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Updated: Mar 24, 2026
High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes
Published on: March 3, 2015
High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility
Samantha G Pattenden1, Jeremy M Simon2, Aminah Wali3
1Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302;
Abstract:
Mutations in chromatin-modifying proteins and transcription factors are commonly associated with a wide variety of cancers. Through gain- or loss-of-function, these mutations may result in characteristic alterations of accessible chromatin, indicative of shifts in the landscape of regulatory elements genome-wide. The identification of compounds that reverse a specific chromatin signature could lead to chemical probes or potential therapies. To explore whether chromatin accessibility could serve as a platform for small molecule screening, we adapted formaldehyde-assisted isolation of regulatory elements (FAIRE), a chemical method to enrich for nucleosome-depleted genomic regions, as a high-throughput, automated assay. After demonstrating the validity and robustness of this approach, we applied this method to screen an epigenetically targeted small molecule library by evaluating regions of aberrant nucleosome depletion mediated by EWSR1-FLI1, the chimeric transcription factor critical for the bone and soft tissue tumor Ewing sarcoma. As a class, histone deacetylase inhibitors were greatly overrepresented among active compounds. These compounds resulted in diminished accessibility at targeted sites by disrupting transcription of EWSR1-FLI1. Capitalizing on precise differences in chromatin accessibility for drug discovery efforts offers significant advantages because it does not depend on the a priori selection of a single molecular target and may detect novel biologically relevant pathways.
Insights
Researchers developed a high-throughput assay using formaldehyde-assisted isolation of regulatory elements (FAIRE) to screen for compounds targeting cancer-associated chromatin changes. Histone deacetylase inhibitors showed promise in reversing aberrant chromatin accessibility in Ewing sarcoma by disrupting EWSR1-FLI1 transcription.
Area of Science:
- Oncology
- Epigenetics
- Chemical Biology
Background:
- Mutations in chromatin-modifying proteins and transcription factors are hallmarks of many cancers, leading to altered genome-wide regulatory element landscapes.
- Aberrant chromatin accessibility, reflecting changes in nucleosome depletion, can serve as a biomarker for cancer and a target for therapeutic intervention.
Purpose of the Study:
- To develop and validate a high-throughput screening platform based on chromatin accessibility.
- To identify small molecules that can reverse aberrant chromatin signatures associated with cancer, specifically Ewing sarcoma.
Main Methods:
- Adapted formaldehyde-assisted isolation of regulatory elements (FAIRE) into a high-throughput, automated assay to enrich for nucleosome-depleted genomic regions.
- Screened an epigenetically targeted small molecule library against aberrant nucleosome depletion mediated by the EWSR1-FLI1 fusion protein in Ewing sarcoma.
Main Results:
- The adapted FAIRE assay proved valid and robust for screening.
- Histone deacetylase inhibitors were identified as a class of compounds significantly effective in reversing aberrant chromatin accessibility.
- These inhibitors diminished chromatin accessibility at targeted sites by disrupting the transcription of EWSR1-FLI1.
Conclusions:
- Chromatin accessibility can serve as a versatile platform for small molecule drug discovery, enabling the identification of compounds that modulate epigenetic states.
- This approach offers advantages by not requiring a priori selection of a single molecular target and potentially uncovering novel biological pathways.
- The findings highlight the therapeutic potential of targeting chromatin accessibility in cancers driven by specific transcription factors like EWSR1-FLI1.
