The human proteome with direct physical access to DNA

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• DNA in human cells is intricately organized by histones, RNA, and proteins, forming chromatin.
• Only a specific subset of cellular proteins physically interacts with DNA to regulate essential functions like transcription, replication, and repair.

Purpose of the Study:

• To develop and apply a novel "zero-distance" photo-crosslinking technique for quantifying proteins in direct contact with DNA in living cells.
• To create a comprehensive atlas of DNA-interacting proteins (DNA interactome) and map their precise binding interfaces.

Main Methods:

• Development of a "zero-distance" photo-crosslinking approach to identify proteins physically associated with DNA.
• Application of the method to human breast cancer cells to generate DNA interactome data.
• Analysis of quantitative interactome data from differentially treated cells to study dynamic protein recruitment.

Main Results:

• Identification of over one thousand proteins with physical access to DNA in human cells.
• Pinpointing of hundreds of protein-DNA interfaces at single-amino-acid resolution using peptide-nucleotide crosslinks.
• Recapitulation of known transcription factor and DNA repair protein recruitment, and discovery of rapid chromatin accessibility regulators (acting within minutes).

Conclusions:

• The developed photo-crosslinking method provides a direct, hypothesis-free approach to explore genomic regulation.
• The DNA interactome atlas offers unprecedented insights into protein-DNA interactions and their dynamic regulation.
• This technique is broadly applicable across various biological systems and organisms for studying genome function.