Human epithelial cell line genome sequence successfully achieved, reaching reference standard quality
Researchers at the University of Rome La Sapienza have made a significant stride in genome sequencing technology, producing the first reference-quality genome assembly of an experimentally relevant human cell line – the retinal pigment epithelial line RPE-1.
Published in Nature Communications under the title, "The reference genome of the human diploid cell line RPE-1," the study led by Simona Giunta, PhD, associate professor of human genomics, aims to improve the precision of genomic and epigenomic studies in the RPE-1 system.
Recent advances in sequencing technology have enabled telomere-to-telomere (T2T) genomes. However, these assemblies do not accurately reflect the precise genomes of the cell lines used in experimental practice. To address this issue, the researchers implemented an approach named isogenomic mapping, which aligns experimental data directly to the RPE-1 reference. This technique reduces alignment errors and improves haplotype resolution.
The new genome assembly, named RPE1v1.1, was generated and validated using high-coverage long-read sequencing and Hi-C chromosome conformation capture. One of the key advantages of this assembly is its ability to resolve the centromeres of RPE-1 chromosomes, which remain fragmented in the current human reference genome. This resolution is crucial for accurate analysis of structural and regulatory variation in the RPE-1 system.
The RPE-1 line, derived from retinal pigment epithelial cells, has a diploid karyotype and is stable under culture conditions. The cell line is closely associated with the population of origin, and comparing the RPE-1 reference genome to the human pangenome shows that the cell line largely retains human-like qualities.
The new assembly enables unprecedented mapping of regulatory and structural features across the genome, including kinetochore assembly. This work lays the groundwork for a larger initiative to assemble high-quality genomes for other commonly used human cell lines. The study also demonstrates the importance of matched references for interpreting experimental data and opens a broader vision of building a Human Pangenome of Experimental Cell Lines.
Read also:
- Is it advisable to utilize your personal health insurance in a publicly-funded medical facility?
- Dietary strategies for IBS elimination: Aims and execution methods
- Benefits, suitable dosage, and safety considerations for utilizing pumpkin seed oil in treating an overactive bladder
- Harmful Medical Remedies: A Misguided Approach to Healing
