Genome-Wide Mapping and Microscopy Visualization of Protein–DNA Interactions by pA-DamID

Tom van Schaik, Stefano G. Manzo, Bas van Steensel*

*Corresponding author for this work

Research output: Chapter/Conference proceedingChapterAcademic

1 Citation (Scopus)
4 Downloads (Pure)

Abstract

Several methods have been developed to map protein–DNA interactions genome-wide in the last decades. Protein A-DamID (pA-DamID) is a recent addition to this list with distinct advantages. pA-DamID relies on antibody-based targeting of the bacterial Dam enzyme, resulting in adenine methylation of DNA in contact with the protein of interest. This m6A can then be visualized by microscopy, or mapped genome-wide. The main advantages of pA-DamID are an easy and direct visualization of DNA that is in contact with the protein of interest, unbiased mapping of protein–DNA interactions, and the possibility to select specific subpopulations of cells by flow cytometry before further sample processing. pA-DamID is particularly suited to study proteins that form large chromatin domains or that are part of distinct nuclear structures such as the nuclear lamina. This chapter describes the pA-DamID procedure from cell harvesting to the preparation of microscopy slides and high-throughput sequencing libraries.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
Chapter12
Pages215-229
Number of pages15
Volume2458
DOIs
Publication statusPublished - 1 Jan 2022

Publication series

SeriesMethods in Molecular Biology
Volume2458
ISSN1064-3745

Bibliographical note

Acknowledgments:
This work was supported by NIH Common Fund “4D Nucleome”
Program grant U54DK107965 (BvS), AIRC-MSCA iCARE2.0
fellowship grant agreement 800924 (SGM) and MSCA Individual
fellowship project number 838555 (SGM). The Oncode Institute
is supported by KWF Dutch Cancer Society.

Publisher Copyright:
© 2022, The Author(s).

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