Reference-Quality Genome Assembly for RPE-1 Cell Line Produced

A research team led by Simona Giunta at the University of Rome La Sapienza has produced the first reference-quality genome assembly for the human retinal pigment epithelial cell line RPE-1, an important model system in biology. Published in Nature Communications, this work provides a matched, high-quality genome for the RPE-1 cell line, which is widely used in experimental settings.

While recent advances in sequencing have produced complete human reference genomes like CHM13, these references do not reflect the precise genomes of commonly used cell lines in labs worldwide. This gap limits experimental accuracy, especially in complex genomic regions such as centromeres. To address this, the team collaborated with experts including Giulio Formenti of Rockefeller University to assemble RPE1v1.1—a near-complete diploid genome of the hTERT-immortalized RPE-1 line. They combined high-coverage long-read sequencing with Hi-C chromosome conformation capture to generate and validate a de novo assembly reaching reference quality. Importantly, this assembly resolves the centromeres on RPE-1 chromosomes and offers haplotype resolution, representing both maternal and paternal genomes.

The RPE-1 cell line, derived from retinal pigment epithelial cells, has been a stable, diploid model system for many years. Until now, researchers studying RPE-1 relied on the human reference genome, which does not capture the line’s unique structural variations and genomic features. This mismatch restricted the accuracy of downstream multi-omics studies, particularly in repetitive and polymorphic regions.

This newly produced assembly attains reference-quality status and significantly advances understanding by resolving RPE-1 centromeres—regions that remain fragmented in the current human reference. This resolution enables detailed mapping of regulatory and structural genomic features, including base-pair level insight into kinetochore assembly, a critical process for chromosome segregation.

Professor Giunta noted, “Cell lines are the workhorses of modern biology, yet their genome assemblies have lagged behind in accuracy and completeness compared to the human reference. By producing a reference-quality assembly of RPE-1 with resolved centromeres, we provide the community with a tool that will drastically improve the precision of genomic and epigenomic studies in this system.”

The study also introduces a practice called isogenomic mapping, which involves aligning experimental data directly to the RPE-1 reference. This approach reduces alignment errors, enhances haplotype resolution, and enables accurate analysis of structural and regulatory variation. It underscores the importance of using matched references for experimental datasets and lays the foundation for composing high-quality genomes of other commonly used human cell lines. 

Beyond its immediate utility, this research sets the stage for creating a Human Pangenome of Experimental Cell Lines. This future resource aims to integrate reference-quality assemblies of commonly used laboratory models into graph-based frameworks, ensuring functional genomic studies are grounded in true genomic architecture. Comparison of the RPE-1 genome to the human pangenome confirms that the cell line retains human-like qualities and is closely related to its population of origin.