ArticleGenomics, proteomics & bioinformatics2024
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome.
Article in Genomics, proteomics & bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Potential Role of Prebiotics and Probiotics on Oocyte Quality, Embryo Development, Endometrial Health, and Fertility Outcomes in Assisted Reproductive Technologies.Probiotics and antimicrobial proteins · 2026Review
- Applications of large-scale artificial intelligence models in bioinformatics.Quantitative biology (Beijing, China) · 2026Review
- CryoPromptSeg: prompt-guided segmentation with integrated denoising for cryo-EM particle picking.Bioinformatics (Oxford, England) · 2026Article
- The uterine and vaginal microbiome in assisted reproductive technologies: implications for maternal and offspring outcomes.Journal of assisted reproduction and genetics · 2026Review
- IFNIKB: a type I interferon database for antitumuor immunity studies.Database : the journal of biological databases and curation · 2026Article
- Network-informed deconvolution of bulk immune gene co-expression reveals single-cell programs and spatial organization.Frontiers in immunology · 2026Article
- How microbiota influence maternal blood disorder in miscarriage.Molecular biology reports · 2025Review
- DGHNN: a deep graph and hypergraph neural network for pan-cancer related gene prediction.Bioinformatics (Oxford, England) · 2025Article
- Developing a multiomics data-based mathematical model to predict colorectal cancer recurrence and metastasis.BMC medical informatics and decision making · 2025Article
- Developing a quantum computing model for sequence annotation of interferon protein.Computational and structural biotechnology journal · 2025Article
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6 authors.
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Abstract
Precisely defining and mapping all cytosine (C) positions and their clusters, known as CpG islands (CGIs), as well as their methylation status, are pivotal for genome-wide epigenetic studies, especially when population-centric reference genomes are ready for timely application. Here, we first align the two high-quality reference genomes, T2T-YAO and T2T-CHM13, from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined CGIs. Second, by mapping some representative genome-wide methylation data from selected organs onto the two genomes, we find that there are about 4.7%-5.8% sequence divergency of variable categories depending on quality cutoffs. Genes among the divergent sequences are mostly associated with neurological functions. Moreover, CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG (O/E) ratio between the two genomes. Finally, we find that the T2T-YAO genome not only has a greater CpG coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing (WGBS) data from the European and American populations are mapped to each reference, but also shows more hyper-methylated CpG sites as compared to the T2T-CHM13 genome. Our study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.
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