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Systems Analysis of Chromatin-Related Protein Complexes in Cancer pp 177–196Cite as

Quantitative Proteomics Characterization of Chromatin-Remodeling Complexes in Health and Disease

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Abstract

Recent advances in the field of chromatin remodeling have elucidated its role in various cellular processes beyond transcription. The intricate dynamics and interplay between several chromatin-remodeling complexes has been shown to be responsible for events ranging from cell differentiation, epigenetic regulation, and human diseases. One of the biggest challenges in understanding the function of these large protein complexes is dissecting their assembly, interactions with other proteins, and identifying the role of individual components. Technological advances in quantitative proteomics make it one of the most sought after technique in identifying and analyzing multiprotein complexes and posttranslational modifications. In particular, multidimensional protein identification technology and spectral counting-based quantitative proteomic analysis is a popular choice for analyzing chromatin remodeling complexes. The reason being they are straightforward approaches and are able to identify and quantify low abundant proteins in a label-free manner. This chapter highlights the recent findings of chromatin-remodeling complexes with respect to cellular processes and disease states and the role of quantitative proteomics has played in these findings.

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Abbreviations

CTCL:

Cutaneous T cell lymphoma

Da:

Daltons

dNSAF:

Distributed normalized spectral abundance factors

DSB:

Double-strand break

ESI:

Electron spray ionization

HATs:

Histone acetyltransferases

HPLC:

High-performance liquid chromatography

ICAT:

Isotope coded affinity tag

iTRAQ:

Isobaric tags for absolute and relative quantitation

LC:

Liquid chromatography

MS:

Mass spectrometry

MudPIT:

Multidimensional protein identification technology

m/z :

Mass to charge

NSAF:

Normalized spectral abundance factor

PFL:

Protein frequency library

PTMs:

Posttranslational modifications

rDNA:

Ribosomal DNA

RP:

Reversed phase

SAHA:

Suberoylanilide hydroxamic acid

SCX:

Strong cation exchange

SILAC:

Stable isotope labeling by amino acids in cell culture

SNAP:

SILAC nucleosome affinity purifications

TAP:

Tandem affinity purification

TMT:

Tandem mass tags

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Acknowledgments

The authors would like to thank the members of Washburn laboratory for critical reading of the manuscript and thoughtful insights. This work was supported by the Stowers Institute for Medical Research.

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Authors and Affiliations

  1. Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA

    Mahadevan Lakshminarasimhan Ph.D. & Michael P. Washburn Ph.D.

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  1. Mahadevan Lakshminarasimhan Ph.D.
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  2. Michael P. Washburn Ph.D.
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Correspondence to Michael P. Washburn Ph.D. .

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Editors and Affiliations

  1. Banting & Best Dept. Medical Research, University of Toronto Donnelly Ctr Cell. & Biomolecular Res., Toronto, Ontario, Canada

    Andrew Emili

  2. University of Toronto Terrence Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada

    Jack Greenblatt

  3. Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario, Canada

    Shoshana Wodak

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Lakshminarasimhan, M., Washburn, M.P. (2014). Quantitative Proteomics Characterization of Chromatin-Remodeling Complexes in Health and Disease. In: Emili, A., Greenblatt, J., Wodak, S. (eds) Systems Analysis of Chromatin-Related Protein Complexes in Cancer. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7931-4_9

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