Accurate identification of centromere locations in yeast genomes using Hi-C

Nelle Varoquaux, Ivan Liachko, Ferhat Ay, Joshua N. Burton, Jay Shendure, Maitreya J. Dunham, Jean Philippe Vert, William S. Noble*

*Corresponding author for this work

    Research output: Contribution to journalArticle

    19 Scopus citations

    Abstract

    Centromeres are essential for proper chromosome segregation. Despite extensive research, centromere locations in yeast genomes remain difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation capture assay, Hi-C, has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single genome from Hi-C data by exploiting the centromeres' tendency to cluster in three-dimensional space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use Centurion to infer centromere locations in 14 yeast species. Across all microbes that we consider, Centurion predicts 89% of centromeres within 5 kb of their known locations. We also demonstrate the robustness of the approach in datasets with low sequencing depth. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results show that Centurion can be used for centromere identification for diverse species of yeast and possibly other microorganisms.

    Original languageEnglish (US)
    Pages (from-to)5331-5339
    Number of pages9
    JournalNucleic acids research
    Volume43
    Issue number11
    DOIs
    StatePublished - Apr 17 2015

    ASJC Scopus subject areas

    • Genetics

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  • Cite this

    Varoquaux, N., Liachko, I., Ay, F., Burton, J. N., Shendure, J., Dunham, M. J., Vert, J. P., & Noble, W. S. (2015). Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic acids research, 43(11), 5331-5339. https://doi.org/10.1093/nar/gkv424