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Related Experiment Video

Updated: Oct 17, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution.

Ting Wu^1,2, Danli Jiang¹, Meijuan Zou¹

¹Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA.

Nucleic Acids Research

|October 11, 2021

Summary

This summary is machine-generated.

Researchers adapted Reel-seq to map functional cis-regulatory elements (cis-REs) in the human genome, including unmarked regions. This method identified novel cis-REs regulating p16INK4a expression, crucial for cellular senescence.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Published on: April 21, 2023

Area of Science:

Genomics
Epigenetics
Molecular Biology

Background:

Functional cis-regulatory elements (cis-REs) are found in both epigenetically marked and unmarked regions of the human genome.
Identifying cis-REs in unmarked genomic sites presents significant challenges.

Purpose of the Study:

To adapt the Reel-seq technique for high-resolution, systematic mapping of cis-REs across large genomic regions.
To identify and characterize cis-REs, particularly in epigenetically unmarked sites, and their role in gene regulation.

Main Methods:

Adaptation of Reel-seq, an in vitro high-throughput technique, for fine-mapping cis-REs.
Coupling Reel-seq with FREP-MS (quantitative proteomics) for cis-RE characterization.
Analysis of the aging-related CDKN2A/B locus, including the p16INK4a gene.

Main Results:

Identified 408 candidate cis-REs within a 58 kb region of the CDKN2A/B locus.
Characterized two cis-REs, one in a marked and one in an unmarked site, regulating p16INK4a expression over ~100 kb.
Demonstrated that PABPC1 and FOXC2 recruitment by these cis-REs controls p16INK4a expression.

Conclusions:

Reel-seq is effective for systematic, high-resolution cis-RE identification across large genomic regions, including challenging unmarked sites.
PABPC1 and FOXC2 are key regulators of p16INK4a expression via cis-REs, impacting cellular senescence.
The combined Reel-seq and FREP-MS approach validates cis-RE function and identifies regulatory mechanisms.