PUB-NChIP--"in Vivo Biotinylation" Approach to Study Chromatin in Proximity to a Protein of Interest

Overview

Journal Genome Res

Specialty Genetics

Date 2012 Oct 6

PMID 23038767

Citations 14

Authors

Muhammad Shoaib

Arman Kulyyassov

Chloe Robin

Kinga Winczura

Pavel Tarlykov

Emmanuelle Despas

Patricia Kannouche

Erlan Ramanculov

Marc Lipinski

Vasily Ogryzko

Affiliations

Soon will be listed here.

Abstract

We have developed an approach termed PUB-NChIP (proximity utilizing biotinylation with native ChIP) to purify and study the protein composition of chromatin in proximity to a nuclear protein of interest. It is based on coexpression of (1) a protein of interest, fused with the bacterial biotin ligase BirA, together with (2) a histone fused to a biotin acceptor peptide (BAP), which is specifically biotinylated by BirA-fusion in the proximity of the protein of interest. Using the RAD18 protein as a model, we demonstrate that the RAD18-proximal chromatin is enriched in some H4 acetylated species. Moreover, the RAD18-proximal chromatin containing a replacement histone H2AZ has a different pattern of H4 acetylation. Finally, biotin pulse-chase experiments show that the H4 acetylation pattern starts to resemble the acetylation pattern of total H4 after the proximity of chromatin to RAD18 has been lost.

Citing Articles

Detection of Recombinant Proteins SOX2 and OCT4 Interacting in HEK293T Cells Using Real-Time Quantitative PCR.

Kanayev D, Abilmazhenova D, Akhmetollayev I, Sekenova A, Ogay V, Kulyyassov A Life (Basel). 2023; 13(1).

PMID: 36676054 PMC: 9862934. DOI: 10.3390/life13010107.

Proximity labeling for investigating protein-protein interactions.

Pfeiffer C, Paulo J, Gygi S, Rockman H Methods Cell Biol. 2022; 169:237-266.

PMID: 35623704 PMC: 10782847. DOI: 10.1016/bs.mcb.2021.12.006.

Generation of Peptides for Highly Efficient Proximity Utilizing Site-Specific Biotinylation in Cells.

Kulyyassov A, Ramankulov Y, Ogryzko V Life (Basel). 2022; 12(2).

PMID: 35207587 PMC: 8875956. DOI: 10.3390/life12020300.

Proximity Labeling Techniques to Study Chromatin.

Ummethum H, Hamperl S Front Genet. 2020; 11:450.

PMID: 32477404 PMC: 7235407. DOI: 10.3389/fgene.2020.00450.

In Vivo Quantitative Estimation of DNA-Dependent Interaction of Sox2 and Oct4 Using BirA-Catalyzed Site-Specific Biotinylation.

Kulyyassov A, Ogryzko V Biomolecules. 2020; 10(1).

PMID: 31963153 PMC: 7022529. DOI: 10.3390/biom10010142.

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