ArticleBioinformatics (Oxford, England)2024
Identification and annotation of centromeric hypomethylated regions with CDR-Finder.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Optimized Genome-Wide Profiling of Centromeric Chromatin Complexes by ChIP-seq.Current protocols · 2026Article
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- Complete chromosome 21 centromere sequencing of families with Down syndrome.American journal of human genetics · 2026Article
- EasyCen: A Lightweight Framework for Centromere Localisation and Repeat-Organisation Profiling in Telomere-to-Telomere Genomes.Molecular ecology resources · 2026Article
- A global map for introgressed structural variation and selection in humans.Science (New York, N.Y.) · 2026Article
- A complete human pancreatic cancer genome.bioRxiv : the preprint server for biology · 2026Article
- A segmental duplication-mediated deletion leads to neocentromere formation in orangutans.bioRxiv : the preprint server for biology · 2026Article
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- Heterochromatin boundaries maintain centromere position, size and number.Nature structural & molecular biology · 2026Article
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- A global view of human centromere variation and evolution.bioRxiv : the preprint server for biology · 2025Article
- Article
- Complete chromosome 21 centromere sequencing of families with Down syndrome reveals centromere size asymmetry.bioRxiv : the preprint server for biology · 2025Article
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6 authors.
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Abstract
motivationCentromeres are chromosomal regions historically understudied with sequencing technologies due to their repetitive nature and short-read mapping limitations. However, recent improvements in long-read sequencing allow for the investigation of complex regions of the genome at the sequence and epigenetic levels.
resultsHere, we present Centromere Dip Region (CDR)-Finder: a tool to identify regions of hypomethylation within the centromeres of high-quality, contiguous genome assemblies. These regions are typically associated with a unique type of chromatin containing the histone H3 variant CENP-A, which marks the location of the kinetochore. CDR-Finder identifies the CDRs in large and short centromeres and generates a BED file indicating the location of the CDRs within the centromere. It also outputs a plot for visualization, validation, and downstream analysis. AVAILABILITY AND IMPLEMENTATION: CDR-Finder is available at https://github.com/EichlerLab/CDR-Finder.
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