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Competitive Genomic Screens of Barcoded Yeast Libraries

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Published on: August 11, 2011

High-throughput Oligopaint screen identifies druggable 3D genome regulators.

Daniel S Park^1,2, Son C Nguyen^1,2, Randi Isenhart^1,2

¹Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

|July 12, 2023

Summary

Researchers identified over 300 factors influencing genome folding using a new imaging pipeline. Inhibiting GSK3A kinase increased chromatin looping, highlighting its role in nuclear architecture.

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Identification of Transcription Factor Regulators using Medium-Throughput Screening of Arrayed Libraries and a Dual-Luciferase-Based Reporter

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Area of Science:

Genomics
Molecular Biology
Cell Biology

Background:

The human genome is a 3D chromatin polymer governed by complex chromosome interactions.
Understanding the proteins regulating these interactions is crucial but limited.
Few regulators of genome folding and nuclear architecture have been identified.

Purpose of the Study:

To identify novel protein factors that regulate genome folding and chromatin interactions.
To develop and utilize an automated imaging pipeline for quantitative measurement of chromatin interactions.
To screen the human druggable genome for regulators of interphase genome organization.

Main Methods:

Developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO) automated imaging pipeline.
Quantitatively measured chromatin interactions in single cells across thousands of samples.
Screened the human druggable genome to identify factors influencing genome folding.

Main Results:

Identified over 300 factors influencing genome folding during interphase.
Validated 43 genes that modulate interactions between topologically associating domains.
Demonstrated that inhibiting GSK3A kinase increases long-range chromatin looping genome-wide in a cohesin-dependent manner.

Conclusions:

GSK3A signaling plays a significant role in maintaining nuclear architecture.
The HiDRO pipeline is effective for identifying mechanisms of spatial genome organization.
Numerous factors regulate genome folding, offering new targets for understanding nuclear organization.