Phylogenetic Analysis of Cell Types Using Histone Modifications

  • Nishanth Ulhas Nair
  • Yu Lin
  • Philipp Bucher
  • Bernard M. E. Moret
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8126)

Abstract

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the differentiation process. In this paper, we present a simple analysis of cell types and differentiation paths using phylogenetic inference based on ChIP-Seq histone modification data. We propose new data representation techniques and new distance measures for ChIP-Seq data and use these together with standard phylogenetic inference methods to build biologically meaningful trees that indicate how diverse types of cells are related. We demonstrate our approach on H3K4me3 and H3K27me3 data for 37 and 13 types of cells respectively, using the dataset to explore various issues surrounding replicate data, variability between cells of the same type, and robustness. The promising results we obtain point the way to a new approach to the study of cell differentiation.

Keywords

cell differentiation cell type epigenomics histone modifications phylogenetics 

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References

  1. 1.
  2. 2.
    Barski, A., et al.: High-resolution profiling of histone methylations in the human genome. Cell 129(4), 823–837 (2007)CrossRefGoogle Scholar
  3. 3.
    Berger, S.L.: Histone modifications in transcriptional regulation. Current Opinion in Genetics & Development 12(2), 142–148 (2002)CrossRefGoogle Scholar
  4. 4.
    Desper, R., Gascuel, O.: Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 357–374. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  5. 5.
    Project Consortium ENCODE: A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9(4), e1001046 (2011)Google Scholar
  6. 6.
    Fishburn, P.C.: Interval orders and interval graphs: A study of partially ordered sets. Wiley New York (1985)Google Scholar
  7. 7.
    Goloboff, P.A.: Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15(4), 415–428 (1999)CrossRefGoogle Scholar
  8. 8.
    Lee, J.-H., Hart, S.R., Skalnik, D.G.: Histone deacetylase activity is required for embryonic stem cell differentiation. Genesis 38(1), 32–38 (2004)CrossRefGoogle Scholar
  9. 9.
    Lister, R., et al.: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471(7336), 68–73 (2011)CrossRefGoogle Scholar
  10. 10.
    Lobe, C.G.: Transcription factors and mammalian development. Current Topics in Developmental Biology 27, 351–351 (1992)CrossRefGoogle Scholar
  11. 11.
    Mardis, E.R., et al.: ChIP-seq: welcome to the new frontier. Nature Methods 4(8), 613–613 (2007)CrossRefGoogle Scholar
  12. 12.
    Martin, C., Zhang, Y.: Mechanisms of epigenetic inheritance. Current Opinions Cell Biology 3(19), 266–272 (2007)CrossRefGoogle Scholar
  13. 13.
    Mikkelsen, T.S., et al.: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153), 553–560 (2007)CrossRefGoogle Scholar
  14. 14.
    Nelson, D.L., Cox, M.M.: Lehninger principles of biochemistry. W.H. Freeman (2010)Google Scholar
  15. 15.
    Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4), 406–425 (1987)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Nishanth Ulhas Nair
    • 1
  • Yu Lin
    • 1
  • Philipp Bucher
    • 2
  • Bernard M. E. Moret
    • 1
  1. 1.School of Computer and Communication SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
  2. 2.School of Life SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland

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