Pathway-Based High-Throughput Chemical Screen Identifies Compounds That Decouple Heterochromatin Transformations

Area of Science:

• Epigenetics and Gene Regulation
• Chemical Biology
• Molecular Biology

Background:

• Heterochromatin Protein 1 (HP1) is crucial for forming repressive heterochromatin domains.
• HP1 recruits histone lysine methyltransferases, increasing H3K9me3 marks and silencing genes.

Purpose of the Study:

• To discover chemical inhibitors of the HP1-mediated heterochromatin gene repression pathway.
• To develop a platform for identifying inhibitors of chromatin modification pathways.

Main Methods:

• Utilized a cell-based assay with chemical-mediated HP1 recruitment to an active gene.
• Employed high-throughput flow cytometry for screening small molecule inhibitors.
• Validated lead compounds in an orthogonal cell-based system and identified binding partners using chemical proteomics.

Main Results:

• Identified novel small molecule inhibitors that block HP1-mediated heterochromatin formation.
• Demonstrated dose-dependent inhibition of HP1-stimulated gene repression by lead compounds.
• Developed compound 2, which helped decouple H3K9 and H3K4 methylation states and identified its molecular interactors.

Conclusions:

• The study successfully discovered new inhibitors of HP1-mediated heterochromatin formation.
• The developed screening platform is modular and can be adapted for other chromatin pathways.
• The findings open avenues for exploring new molecular interactions within the HP1 pathway and developing cell-permeable inhibitors.