42. Marlow, H. & Arendt, D. Evolution: ctenophore genomes and the origin of neurons. Curr. Biol. 24, R757–R761 (2014).

    CAS  PubMed  Google Scholar 

  43. Smith, C. L. et al. Novel cell types, neurosecretory cells, and body plan of the early-diverging metazoan Trichoplax adhaerens. Curr. Biol. 24, 1565–1572 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Ganz, T. Defensins: antimicrobial peptides of innate immunity. Nat. Rev. Immunol. 3, 710–720 (2003).

    CAS  PubMed  Google Scholar 

  45. Senatore, A., Reese, T. S. & Smith, C. L. Neuropeptidergic integration of behavior in Trichoplax adhaerens, an animal without synapses. J. Exp. Biol. 220, 3381–3390 (2017).

    PubMed  PubMed Central  Google Scholar 

  46. Nikitin, M. Bioinformatic prediction of Trichoplax adhaerens regulatory peptides. Gen. Comp. Endocrinol. 212, 145–155 (2015).

    CAS  PubMed  Google Scholar 

  47. Riesgo, A., Farrar, N., Windsor, P. J., Giribet, G. & Leys, S. P. The analysis of eight transcriptomes from all poriferan classes reveals surprising genetic complexity in sponges. Mol. Biol. Evol. 31, 1102–1120 (2014).

    CAS  PubMed  Google Scholar 

  48. Tautz, D. & Domazet-Lošo, T. The evolutionary origin of orphan genes. Nat. Rev. Genet. 12, 692–702 (2011).

    CAS  PubMed  Google Scholar 

  49. Sebé-Pedrós, A. et al. High-throughput proteomics reveals the unicellular roots of animal phosphosignaling and cell differentiation. Dev. Cell 39, 186–197 (2016).

    PubMed  Google Scholar 

  50. Levine, M. & Tjian, R. Transcription regulation and animal diversity. Nature 424, 147–151 (2003).

    CAS  PubMed  Google Scholar 

  51. Piasecki, B. P., Burghoorn, J. & Swoboda, P. Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals. Proc. Natl Acad. Sci. USA 107, 12969–12974 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Wang, S. & Samakovlis, C. Grainy head and its target genes in epithelial morphogenesis and wound healing. Curr. Top. Dev. Biol. 98, 35–63 (2012).

    CAS  PubMed  Google Scholar 

  53. Peter, I. S. & Davidson, E. H. Evolution of gene regulatory networks controlling body plan development. Cell 144, 970–985 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    PubMed  PubMed Central  Google Scholar 

  55. Lara-Astiaso, D. et al. Chromatin state dynamics during blood formation. Science 345, 943–949 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Nora, E. P. et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169, 930–944 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Wang, Q., Sun, Q., Czajkowsky, D. M. & Shao, Z. Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells. Nat. Commun. 9, 188 (2018).

    PubMed  PubMed Central  Google Scholar 

  58. Ramírez, F. et al. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat. Commun. 9, 189 (2018).

    PubMed  PubMed Central  Google Scholar 

  59. Grell, K. G. & Benwitz, G. Ultrastruktur von Trichoplax adhaerens F.E. Schulze. Cytobiologie 4, 216–240 (1971).

    Google Scholar 

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

    PubMed  PubMed Central  Google Scholar 

  61. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed  PubMed Central  Google Scholar 

  62. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327–339 (2013).

    CAS  PubMed  Google Scholar 

  64. Jolma, A. et al. DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature 527, 384–388 (2015).

    CAS  PubMed  Google Scholar 

  65. Kulakovskiy, I. V. et al. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. 41, D195–D202 (2013).

    CAS  PubMed  Google Scholar 

  66. Tanay, A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res. 16, 962–972 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Punta, M. et al. The Pfam protein families database. Nucleic Acids Res. 40, D290–D301 (2012).

    CAS  PubMed  Google Scholar 

  68. De Mendoza, A. et al. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proc. Natl Acad. Sci. USA 110, E4858–E4866 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Katoh, K. & Toh, H. Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 9, 286–298 (2008).

    CAS  PubMed  Google Scholar 

  70. Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164–1165 (2011).

    CAS  PubMed  Google Scholar 

  71. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006).

    CAS  PubMed  Google Scholar 

  72. Lartillot, N., Lepage, T. & Blanquart, S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288 (2009).

    CAS  PubMed  Google Scholar 

  73. Li, L., Stoeckert, C. J. Jr & Roos, D. S. D. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    PubMed  PubMed Central  Google Scholar 

  75. Booth, D. S. & King, N. Evolution: gene regulation in transition. Nature 534, 482–483 (2016).

    CAS  PubMed  Google Scholar 

  76. Vij, S. et al. Evolutionarily ancient association of the FoxJ1 transcription factor with the motile ciliogenic program. PLoS Genet. 8, e1003019 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank all members of the Tanay laboratory for comments and discussion, X. Grau-Bové for genome statistics in different species, A. Furu for help with M. leidyi, and H.-J. Osigus and B. Schierwater for providing T. adharens starting culture. Research in A.H.’s group was supported by the European Research Council Community’s Framework Program Horizon 2020 (2014–2020) ERC grant agreement 648861 and an NSF IRFP Postdoctoral Fellowship (1158629) to K.P. Research by B.M.D. is supported by the Australian Research Council. A.S.-P. was supported by an EMBO Long-Term Fellowship (ALTF 841-2014). Research in A.T.’s group was supported by the European Research Council Community’s Framework Program Horizon 2020 (2014–2020) ERC grant agreement 724824. A.T. is a Kimmel investigator.

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Author notes

  1. Federico Gaiti

    Present address: Department of Medicine, Weill Cornell Medicine and New York Genome Center, New York, NY, USA

Authors and Affiliations

  1. Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel

    Arnau Sebé-Pedrós, Elad Chomsky, Zohar Mukamel & Amos Tanay

  2. Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel

    Arnau Sebé-Pedrós, Elad Chomsky, Zohar Mukamel & Amos Tanay

  3. Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway

    Kevin Pang & Andreas Hejnol

  4. Department of Immunology, Weizmann Institute of Science, Rehovot, Israel

    David Lara-Astiaso & Ido Amit

  5. School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia

    Federico Gaiti & Bernard M. Degnan

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Contributions

A.S.-P. and A.T. conceived the project. K.P., A.H., B.M.D. and F.G. provided animal specimens and chromatin material. Z.M. and E.C. assisted with experimental setup and analysis tools. I.A. assisted with iChIP and MARS-seq setup and reagents. A.S.-P. performed the MARS-seq experiments. A.S.-P. and D.L.-A. performed the iChIP experiments. A.S.-P. and A.T. analysed the data and wrote the manuscript. All authors discussed and commented on the data.

Corresponding authors

Correspondence to Arnau Sebé-Pedrós or Amos Tanay.

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Supplementary information

Supplementary Information

Supplementary figures 1–8, Legends for Supplementary tables 1–7.

Reporting Summary

Appendix

MetaCell guide.

Supplementary table 1

A. queenslandica, M. leidyi and T. adharens scRNA sequencing library statistics.

Supplementary table 2

A. queenslandica adult cell clusters enriched gene lists.

Supplementary table 3

A. queenslandica larva cell clusters enriched gene lists.

Supplementary table 4

M. leidyi cell clusters enriched gene lists.

Supplementary table 5

T. adhaerens cell clusters enriched gene lists.

Supplementary table 6

Taxon sampling employed in the orthoclustering analysis.

Supplementary table 7

A. queenslandica, M. leidyi and T. adharens de novo motifs.

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Sebé-Pedrós, A., Chomsky, E., Pang, K. et al. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat Ecol Evol 2, 1176–1188 (2018). https://doi.org/10.1038/s41559-018-0575-6

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