Reference-quality genome meeting created for extensively used RPE-1 human cell line

A analysis group led by Professor Simona Giunta on the University of Rome La Sapienza has produced the primary reference-quality genome meeting of an experimentally related human cell line, the extensively used retinal pigment epithelial line RPE-1. The work, published in Nature Communications, marks a milestone in practical genomics by offering a matched, high-quality genome for considered one of biology’s most necessary mannequin programs.

Recent advances in sequencing know-how have enabled telomere-to-telomere (T2T) genomes, corresponding to the present CHM13 human reference. Yet these assemblies, whereas full, don’t mirror the exact genomes of the cell strains that scientists truly use in laboratories all over the world. This mismatch has constrained the accuracy of experimental research, notably in extremely variable and structurally complicated areas corresponding to centromeres.

To shut this hole, the analysis group labored with consultants in genomics, together with Giulio Formenti on 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 seize, the researchers generated and validated a de novo meeting at reference high quality. Crucially, their meeting resolves the centromeres of RPE-1 chromosomes, providing a haplotype-resolved human reference—with maternal and paternal genomes represented.

The RPE-1 line, derived from retinal pigment epithelial cells, has lengthy served as a mannequin system on account of its diploid karyotype and stability underneath tradition situations. Until now, nevertheless, scientists finding out RPE-1 relied on the human reference genome, which doesn’t totally seize the structural variation or distinctive genomic options of this experimental mannequin. This mismatch has restricted the accuracy of downstream multi-omics analyses, notably in repetitive and polymorphic areas.

The new meeting reaches reference high quality, with a key advance in resolving the centromeres of RPE-1 chromosomes—areas that stay fragmented within the present human reference genome. This achievement allows unprecedented mapping of regulatory and structural options throughout the genome, together with base-pair–degree perception into kinetochore meeting, the important course of that governs devoted 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,” mentioned 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 information on to the RPE-1 reference, a follow the researchers named isogenomic mapping, reduces alignment errors, improves haplotype decision, and allows correct evaluation of structural and regulatory variation. This technique highlights the significance of matched references for deciphering experimental information and lays the groundwork for a bigger initiative to assemble high-quality genomes for different generally used human cell strains.

Beyond its technical influence, the research opens the door to a broader imaginative and prescient: constructing a Human Pangenome of Experimental Cell Lines. Such a useful resource would systematically combine reference-quality assemblies of extensively used laboratory fashions into graph-based frameworks, guaranteeing that practical genomic research are grounded within the true genomic structure of the programs through which they’re carried out.

Indeed, evaluating the RPE-1 reference genome to the human pangenome reveals that the cell line largely retains humanlike qualities, with the cell line carefully related to the inhabitants of origin.