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Updated: Mar 14, 2026

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

High-resolution interrogation of functional elements in the noncoding genome.

Neville E Sanjana¹, Jason Wright², Kaijie Zheng²

¹Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. nsanjana@nygenome.org zhang@broadinstitute.org.

Science (New York, N.Y.)

|October 7, 2016

Summary

This summary is machine-generated.

Researchers developed CRISPR screens to identify noncoding elements that influence melanoma drug resistance. These functional noncoding regions impact gene regulation and could be targeted for new therapies.

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

Area of Science:

Genomics
Molecular Biology
Cancer Research

Background:

The noncoding genome plays a crucial role in gene regulation and disease pathogenesis.
Current tools for identifying and manipulating noncoding elements are limited, hindering research.
Melanoma BRAF inhibitor resistance is a significant clinical challenge.

Purpose of the Study:

To develop and apply CRISPR screening methods for the rapid identification and functional characterization of noncoding genomic elements.
To investigate the role of noncoding regions in BRAF inhibitor resistance in melanoma.
To explore the potential of targeting noncoding elements for therapeutic strategies.

Main Methods:

Utilized pooled CRISPR screens with approximately 18,000 single guide RNAs targeting over 700 kilobases surrounding the NF1, NF2, and CUL3 genes.
Analyzed noncoding regions for hallmarks of functional importance in modulating drug resistance.
Performed engineered mutations at specific CUL3 locus regions to assess effects on transcription factor binding and epigenetic modifications.

Main Results:

Identified noncoding locations that significantly modulate BRAF inhibitor resistance in melanoma.
Discovered that these functional noncoding regions possess predictive hallmarks of regulatory activity.
Demonstrated that engineered mutations in CUL3 locus noncoding regions alter transcription factor occupancy and epigenetic landscapes, impacting gene regulation and drug resistance.

Conclusions:

Developed novel CRISPR screening tools for efficient discovery of functional noncoding elements.
Established the link between specific noncoding regions, gene regulation, and melanoma chemotherapeutic resistance.
Implicated noncoding elements as potential therapeutic targets for overcoming drug resistance in cancer.