空间相关性对甲基化熵的影响及其在小鼠脑甲基组中的应用。

IF 4.2 2区 生物学 Q1 GENETICS & HEREDITY Epigenetics & Chromatin Pub Date : 2023-02-04 DOI:10.1186/s13072-023-00479-6
Xiaowei Wu, Joung Min Choi
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引用次数: 0

摘要

背景:随着亚硫酸酯测序技术的发展,大量甲基化数据的产生,为研究亚硫酸酯的表观遗传机制及其与其他生物过程的关系提供了前所未有的机会。甲基化数据的一个常见特征是附近CpG位点之间的相关性。尽管这种空间相关性在一些表观遗传学研究中被利用,但其与甲基化数据的其他特征的相互作用尚未得到充分研究。结果:从信息论的角度探讨空间相关性对甲基化熵的影响,填补了这一研究空白。考虑到空间相关性,我们推导了ME与另一个关键参数甲基化概率之间的解析关系。通过对比观察到的ME与平均甲基化水平这两个相应统计量之间的经验关系,可以鉴定出受强表观遗传控制的基因组位点,这些位点可能作为细胞类型特异性甲基化的潜在标记。通过模拟研究验证了该方法的有效性,并应用于分析已发表的小鼠脑甲基组数据集。结论:与文献中开发的其他复杂方法相比,该方法提供了一种简单而有效的方法来检测受强表观遗传控制(例如双极甲基化模式)的CpG片段。这项研究的发现揭示了基于混合细胞群体甲基化数据的细胞类型特异性基因/途径的鉴定。
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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The impact of spatial correlation on methylation entropy with application to mouse brain methylome.

Background: With the advance of bisulfite sequencing technologies, massive amount of methylation data have been generated, which provide unprecedented opportunities to study the epigenetic mechanism and its relationship to other biological processes. A commonly seen feature of the methylation data is the correlation between nearby CpG sites. Although such a spatial correlation was utilized in several epigenetic studies, its interaction to other characteristics of the methylation data has not been fully investigated.

Results: We filled this research gap from an information theoretic perspective, by exploring the impact of the spatial correlation on the methylation entropy (ME). With the spatial correlation taken into account, we derived the analytical relation between the ME and another key parameter, the methylation probability. By comparing it to the empirical relation between the two corresponding statistics, the observed ME and the mean methylation level, genomic loci under strong epigenetic control can be identified, which may serve as potential markers for cell-type specific methylation. The proposed method was validated by simulation studies, and applied to analyze a published dataset of mouse brain methylome.

Conclusions: Compared to other sophisticated methods developed in literature, the proposed method provides a simple but effective way to detect CpG segments under strong epigenetic control (e.g., with bipolar methylation pattern). Findings from this study shed light on the identification of cell-type specific genes/pathways based on methylation data from a mixed cell population.

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来源期刊
Epigenetics & Chromatin
Epigenetics & Chromatin GENETICS & HEREDITY-
CiteScore
7.00
自引率
0.00%
发文量
35
审稿时长
1 months
期刊介绍: Epigenetics & Chromatin is a peer-reviewed, open access, online journal that publishes research, and reviews, providing novel insights into epigenetic inheritance and chromatin-based interactions. The journal aims to understand how gene and chromosomal elements are regulated and their activities maintained during processes such as cell division, differentiation and environmental alteration.
期刊最新文献
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