Histone Methyltransferases: Methods and Protocols

ISBN-13: 9781071624807 / Angielski / Twarda / 2022

Margueron, Raphaël

Opis

This volume provides methods used to investigate histone methyltransferase function. Chapters guide readers through a comprehensive set of approaches that detail phylogenetic diversity, histone demethylase activities in vitro, generating chromatin substrates, auto-methylation, quantification of metabolites, protein purification, crystallization, X-ray structure, cryogenic electron microscopy, assessing genome-wide patterns, CUT&Tag in mouse embryonic tissues, chemical biology approaches, peptide SPOT arrays, nascent chromatin capture, ectopic protein tethering, computational models, and development of methyltransferase inhibitors. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Histone Methyltransferases: Methods and Protocols aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

Spis treści

Part I: Introduction and biological context

1.      Not all is SET for methylation: Evolution of eukaryotic protein methyltransferases

Allyson A. Erlendson and Michael Freitag

 

Part II: In vitro Enzymatic Assays

2.      Detection and quantification of histone methyltransferase activity in vitro

Nwamaka J. Idigo and Philipp Voigt

 

3.      In Vitro Histone Demethylase Assays

Shengjiang Tu

 

Part III: Exploring the regulation of histone methyltransferase enzymatic activity

4.      Preparation and characterization of chromatin templates for histone methylation assays

Cuifang Liu, Jicheng Zhao, and Guohong Li

 

5.      Techniques to study automethylation of histone methyltransferases and its functional impact

Luis Popoca and Chul-Hwan Lee

 

6.      Rodriguez Profiling the regulation of histone methylation and demethylation by metabolites and metals

Sebastian Müller, Fabien Sindikubwabo, Tatiana Cañeque, and Raphaël

 

Part IV: Structural investigation of histone methyltransferases

7.      Determination of histone methyltransferase structure by crystallography

Jon R. Wilson

 

8.      Determination of histone methyltransferase structures in complex with the nucleosome by cryogenic electron microscopy

Cathy J. Spangler & Robert K. McGinty

 

Part V: Analysis of histone methylation in cells and genomes

9.      Development and validation of antibodies targeting site-specific histone methylation

Lara Zorro Shahidian and Sylvain Daujat

 

10.  Genetic, genomic and imaging approaches to dissect the role of Polycomb group epigenetic regulators in mice

Nayuta Yakushiji-Kaminatsui, Takashi Kondo, Yasuhide Ohinata, Junichiro Takano, and Haruhiko Koseki

 

11.  Profiling histone methylation in low numbers of cells

Julie Brind’Amour and Matthew Lorincz

 

12.  Automated CUT&RUN using the KingFisher Duo Prime

Setareh Aflaki, Raphaël Margueron, and Daniel Holoch

 

13.  Bioinformatics methods for ChIP-seq histone analysis

Nicolas Servant

Part VI: Discovery of histone methyltransferase substrates and methylated histone interactors

14.  Characterization of SET-domain histone lysine methyltransferase substrates using a cofactor S-adenosyl-L-methionine surrogate

Alexandre Désert, Karine Guitot, Audrey Michaud, Daniel Holoch, Raphaël Margueron, Fabienne Burlina, and Dominique Guianvarc’h

 

15.  Specificity analysis of protein methyltransferases and discovery of novel substrates using SPOT peptide arrays

Sara Weirich and Albert Jeltsch

 

16.  Identifying specific protein interactors of nucleosomes carrying methylated histones using mass spectrometr

Andrey Tvardovskiy, Nhuong Nguyen, and Till Bartke

 

Part VII: Inheritance of histone methylation patterns

17.  Investigating mitotic inheritance of histone post-translational modifications by triple pSILAC coupled to Nascent Chromatin Capture

Kyosuke Nakamura, Anja Groth, and Constance Alabert

 

18.  Investigating mitotic inheritance of histone modifications using tethering

Ajay Larkin, Amanda Ames, Melissa Seman, and Kaushik Ragunathan

 

19.  Investigating histone modification dynamics by mechanistic computational modelling

Govind Menon and Martin Howard

 

Part VIII: Finding inhibitors of histone methyltransferases

20.  Screening for small molecule inhibitors of histone methyltransferases

Nico Cantone, Richard T. Cummings, and Patrick Trojer