Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Parallel evolution of male germline epigenetic poising and somatic development in animals

Nature Genetics volume 48, pages 888–894 (2016)Cite this article

Subjects

A Corrigendum to this article was published on 28 September 2016

This article has been updated

Abstract

Changes in gene regulation frequently underlie changes in morphology during evolution, and differences in chromatin state have been linked with changes in anatomical structure and gene expression across evolutionary time. Here we assess the relationship between evolution of chromatin state in germ cells and evolution of gene regulatory programs governing somatic development. We examined the poised (H3K4me3/H3K27me3 bivalent) epigenetic state in male germ cells from five mammalian and one avian species. We find that core genes poised in germ cells from multiple amniote species are ancient regulators of morphogenesis that sit at the top of transcriptional hierarchies controlling somatic tissue development, whereas genes that gain poising in germ cells from individual species act downstream of core poised genes during development in a species-specific fashion. We propose that critical regulators of animal development gained an epigenetically privileged state in germ cells, manifested in amniotes by H3K4me3/H3K27me3 poising, early in metazoan evolution.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Gene expression and chromatin state in the mammalian germ line.
Figure 2: The poised chromatin state in the mammalian germ line.
Figure 3: Core poised genes are conserved regulators of tissue patterning.
Figure 4: Gain of poising at genes with species-specific developmental roles.
Figure 5: Conservation of poising in the metazoan germ line.

Similar content being viewed by others

Accession codes

Primary accessions

Sequence Read Archive

Change history

  • 18 July 2016

    In the version of this article initially published online, the following callouts to supplementary items or main figure panels were incorrect: in the legend to Figure 1, the callout to Supplementary Figure 4 should have referred to Supplementary Figure 2; on page 4 of the PDF, the callout to Figure 4a should have also called out Figure 4b; on page 6 of the PDF, the callout to Supplementary Table 4 should have referred to Supplementary Table 5 and the callout to Supplementary Figure 9b should have referred to Supplementary Figure 10b; and on page 9 of the PDF, the callout to Supplementary Table 2 should have referred to Supplementary Data. The errors have been corrected for the print, PDF and HTML versions of this article.

References

  1. Kimmins, S. & Sassone-Corsi, P. Chromatin remodelling and epigenetic features of germ cells. Nature 434, 583–589 (2005).

    Article  CAS  PubMed  Google Scholar 

  2. Kurimoto, K. et al. Quantitative dynamics of chromatin remodeling during germ cell specification from mouse embryonic stem cells. Cell Stem Cell 16, 517–532 (2015).

    Article  CAS  PubMed  Google Scholar 

  3. Siklenka, K. et al. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science 350, aab2006 (2015).

    Article  CAS  PubMed  Google Scholar 

  4. Arico, J.K., Katz, D.J., van der Vlag, J. & Kelly, W.G. Epigenetic patterns maintained in early Caenorhabditis elegans embryos can be established by gene activity in the parental germ cells. PLoS Genet. 7, e1001391 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ihara, M. et al. Paternal poly (ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression. PLoS Genet. 10, e1004317 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. King, M.C. & Wilson, A.C. Evolution at two levels in humans and chimpanzees. Science 188, 107–116 (1975).

    Article  CAS  PubMed  Google Scholar 

  7. Wray, G.A. The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8, 206–216 (2007).

    Article  CAS  PubMed  Google Scholar 

  8. Cotney, J. et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154, 185–196 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Reilly, S.K. et al. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 347, 1155–1159 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Villar, D. et al. Enhancer evolution across 20 mammalian species. Cell 160, 554–566 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Prescott, S.L. et al. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell 163, 68–83 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).

    Article  CAS  PubMed  Google Scholar 

  13. Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Azuara, V. et al. Chromatin signatures of pluripotent cell lines. Nat. Cell Biol. 8, 532–538 (2006).

    Article  CAS  PubMed  Google Scholar 

  15. Soshnikova, N. & Duboule, D. Epigenetic temporal control of mouse Hox genes in vivo. Science 324, 1320–1323 (2009).

    Article  CAS  PubMed  Google Scholar 

  16. Noordermeer, D. et al. Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci. eLife 3, e02557 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Lesch, B.J., Dokshin, G.A., Young, R.A., McCarrey, J.R. & Page, D.C. A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis. Proc. Natl. Acad. Sci. USA 110, 16061–16066 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Sachs, M. et al. Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo. Cell Rep. 3, 1777–1784 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hammoud, S.S. et al. Distinctive chromatin in human sperm packages genes for embryo development. Nature 460, 473–478 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Erkek, S. et al. Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa. Nat. Struct. Mol. Biol. 20, 868–875 (2013).

    Article  CAS  PubMed  Google Scholar 

  21. Smith, C.M. et al. The mouse Gene Expression Database (GXD): 2014 update. Nucleic Acids Res. 42, D818–D824 (2014).

    Article  CAS  PubMed  Google Scholar 

  22. Richardson, L. et al. EMAGE mouse embryo spatial gene expression database: 2014 update. Nucleic Acids Res. 42, D835–D844 (2014).

    Article  CAS  PubMed  Google Scholar 

  23. Arda, H.E., Benitez, C.M. & Kim, S.K. Gene regulatory networks governing pancreas development. Dev. Cell 25, 5–13 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Oberdick, J. in Handbook of the Cerebellum and Cerebellar Disorders (eds. Manto, M., Schmahmann, J., Rossi, F., Gruol, D. & Koibuchi, N.) 127–145 (Springer Netherlands, 2013).

  25. Cripps, R.M. & Olson, E.N. Control of cardiac development by an evolutionarily conserved transcriptional network. Dev. Biol. 246, 14–28 (2002).

    Article  CAS  PubMed  Google Scholar 

  26. Olson, E.N. Gene regulatory networks in the evolution and development of the heart. Science 313, 1922–1927 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Arendt, D. & Nübler-Jung, K. Comparison of early nerve cord development in insects and vertebrates. Development 126, 2309–2325 (1999).

    CAS  PubMed  Google Scholar 

  28. van de Leemput, J. et al. CORTECON: a temporal transcriptome analysis of in vitro human cerebral cortex development from human embryonic stem cells. Neuron 83, 51–68 (2014).

    Article  CAS  PubMed  Google Scholar 

  29. Davidson, E.H. & Erwin, D.H. Gene regulatory networks and the evolution of animal body plans. Science 311, 796–800 (2006).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Bult, C.J. et al. Mouse genome database 2016. Nucleic Acids Res. 44 D1, D840–D847 (2016).

    Article  CAS  Google Scholar 

  32. Hou, Z.C. et al. Elephant transcriptome provides insights into the evolution of eutherian placentation. Genome Biol. Evol. 4, 713–725 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Ozawa, M. et al. Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst. BMC Dev. Biol. 12, 33 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Das, R. et al. DNMT1 and AIM1 imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation. BMC Genomics 14, 685 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Cáceres, M., Suwyn, C., Maddox, M., Thomas, J.W. & Preuss, T.M. Increased cortical expression of two synaptogenic thrombospondins in human brain evolution. Cereb. Cortex 17, 2312–2321 (2007).

    Article  PubMed  Google Scholar 

  36. Olivieri, G. & Miescher, G.C. Immunohistochemical localization of EphA5 in the adult human central nervous system. J. Histochem. Cytochem. 47, 855–861 (1999).

    Article  CAS  PubMed  Google Scholar 

  37. McGhee, S.A. & Chatila, T.A. DOCK8 immune deficiency as a model for primary cytoskeletal dysfunction. Dis. Markers 29, 151–156 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Soejima, M., Tachida, H., Ishida, T., Sano, A. & Koda, Y. Evidence for recent positive selection at the human AIM1 locus in a European population. Mol. Biol. Evol. 23, 179–188 (2006).

    Article  CAS  PubMed  Google Scholar 

  39. Liu, X. et al. Detecting signatures of positive selection associated with musical aptitude in the human genome. Sci. Rep. 6, 21198 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Capra, J.A., Erwin, G.D., McKinsey, G., Rubenstein, J.L. & Pollard, K.S. Many human accelerated regions are developmental enhancers. Phil. Trans. R. Soc. Lond. B 368, 20130025 (2013).

    Article  CAS  Google Scholar 

  41. Hedges, S.B., Marin, J., Suleski, M., Paymer, M. & Kumar, S. Tree of life reveals clock-like speciation and diversification. Mol. Biol. Evol. 32, 835–845 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Lynch, V.J. et al. Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals. Proc. Natl. Acad. Sci. USA 105, 14928–14933 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Krol, A.J. et al. Evolutionary plasticity of segmentation clock networks. Development 138, 2783–2792 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Zhang, X.M., Ramalho-Santos, M. & McMahon, A.P. Smoothened mutants reveal redundant roles for Shh and Ihh signaling including regulation of L/R asymmetry by the mouse node. Cell 105, 781–792 (2001).

    Article  CAS  PubMed  Google Scholar 

  45. Barrow, K.M., Ward, C.M., Rutter, J., Ali, S. & Stern, P.L. Embryonic expression of murine 5T4 oncofoetal antigen is associated with morphogenetic events at implantation and in developing epithelia. Dev. Dyn. 233, 1535–1545 (2005).

    Article  CAS  PubMed  Google Scholar 

  46. Sheng, G. & Foley, A.C. Diversification and conservation of the extraembryonic tissues in mediating nutrient uptake during amniote development. Ann. NY Acad. Sci. 1271, 97–103 (2012).

    Article  PubMed  Google Scholar 

  47. Wu, S.F., Zhang, H. & Cairns, B.R. Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome Res. 21, 578–589 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Chen, C. et al. Human neuronal calcium sensor-1 shows the highest expression level in cerebral cortex. Neurosci. Lett. 319, 67–70 (2002).

    Article  CAS  PubMed  Google Scholar 

  49. Brawand, D. et al. The evolution of gene expression levels in mammalian organs. Nature 478, 343–348 (2011).

    Article  CAS  PubMed  Google Scholar 

  50. El-Sharnouby, S., Redhouse, J. & White, R.A. Genome-wide and cell-specific epigenetic analysis challenges the role of polycomb in Drosophila spermatogenesis. PLoS Genet. 9, e1003842 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Arthur, R.K. et al. Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification. Genome Res. 24, 1115–1124 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Lesch, B.J. & Page, D.C. Poised chromatin in the mammalian germ line. Development 141, 3619–3626 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Brykczynska, U. et al. Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nat. Struct. Mol. Biol. 17, 679–687 (2010).

    Article  CAS  PubMed  Google Scholar 

  54. Fortunato, S. et al. Genome-wide analysis of the sox family in the calcareous sponge Sycon ciliatum: multiple genes with unique expression patterns. Evodevo 3, 14 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  56. Saudemont, A. et al. Complementary striped expression patterns of NK homeobox genes during segment formation in the annelid Platynereis. Dev. Biol. 317, 430–443 (2008).

    Article  CAS  PubMed  Google Scholar 

  57. Larroux, C. et al. Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity. Evol. Dev. 8, 150–173 (2006).

    Article  CAS  PubMed  Google Scholar 

  58. Larroux, C. et al. Genesis and expansion of metazoan transcription factor gene classes. Mol. Biol. Evol. 25, 980–996 (2008).

    Article  CAS  PubMed  Google Scholar 

  59. Bellvé, A.R. Purification, culture, and fractionation of spermatogenic cells. Methods Enzymol. 225, 84–113 (1993).

    Article  PubMed  Google Scholar 

  60. Shepherd, R.W., Millette, C.F. & DeWolf, W.C. Enrichment of primary pachytene spermatocytes from the human testes. Mol. Reprod. Dev. 4, 487–498 (1981).

    Google Scholar 

  61. Liu, Y. et al. Fractionation of human spermatogenic cells using STA-PUT gravity sedimentation and their miRNA profiling. Sci. Rep. 5, 8084 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Lam, D.M., Furrer, R. & Bruce, W.R. The separation, physical characterization, and differentiation kinetics of spermatogonial cells of the mouse. Proc. Natl. Acad. Sci. USA 65, 192–199 (1970).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Longo, F.J., Cook, S. & Baillie, R. Characterization of an acrosomal matrix protein in hamster and bovine spermatids and spermatozoa. Biol. Reprod. 42, 553–562 (1990).

    Article  CAS  PubMed  Google Scholar 

  64. Chan, J. et al. Characterization of the CDKN2A and ARF genes in UV-induced melanocytic hyperplasias and melanomas of an opossum (Monodelphis domestica). Mol. Carcinog. 31, 16–26 (2001).

    Article  CAS  PubMed  Google Scholar 

  65. Oliva, R., Mezquita, J., Mezquita, C. & Dixon, G.H. Haploid expression of the rooster protamine mRNA in the postmeiotic stages of spermatogenesis. Dev. Biol. 125, 332–340 (1988).

    Article  CAS  PubMed  Google Scholar 

  66. Egelhofer, T.A. et al. An assessment of histone-modification antibody quality. Nat. Struct. Mol. Biol. 18, 91–93 (2011).

    Article  CAS  PubMed  Google Scholar 

  67. Liu, Y. et al. Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Res. 39, 1408–1418 (2011).

    Article  CAS  PubMed  Google Scholar 

  68. Goldberg, A.D. et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140, 678–691 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Guenther, M.G. et al. Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 7, 249–257 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Shpargel, K.B., Starmer, J., Yee, D., Pohlers, M. & Magnuson, T. KDM6 demethylase independent loss of histone H3 lysine 27 trimethylation during early embryonic development. PLoS Genet. 10, e1004507 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Mitra, A. et al. Marek's disease virus infection induces widespread differential chromatin marks in inbred chicken lines. BMC Genomics 13, 557 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Rebollo, R. et al. A snapshot of histone modifications within transposable elements in Drosophila wild type strains. PLoS One 7, e44253 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Yates, A. et al. Ensembl 2016. Nucleic Acids Res. 44 D1, D710–D716 (2016).

    Article  CAS  Google Scholar 

  77. Zhao, H. et al. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics 30, 1006–1007 (2014).

    Article  CAS  PubMed  Google Scholar 

  78. Anders, S., Pyl, P.T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

    Article  CAS  PubMed  Google Scholar 

  79. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Durinck, S. et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21, 3439–3440 (2005).

    Article  CAS  PubMed  Google Scholar 

  81. Falcon, S. & Gentleman, R. Using GOstats to test gene lists for GO term association. Bioinformatics 23, 257–258 (2007).

    Article  CAS  PubMed  Google Scholar 

  82. Wingender, E., Schoeps, T. & Dönitz, J. TFClass: an expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165–D170 (2013).

    Article  CAS  PubMed  Google Scholar 

  83. Bailey, T.L. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27, 1653–1659 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. McLeay, R.C. & Bailey, T.L. Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics 11, 165 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Gupta, S., Stamatoyannopoulos, J.A., Bailey, T.L. & Noble, W.S. Quantifying similarity between motifs. Genome Biol. 8, R24 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Mathelier, A. et al. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 44 D1, D110–D115 (2016).

    Article  CAS  Google Scholar 

  87. Badis, G. et al. Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720–1723 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Berger, M.F. et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133, 1266–1276 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Hume, M.A., Barrera, L.A., Gisselbrecht, S.S. & Bulyk, M.L. UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions. Nucleic Acids Res. 43, D117–D122 (2015).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank H. Skaletsky for statistical advice and analysis; R. Young for advice on ChIP-seq analysis and critical reading of the manuscript; and P. Reddien for critical reading of the manuscript. This project was funded by an HHMI award to D.C.P., by a Hope Funds for Cancer Research postdoctoral fellowship to B.J.L., and by a Burroughs-Wellcome Career Award to B.J.L.

Author information

Authors and Affiliations

  1. Whitehead Institute, Cambridge, Massachusetts, USA

    Bluma J Lesch & David C Page

  2. Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, Missouri, USA

    Sherman J Silber

  3. Department of Biology, University of Texas at San Antonio, San Antonio, Texas, USA

    John R McCarrey

  4. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    David C Page

  5. Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, USA

    David C Page

Authors
  1. Bluma J Lesch
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sherman J Silber
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John R McCarrey
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. David C Page
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

B.J.L. designed the project, conducted experiments, analyzed data, and wrote the manuscript. D.C.P. designed the project and wrote the manuscript. S.J.S. provided human testis samples and contributed to writing the manuscript. J.R.M. isolated germ cells for all samples and contributed to writing the manuscript.

Corresponding author

Correspondence to David C Page.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Assessment of sample purity and quality.

(a) Hematoxylin and eosin staining of formaldehyde-fixed, paraffin-embedded sections from a human testis biopsy collected concurrently with the sample used for cell sorting. Left, 10× magnification; right, 40× magnification of the boxed region at left. (b) Phase-contrast microscopy images of dissociated spermatogenic cells before StaPut and of sorted pachytene spermatocyte and round spermatid populations after StaPut. All images are shown at 40× magnification. A small population of contaminating red blood cells, which do not contain chromatin, was present in the human round spermatid sample shown (arrows). (c) Numbers of sorted cells (of a total of 100) from the fractions shown that are identifiable as belonging to the reported cell type population in each fraction.

Supplementary Figure 2 Correspondence between H3K4me3, H3K27me3, and expression levels.

(a–e) Heat maps showing mean expression level as a function of H3K4me3 and H3K27me3 quantile, as shown in Figure 1b. Each pachytene spermatocyte and round spermatid sample is shown separately for human (a), rhesus (b), mouse (c), bull (d), and opossum (e). The plots for human replicate 2 are identical to those shown in Figure 1b and are reproduced here for comparison.

Supplementary Figure 3 Correlations between biological replicates.

(a) Correlation of normalized, input-subtracted ChIP-seq signal or normalized RNA-seq counts by gene. Pearson’s correlation coefficient (r) is shown for each. P < 2.2 × 10−16 for all correlations. (b) Overlap between poised gene sets called for each human, rhesus, mouse, or opossum replicate.

Supplementary Figure 4 Principal-component and clustering analysis of H3K4me3, H3K27me3, and RNA-seq data.

(a) Principal-component analysis. Axes represent the first two principal components, labeled with the percentage of total variance explained by each. Left, H3K4me3 signal; middle, H3K27me3 signal; right, expression (FPKM). (b) Clustering of H3K4me3 data with and without inclusion of an outlier data set. Top, clustering of H3K4me3 data reproduced from Figure 1c; bottom, the same clustering analysis after removal of the pachytene sample from human replicate 1 (“human 1 p.s.”), the least well correlated of the biological replicates. Removal of the outlier does not alter the clustering result.

Supplementary Figure 5 Effect of changing ChIP and expression thresholds on the number of poised genes called.

(a) Top left, numbers of five-mammal poised genes called as expression and ChIP thresholds vary; H3K4me3 and H3K27me3 thresholds are set as equal in all conditions. Top right, numbers of five-mammal poised genes called as H3K4me3 and H3K27me3 thresholds vary relative to each other; the expression threshold is held constant at FPKM ≤ 5. Dashed lines show the gene space included by the criteria used in this study. Bottom, example values for numbers of five-mammal poised genes called using different combinations of H3K4me3, H3K27me3, and expression thresholds. (b) Numbers of genes meeting each threshold independently (expression, H3K4me3, or H3K27me3) in each sample. (c) Numbers of poised genes for each overlap condition among five mammalian species.

Source data

Supplementary Figure 6 Effect of changing ChIP and expression thresholds on the number of poised genes called in only one of five mammalian species.

(a) Left, total numbers of species-specific poised genes called as H3K4me3 and H3K27me3 ChIP thresholds vary; the expression threshold is held constant at FPKM ≤ 5. The red dashed line on the plot shows the gene space included by the criteria in this study. Right, sample values for numbers of total species-specific poised genes called using different combinations of H3K4me3, H3K27me3, and expression thresholds. (b) Numbers of species-specific poised genes called for individual species as H3K4me3 and H3K27me3 ChIP thresholds vary, with the expression threshold held constant at FPKM ≤ 5.

Supplementary Figure 7 ChIP signal at sequential ChIP–qPCR targets.

(a) Input-subtracted ChIP signal tracks for the promoters targeted in mouse sequential ChIP–qPCR experiments (Fig. 2c). (b) Input-subtracted ChIP signal tracks for the promoters targeted in opossum sequential ChIP–qPCR experiments (Fig. 2d).

Supplementary Figure 8 Characteristics of core poised genes.

(a) Distribution of core poised genes on human chromosomes. Top, absolute numbers of poised genes on each human chromosome; middle, numbers of poised genes corrected for chromosome length; bottom, numbers of poised genes corrected for chromosome gene density, expressed as the percentage of all genes on the chromosome that are poised. (b) Conservation of promoter regions (1 kb upstream of the transcription start site) for human core poised genes, human genes with conserved retention of H3K27me3 only, human-specific poised genes, and all other genes. Horizontal bars represent the median. ***P < 0.001 by two-sided Welch t test. phastCons score is derived from multiple alignments of 99 vertebrate genomes to the human genome. (c) Class distribution of all transcription factors encoded in the human genome (compare to Fig. 3b).

Source data

Supplementary Figure 9 Additional examples of genes poised specifically in only one of five mammalian species.

(a) Human-specific poised genes. HIPK2 has gained a human-specific enhancer that functions in early limb development8. ITGB2 exhibits human-specific gain of active chromatin at its promoter in developing brain9. LMF1 is expressed in human but not mouse or bull placenta32. (b) Mouse-specific poised gene. Smug1 is expressed in mouse but not human or bovine placenta32. For HIPK2, ITGB2, and LMF1, only the region surrounding the TSS is shown to fit all tracks on the same page.

Supplementary Figure 10 Poised genes in Drosophila germ cells and in human and mouse spermatozoa.

(a) Polycomb enrichment at orthologs of five-mammal poised genes in the Drosophila melanogaster germ line. ChIP–microarray data are from ref. 50. P value was calculated by two-sided Welch t test. (b) Fraction of poised genes marked by both H3K4me3 and H3K27me3 in mature human and mouse spermatozoa. Data are from ref. 19 (human) and ref. 20 (mouse). ***P < 1 × 10−15 (Fisher’s exact test).

Source data

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10, Supplementary Note and Supplementary Table 10. (PDF 3986 kb)

Supplementary Table 1

Summary of Illumina libraries and alignments. (XLSX 47 kb)

Supplementary Table 2

Poised genes by species. (XLSX 318 kb)

Supplementary Table 3

Two-way poised gene overlaps. (XLSX 46 kb)

Supplementary Table 4

Core poised genes and assigned protein function categories. (XLSX 63 kb)

Supplementary Table 5

GO category enrichments. (XLSX 387 kb)

Supplementary Table 6

Genes poised in only one of five mammalian species. (XLSX 115 kb)

Supplementary Table 7

Motifs gained in promoters of genes poised in only one of five mammalian species. (XLSX 57 kb)

Supplementary Table 8

Poised gene set overlaps among five mammalian species. (XLSX 49 kb)

Supplementary Table 9

Poised genes in chicken male germ cells and gene set overlaps among six amniote species. (XLSX 218 kb)

Supplementary Data

Tab-delimited text files containing input data. (ZIP 8609 kb)

Supplementary Code

R scripts used for analyses in the manuscript. (ZIP 20 kb)

Source data

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lesch, B., Silber, S., McCarrey, J. et al. Parallel evolution of male germline epigenetic poising and somatic development in animals. Nat Genet 48, 888–894 (2016). https://doi.org/10.1038/ng.3591

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3591

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing