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.

Genome-Wide Mapping and Microscopy Visualization of Protein-DNA Interactions by pA-DamID / T. van Schaik, S.G. Manzo, B. van Steensel (METHODS IN MOLECULAR BIOLOGY). - In: Chromatin / [a cura di] J. Horsfield, J. Marsman. - [s.l] : Springer, 2022. - ISBN 978-1-0716-2139-4. - pp. 215-229 [10.1007/978-1-0716-2140-0_12]

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

S.G. Manzo
Secondo
;
2022

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.
English
Chromatin; Fluorescence microscopy; Genome-wide mapping; High-throughput sequencing; Nuclear lamina; Protein A-DamID (pA-DamID); Protein–DNA interactions; m6A-tracer
Settore BIO/11 - Biologia Molecolare
Capitolo o Saggio
Sì, ma tipo non specificato
Pubblicazione scientifica
Chromatin
J. Horsfield, J. Marsman
Springer
2022
215
229
15
978-1-0716-2139-4
978-1-0716-2140-0
2458
Volume a diffusione internazionale
Gold
pubmed
scopus
crossref
datacite
Aderisco
T. van Schaik, S.G. Manzo, B. van Steensel
Book Part (author)
open
268
Genome-Wide Mapping and Microscopy Visualization of Protein-DNA Interactions by pA-DamID / T. van Schaik, S.G. Manzo, B. van Steensel (METHODS IN MOLECULAR BIOLOGY). - In: Chromatin / [a cura di] J. Horsfield, J. Marsman. - [s.l] : Springer, 2022. - ISBN 978-1-0716-2139-4. - pp. 215-229 [10.1007/978-1-0716-2140-0_12]
info:eu-repo/semantics/bookPart
3
Prodotti della ricerca::03 - Contributo in volume
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/956622
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