Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry

Proceedings of the National Academy of Sciences of the United States of America
Barry M ZeeMitzi I Kuroda

Abstract

Posttranslational modifications (PTMs) are key contributors to chromatin function. The ability to comprehensively link specific histone PTMs with specific chromatin factors would be an important advance in understanding the functions and genomic targeting mechanisms of those factors. We recently introduced a cross-linked affinity technique, BioTAP-XL, to identify chromatin-bound protein interactions that can be difficult to capture with native affinity techniques. However, BioTAP-XL was not strictly compatible with similarly comprehensive analyses of associated histone PTMs. Here we advance BioTAP-XL by demonstrating the ability to quantify histone PTMs linked to specific chromatin factors in parallel with the ability to identify nonhistone binding partners. Furthermore we demonstrate that the initially published quantity of starting material can be scaled down orders of magnitude without loss in proteomic sensitivity. We also integrate hydrophilic interaction chromatography to mitigate detergent carryover and improve liquid chromatography-mass spectrometric performance. In summary, we greatly extend the practicality of BioTAP-XL to enable comprehensive identification of protein complexes and their local chromatin environment.

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Citations

Sep 13, 2017·Expert Review of Proteomics·Cassandra G EubanksMichael P Washburn
Jul 13, 2016·Human Molecular Genetics·Michael Wierer, Matthias Mann
Jul 14, 2018·PeerJ·Saniya DeshmukhDeepti Deobagkar
Feb 9, 2021·Molecular & Cellular Proteomics : MCP·Guido van Mierlo, Michiel Vermeulen
Oct 17, 2020·Molecular & Cellular Proteomics : MCP·Guido van Mierlo, Michiel Vermeulen
Sep 28, 2017·Journal of Proteome Research·Malte SielaffUte Distler

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