We report flow cytometric protocols that quantitatively display the levels of different histone modifications on the single cell level. This method allows the rapid and simultaneous analysis of the global levels of chromatin marks in combination with other flow cytometric features. We show that chromatin flow cytometry identifies changes in epigenetic marks, such as histone acetylation and methylation, in drug-treated and differentiated mouse embryonic stem cell populations.

Baerlocher, G.M., I. Vulto, G. de Jong, P.M. Lansdorp (2006) Flow cytometry and FISH to measure the average length of telomeres (flow FISH). Nat Protoc 1: 2365–2376.
Berger, S.L. (2007) The complex language of chromatin regulation during transcription. Nature 447: 407–412.
Brambrink, T., R. Foreman, G.G. Welstead, C.J. Lengner, M. Wernig, H. Suh, R. Jaenisch (2008) Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. Cell Stem Cells 2: 151–159.
Cao, R., L. Wang, H. Wang, L. Xia, H. Erdjument-Bromage, P. Tempst, R.S. Jones, Y. Zhang (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298: 1039–1043.
Cui, L., K. Johkura, F. Yue, N. Ogiwara, Y. Okouchi, K. Asanuma, K. Sasaki (2004) Spatial distribution and initial changes of SSEA-1 and other cell adhesion-related molecules on mouse embryonic stem cells before and during differentiation. J Histochem Cytochem 52: 1447–1457.
Dai, B., T.P. Rasmussen (2007) Global epiproteomic signatures distinguish embryonic stem cells from differentiated cells. Stem Cells 25: 2567–2574.
Doan, L.L., M.K. Tanner, H.L. Grimes (2003) Intranuclear staining of proteins in heterogeneous cell populations and verification of nuclear localization by flow cytometric analysis. J Immunol Methods 279: 193–198.
Fischle, W. (2008) Talk is cheap – cross-talk in establishment, maintenance, and readout of chromatin modifications. Genes Dev 22: 3375–3382.
Gernez, Y., L.A. Herzenberg, L.A. Herzenberg, R. Tirouvanziam (2007) Phospho-FACS: a powerful tool for exploring intracellular transduction cascades. Rev Mal Respir 24: 955–964.
Hasbold, J., P.D. Hodgkin (2000) Flow cytometric cell division tracking using nuclei. Cytometry 40: 230–237.
Kubicek, S., R.J. O’Sullivan, E.M. August, E.R. Hickey, Q. Zhang, M.L. Teodoro, S. Rea, K. Mechtler, J.A. Kowalski, C.A. Homon, T.A. Kelly, T. Jenuwein (2007) Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase. Mol Cell 25: 473–481.
Lo, W.S., K.W. Henry, M.F. Schwartz, S.L. Berger (2004) Histone modification patterns during gene activation. Methods Enzymol 377: 130–153.
Meshorer, E., D. Yellajoshula, E. George, P.J. Scambler, D.T. Brown, T. Misteli (2006) Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev Cell 10: 105–110.
Nightingale, K.P., S. Gendreizig, D.A. White, C. Bradbury, F. Hollfelder, B.M. Turner (2007) Cross-talk between histone modifications in response to histone deacetylase inhibitors: MLL4 links histone H3 acetylation and histone H3K4 methylation. J Biol Chem 282: 4408–4416.
Ronzoni, S., M. Faretta, M. Ballarini, P. Pelicci, S. Minucci (2005) New method to detect histone acetylation levels by flow cytometry. Cytometry A 66: 52–61.
Schoeftner, S., A.K. Sengupta, S. Kubicek, K. Mechtler, L. Spahn, H. Koseki, T. Jenuwein, A. Wutz (2006) Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J 25: 3110–3122.
Schones, D.E., K. Zhao (2008) Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9: 179–191.
Spivakov, M., A.G. Fisher (2007) Epigenetic signatures of stem-cell identity. Nat Rev Genet 8: 263–271.
Copyright / Drug Dosage / Disclaimer
Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.
You do not currently have access to this content.