ArticleNature communications2025
The reference genome of the human diploid cell line RPE-1.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Allele-resolved monosome and polysome sequencing identifies cis-variants affecting mRNA translation.Life science alliance · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
- Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome.Cell genomics · 2026Article
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- Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregation.Cell reports · 2026Article
- ChromoMapperWeb: evaluate genome alignments and track assembly steps within an interactive graphic environment.Nucleic acids research · 2026Article
- HOROSCOPE: Decoding human centromere architecture from short reads usingbioRxiv : the preprint server for biology · 2026Article
- Quantitative analysis of autophagic flux reveals radiation-induced activation of SQSTM1-mediated degradation of protein aggregates and ER-phagy.Journal of radiation research · 2026Article
- Using combined RNA/DNA short read sequencing to investigate allele-specific expression from the inactive X chromosome in human cells.bioRxiv : the preprint server for biology · 2026Article
- A genomic and epigenomic view of human centromeres.Nature reviews. Genetics · 2026Review
- Haplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing data.Nucleic acids research · 2026Article
- Chromatin Remodeling, DNA Double-Strand Break Repair, and Human Disease: How a Breakup Changes You.Biomolecules · 2026Review
- Chronic PFOA and PFOS exposure triggers cellular oxidative stress and alters lipid levels as revealed through multi-omics analysis.Environmental science. Advances · 2026Article
- Haplotype-resolved centromeric chromatin organization from a complete diploid human genome.bioRxiv : the preprint server for biology · 2026Article
- The complete genome of the KOLF2.1J reference iPSC line.bioRxiv : the preprint server for biology · 2026Article
- Heterochromatin boundaries maintain centromere position, size and number.Nature structural & molecular biology · 2026Article
- 40 years of CENP-A: the foundation of a new era of centromere biology.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Article
- Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.bioRxiv : the preprint server for biology · 2025Article
- Chromatin remodeling activity of EP400 safeguards chromosomal stability by preventing CENP-A mislocalization.Cell reports · 2025Article
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Authors and funding
13 authors.
Funding
Abstract
Recent technological advances have facilitated the assembly of telomere-to-telomere (T2T) genomes. The current T2T CHM13 showcases the complete architecture of the human genome, yet its use in functional experiments is limited by discrepancies with the actual genome of the specific biological system under study. Access to reference assemblies for experimentally relevant cell lines is therefore essential in advancing sequencing-based analyses and precise manipulation, particularly in highly variable regions such as centromeres. Here, we present RPE1v1.1, the near-complete diploid genome assembly of the hTERT RPE-1 cell line, a non-cancerous human retinal epithelial model with a stable karyotype. Using high-coverage Pacific Biosciences and Oxford Nanopore Technologies long-read sequencing, we generate a high-quality de novo assembly, validate it through multiple methods, and phase it by integrating high-throughput chromosome conformation capture (Hi-C) data. Our assembly includes chromosome-level scaffolds that span centromeres for all chromosomes. Comparing both haplotypes with the CHM13 genome, we detect haplotype-specific genomic variations, including the translocation between chromosome 10 and chromosome X t(X;10)(Xq28;10q21.2) characteristic of RPE-1 cells, and divergence peaking at centromeres. Altogether, the RPE1v1.1 genome provides a reference-quality diploid assembly of a widely used cell line, supporting high-precision genetic and epigenetic studies in this model system.
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