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Related Experiment Video

Updated: Jan 17, 2026

Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization

Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization

Published on: December 10, 2012

PARTAGE: Parallel analysis of replication timing and gene expression.

Lakshana Sruthi Sadu Murari¹, Quinn Dickinson¹, Silvia Meyer-Nava¹

¹Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota.

Biorxiv : the Preprint Server for Biology

|September 15, 2025

Summary

This summary is machine-generated.

Replication timing (RT) and genome organization are linked to gene expression and disease. A new method, PARTAGE, jointly profiles copy number variation, RT, and gene expression from single samples for better insights.

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Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

The human genome is organized into functional compartments that replicate during S-phase, a process known as replication timing (RT).
RT is cell-type specific, coordinated with 3D genome organization and gene expression, and altered in diseases like cancer.
Current methods analyze RT and gene expression separately, hindering understanding of their co-regulation.

Purpose of the Study:

To develop a multiomics approach for simultaneous profiling of copy number variation (CNV), RT, and gene expression.
To provide an integrated view of the relationships between RT, genome architecture, and transcriptional regulation.

Main Methods:

Developed PARTAGE, a novel multiomics technique.
Enabled joint profiling of CNV, RT, and gene expression from identical biological samples.

Main Results:

PARTAGE allows for a more accurate and integrated analysis of RT and gene regulation.
Overcomes limitations of separate sample profiling, revealing complex co-regulatory mechanisms.

Conclusions:

The PARTAGE approach facilitates a deeper understanding of the mechanistic links between replication timing, 3D genome organization, and gene expression.
This method is crucial for studying genome regulation in health and disease contexts, particularly cancer.