DamID-seq: A genome-wide DNA methylation method that captures both transient and stable TF-DNA interactions in plant cells

Authors: ALVAREZ, JOSE - Universidad Andres Bello (UNAB); HINCKLEY, WILL - New York University; LEONELLI, LAURIEBETH - University Of Illinois; Brooks, Matthew; CORUZZI, GLORIA - New York University

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 9/24/2022
Publication Date: 9/9/2023
Citation: Alvarez, J.M., Hinckley, W., Leonelli, L., Brooks, M.D., Coruzzi, G.M. 2023. DamID-seq: A genome-wide DNA methylation method that captures both transient and stable TF-DNA interactions in plant cells. Book Chapter. p. 87-107. https://doi.org/10.1007/978-1-0716-3354-0.
DOI: https://doi.org/10.1007/978-1-0716-3354-0

Interpretive Summary:

Technical Abstract: Capturing the dynamic and transient interactions of a transcription factor (TF) and its genome-wide targets whose regulation leads to plants adaptation to their changing environment is a major technical challenge. We describe how a DNA adenine methyltransferase identification and sequencing (DamID-seq) approach can be used to capture both transient and stable TF-target interactions by DNA methylation. The DamID technique uses a TF-fusion protein to a DNA adenine methyltransferase (Dam) from E. coli. When expressed in a plant cell, the Dam-TF fusion protein will methylate adenine bases near the sites of TF-DNA interactions. In this way, DamID can leave a permanent stable DNA methylation mark on gene promoters, even if the target gene is only transiently “touched” by the Dam-TF fusion protein. In this paper, we provide a step-by-step protocol to perform DamID-seq experiments in isolated plant cells for any Dam-TF fusion protein of interest. The example in this chapter is for Arabidopsis thaliana, however the DamID-seq workflow is broadly applicable to other plants and organisms.