Native, Spatiotemporal Profiling of the Global Human Regulome

Area of Science:

• Molecular Biology
• Proteomics
• Genomics

Background:

• The cell's regulome, including transcription factors (TFs) and regulatory proteins, controls gene expression but is difficult to study at scale.
• Its dynamic, low-abundance, and chromatin-associated nature presents significant challenges for comprehensive analysis.

Purpose of the Study:

• To develop a scalable method for profiling the regulome, enabling global and compartment-resolved quantification of native regulatory proteins.
• To create a foundational resource for decoding the regulatory proteome and integrating this data into cellular behavior models.

Main Methods:

• Enrichment of DNA- and chromatin-associated proteins.
• High-throughput, label-free DIA mass spectrometry for protein quantification.
• Profiling across 36 human cell lines and thousands of perturbations.

Main Results:

• The developed method, Regulome Profiling, captures chromatin-associated proteins and creates a Regulome Atlas.
• The Atlas includes nearly 60% of known human TFs, reveals lineage-specific TF localization, and distinguishes active from latent TF states.
• Regulome profiles detected immune pathway activation before transcriptional changes and identified novel drug responses.

Conclusions:

• This work establishes a scalable method for regulome profiling, providing a comprehensive resource for understanding gene regulation.
• The Regulome Atlas offers insights into TF dynamics, cellular responses to stimuli, and drug target engagement.
• The findings provide a blueprint for integrating proteomic regulome data into advanced cellular models.