Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China.
Sci Data. 2023 Aug 10;10(1):532. doi: 10.1038/s41597-023-02431-5.
Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%-80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders.
斑马鱼是一种广泛用于研究人类疾病的模式生物，包括血液系统疾病。然而，斑马鱼主要造血器官——肾脏骨髓（KM）的综合甲基化基准仍然缺乏。我们通过生成四个 KM 数据集，利用牛津纳米孔技术（ONT）测序对斑马鱼 KM 中的 DNA 甲基化进行了分析，这两个数据集是基于是否存在红细胞来分组的。我们的研究结果表明，KM 样本中的血液污染会降低读取质量并改变甲基化模式。与全基因组亚硫酸氢盐测序（WGBS）相比，基于 ONT 的甲基化分析可以覆盖更多的 CpG 位点（92.4%对 70%-80%），并且具有更少的 GC 偏倚和更均匀的基因组覆盖度。并且，当使用共享位点时，ONT 甲基化调用结果与 WGBS 结果具有高度相关性。本研究为斑马鱼 KM 建立了一个全面的甲基化图谱，为进一步研究表观遗传调控和血液系统疾病的靶向治疗铺平了道路。
