Tools and Strategies for Analysis of Genome-Wide and Gene-Specific DNA Methylation Patterns
Tools and Strategies for Analysis of Genome-Wide and Gene-Specific DNA Methylation Patterns
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DOI：
10.1007/978-1-4939-6685-1_15
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发表时间：
2017-01-01
期刊：
影响因子：
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通讯作者：
Stockwell, Peter A.
中科院分区：
文献类型：
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作者：
Chatterjee, Aniruddha;Rodger, Euan J.;Stockwell, Peter A.
DNA甲基化是一种稳定的表观遗传机制，在细胞的正常功能中具有重要作用，因此也在疾病病因学中具有重要作用。准确测量正常和改变的DNA甲基化模式对于理解其在调节基因表达和细胞表型中的作用是重要的。在过去的十年中，在开发研究DNA甲基化的方法方面取得了显着进展。下一代测序的可用性使得能够以前所未有的规模对甲基化标记进行分析。以前用于分析基因座特异性甲基化的几种方法现在已经使用高通量测序或阵列平台升级到全基因组范围。然而，由于有这么多的技术，研究人员面临着评估每种技术的潜在优点或局限性，并选择适当的方法进行分析的挑战。在这篇综述中，我们讨论了询问DNA甲基化的全基因组和基因特异性分析工具的优点和缺点。我们特别关注所涉及的设计和分析策略。本文的综述将为大规模基因座特异性DNA甲基化分析选择合适的方法和工具提供指导。
DNA methylation is a stable epigenetic mechanism that has important roles in the normal function of a cell and therefore also in disease etiology. Accurate measurements of normal and altered DNA methylation patterns are important to understand its role in regulating gene expression and cell phenotype. Remarkable progress has been made over the last decade in developing methodologies to investigate DNA methylation. The availability of next-generation sequencing has enabled the profiling of methylation marks at an unprecedented scale. Several methods that were previously used to profile locus-specific methylation have now been upgraded to a genome-wide scale using high-throughput sequencing or array platforms. However, because there are so many techniques available, researchers are faced with the challenge of assessing the potential merits or limitations of each technique and selecting the appropriate method for their analysis. In this review we discuss the strengths and weaknesses of genome-wide and gene-specific analysis tools for interrogating DNA methylation. We particularly focus on the design and analysis strategies involved. This review will provide a guideline for selecting the appropriate methods and tools for large-scale and locus-specific DNA methylation analysis.