麻豆淫院

A research team led by Professor Simona Giunta at the University of Rome La Sapienza has produced the first reference-quality genome assembly of an experimentally relevant human cell line, the widely used retinal pigment epithelial line RPE-1. The work, in Nature Communications, marks a milestone in functional genomics by providing a matched, high-quality genome for one of biology's most important model systems.

Recent advances in sequencing technology have enabled telomere-to-telomere (T2T) genomes, such as the current CHM13 human reference. Yet these assemblies, while complete, do not reflect the precise genomes of the cell lines that scientists actually use in laboratories around the world. This mismatch has constrained the accuracy of experimental studies, particularly in highly variable and structurally complex regions such as centromeres.

To close this gap, the research team worked with experts in genomics, including Giulio Formenti at the Rockefeller University in New York, to assemble RPE1v1.1, a near-complete diploid genome of the hTERT RPE-1 cell line. By integrating high-coverage long-read sequencing with Hi-C chromosome conformation capture, the researchers generated and validated a de novo assembly at reference quality. Crucially, their assembly resolves the centromeres of RPE-1 chromosomes, offering a haplotype-resolved human reference鈥攚ith maternal and paternal genomes represented.

The RPE-1 line, derived from retinal pigment epithelial cells, has long served as a model system due to its diploid karyotype and stability under culture conditions. Until now, however, scientists studying RPE-1 relied on the human reference genome, which does not fully capture the structural variation or unique genomic features of this experimental model. This mismatch has limited the accuracy of downstream multi-omics analyses, particularly in repetitive and polymorphic regions.

The new assembly reaches reference quality, with a key advance in resolving the centromeres of RPE-1 chromosomes鈥攔egions that remain fragmented in the current human reference genome. This achievement enables unprecedented mapping of regulatory and structural features across the genome, including base-pair鈥搇evel insight into kinetochore assembly, the essential process that governs faithful chromosome segregation.

"Cell lines are the workhorses of modern biology, yet their genome assemblies have lagged behind in accuracy and completeness compared to the human reference," said Giunta. "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 work demonstrates that aligning experimental data directly to the RPE-1 reference, a practice the researchers named isogenomic mapping, reduces alignment errors, improves haplotype resolution, and enables accurate analysis of structural and regulatory variation. This strategy highlights the importance of matched references for interpreting experimental data and lays the groundwork for a larger initiative to assemble high-quality genomes for other commonly used human cell lines.

Beyond its technical impact, the study opens the door to a broader vision: building a Human Pangenome of Experimental Cell Lines. Such a resource would systematically integrate reference-quality assemblies of widely used laboratory models into graph-based frameworks, ensuring that functional genomic studies are grounded in the true genomic architecture of the systems in which they are performed.

Indeed, comparing the RPE-1 reference genome to the human pangenome shows that the cell line largely retains humanlike qualities, with the cell line closely associated with the population of origin.