Single-molecule tools elucidate H2A.Z nucleosome composition

Jiji Chen, Birck Nanotechnology Center, Purdue University
Andrew Miller, Purdue University
Ann L. Kirchmaier, Purdue University
Joseph M.K. Irudayaraj, Birck Nanotechnology Center, Purdue University

Date of this Version



Jiji Chen, Andrew Miller, Ann L. Kirchmaier, Joseph M. K. Irudayaraj J Cell Sci 2012 125: 2954-2964; doi: 10.1242/jcs.101592


Copyright 2012. Jiji Chen, Andrew Miller, Ann L. Kirchmaier , Joseph M.K. Irudayaraj.

This article was first published in the Journal of Cell Science and is available online at:

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Although distinct epigenetic marks correlate with different chromatin states, how they are integrated within single nucleosomes to generate combinatorial signals remains largely unknown. We report the successful implementation of single molecule tools constituting fluorescence correlation spectroscopy (FCS), pulse interleave excitation-based Forster resonance energy transfer (PIE-FRET) and fluorescence lifetime imaging-based FRET (FLIM-FRET) to elucidate the composition of single nucleosomes containing histone variant H2A.Z (Htz1p in yeast) in vitro and in vivo. We demonstrate that yeast nucleosomes containing Htz1p are primarily composed of H4 K12ac and H3 K4me3 but not H3 K36me3 and that these patterns are conserved in mammalian cells. Quantification of epigenetic modifications in nucleosomes will provide a new dimension to epigenetics research and lead to a better understanding of how these patterns contribute to the targeting of chromatin-binding proteins and chromatin structure during gene regulation.


Nanoscience and Nanotechnology