Mastrorosa Francesco Kumara, Oshima Keisuke K, Rozanski Allison N, Harvey William T, Eichler Evan E, Logsdon Glennis A
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, United States.
Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
Bioinformatics. 2024 Nov 28;40(12). doi: 10.1093/bioinformatics/btae733.
Centromeres 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.
Here, 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.
CDR-Finder is available at https://github.com/EichlerLab/CDR-Finder.
由于着丝粒的重复性质和短读长映射限制，其在历史上一直是测序技术较少研究的染色体区域。然而，长读长测序技术的最新进展使得能够在序列和表观遗传水平上研究基因组的复杂区域。
在此，我们展示了着丝粒双区域（CDR）查找器：一种用于在高质量、连续的基因组组装体的着丝粒内识别低甲基化区域的工具。这些区域通常与一种独特类型的染色质相关，该染色质包含组蛋白H3变体CENP - A，它标记着动粒的位置。CDR查找器可识别大型和小型着丝粒中的CDR，并生成一个BED文件，指示CDR在着丝粒内的位置。它还输出一个用于可视化、验证和下游分析的图表。
