PARTAGE Method Reveals Genome Regulation in Single Approach

April 14, 2026

By Bio-IT World Staff 

April 14, 2026 | Researchers at the University of Minnesota Medical School propose PARTAGE, a multiomics approach that allows researchers to measure replication timing, changes in copy number, and gene activity from the same DNA sample. Their method was published last month in Genome Research (DOI: 10.1101/gr.281532.125).  

The human genome is partitioned into functional compartments that replicate at specific times called replication timing (RT). “Replication timing is coregulated with the 3D genome organization, is cell type–specific, and changes during development in coordination with gene expression,” the paper authors write. “RT alterations are linked to abnormal gene expression, genome instability, and structural variation in multiple diseases, including cancer. However, mechanistic links between RT, large-scale 3D genome architecture, and transcriptional regulation remain poorly understood.”  

“PARTAGE lets us connect DNA replication, genomic alterations, and gene activity in a single experiment — giving us a more complete view of how the genome is regulated and how it is altered in disease, like in cancer cells,” said Juan Carlos Rivera-Mulia, PhD, an assistant professor at the University of Minnesota Medical School and principal investigator of the study in a press release. “This work could help identify new biomarkers and uncover potential therapeutic targets.”  

Parallel Workflow 

The approach, the authors write, “is based on sample preparation under conditions that enable the preservation of both nucleic acids, enabling joint profiling of RT and transcriptome programs.” It’s done on asynchronous cultures of cells, which eliminates the need for cell cycle synchronization.  

First, cells are labeled with the nucleotide analog BrdU to label nascent DNA. Intact nuclei are purified from single cell suspensions, stained, and sorted by fluorescence-activated cell sorting (FACS). Next, genomic DNA and nuclear RNA are copurified. Genomic DNA is processed following the optimized Repli-seq method. Nuclear RNA is processed by standard RNA-seq. Finally, from the genomic DNA, researchers can map CNVs and measure replication timing, and the RNA enables transcriptome profiling.  

The approach has several advantages over other options, the authors outline. Among them:  

  • the researchers used nontoxic, cell-permeant dyes with narrow emission spectra to enable the stoichiometric DNA staining for accurate cell cycle analysis based in DNA content; 
  • they processed isolated nuclei in order to enrich for nuclear RNA, which is closer to ongoing transcriptional activity and less influenced by cytoplasmic mRNA stability and export; and
  • they applied the multifraction Repli-seq approach and exploited the data from the G1-purified nuclei to normalize signals and generate accurate heat maps of RT.  

“We demonstrated that PARTAGE sample preparation allows the copurification of DNA and RNA of high quality and in sufficient amounts for parallel processing for Repli-seq and RNA-seq,” the authors write.  

“Importantly, PARTAGE’s capacity to detect CNVs with this sequencing depth makes this approach cost-effective and scalable for clonal tracking, genome integrity screenings, and cancer alterations studies, with the addition of joint profiling of RT and gene regulation.” 

Researchers found that PARTAGE produces results just as accurate as current gold-standard methods performed separately. The method also shows a strong link between early DNA replication and active gene expression, and precisely detects genome alterations, such as extra or missing pieces of DNA in cancer cells.  

“In disease contexts, such as cancer and other conditions characterized by genome instability, PARTAGE provides a practical approach to concurrently monitor RT alterations, CNV burden, and transcriptional dysregulation, thereby enabling more comprehensive assessments of genome integrity and its functional implications,” the authors conclude.