Unraveling the DNA methylation landscape in dog blood across breeds.

IF 3.5 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

BMC Genomics Pub Date : 2024-11-15 DOI:10.1186/s12864-024-10963-2

Miyuki Nakamura, Yuki Matsumoto, Keiji Yasuda, Masatoshi Nagata, Ryo Nakaki, Masahiro Okumura, Jumpei Yamazaki

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引用次数: 0

Abstract

Background: DNA methylation is a covalent bond modification that is observed mainly at cytosine bases in the context of CG pairs. DNA methylation patterns reflect the status of individual tissues, such as cell composition, age, and the local environment, in mammals. Genetic factors also impact DNA methylation, and the genetic diversity among various dog breeds provides a valuable platform for exploring this topic. Compared to those in the human genome, studies on the profiling of methylation in the dog genome have been less comprehensive.

Results: Our study provides extensive profiling of DNA methylation in the whole blood of three dog breeds using whole-genome bisulfite sequencing. The difference in DNA methylation between breeds was moderate after removing CpGs overlapping with potential genetic variation. However, variance in methylation between individuals was common and often occurred in promoters and CpG islands (CGIs). Moreover, we adopted contextual awareness methodology to characterize DNA primary sequences using natural language processing (NLP). This method could be used to effectively separate unmethylated CGIs from highly methylated CGIs in the sequences that are identified by the conventional criteria.

Conclusions: This study presents a comprehensive DNA methylation landscape in the dog blood. Our observations reveal the similar methylation patterns across dog breeds, while CGI regions showed high variations in DNA methylation level between individuals. Our study also highlights the potential of NLP approach for analyzing low-complexity DNA sequences, such as CGIs.

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揭示不同品种犬血液中的 DNA 甲基化状况。

背景：DNA 甲基化是一种共价键修饰，主要出现在 CG 对背景下的胞嘧啶碱基上。DNA 甲基化模式反映了哺乳动物个体组织的状况，如细胞组成、年龄和当地环境。遗传因素也会影响 DNA 甲基化，而各种犬种之间的遗传多样性为探讨这一课题提供了一个宝贵的平台。与人类基因组相比，有关狗基因组甲基化的研究还不够全面：结果：我们的研究利用全基因组亚硫酸氢盐测序技术对三个犬种的全血进行了广泛的 DNA 甲基化分析。在去除与潜在遗传变异重叠的 CpGs 后，不同品种之间的 DNA 甲基化差异不大。然而，个体间的甲基化差异很常见，而且通常发生在启动子和 CpG 岛（CGI）上。此外，我们还采用了上下文感知方法，利用自然语言处理（NLP）来描述 DNA 主序列的特征。这种方法可用于有效区分传统标准所识别序列中的未甲基化CGI和高度甲基化CGI：本研究展示了狗血液中全面的 DNA 甲基化图谱。我们的观察结果表明，不同品种的狗具有相似的甲基化模式，而不同个体的 CGI 区域在 DNA 甲基化水平上存在很大差异。我们的研究还凸显了 NLP 方法在分析 CGI 等低复杂度 DNA 序列方面的潜力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

BMC Genomics 生物-生物工程与应用微生物

CiteScore

7.40

自引率

4.50%

发文量

769

审稿时长

6.4 months

期刊介绍： BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.