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Optical mapping discerns genome wide DNA methylation profiles.
BMC Molecular Biology Pub Date : 2008-07-30 , DOI: 10.1186/1471-2199-9-68
Gene E Ananiev 1 , Steve Goldstein , Rod Runnheim , Dan K Forrest , Shiguo Zhou , Konstantinos Potamousis , Chris P Churas , Veit Bergendahl , James A Thomson , David C Schwartz
Affiliation  

BACKGROUND Methylation of CpG dinucleotides is a fundamental mechanism of epigenetic regulation in eukaryotic genomes. Development of methods for rapid genome wide methylation profiling will greatly facilitate both hypothesis and discovery driven research in the field of epigenetics. In this regard, a single molecule approach to methylation profiling offers several unique advantages that include elimination of chemical DNA modification steps and PCR amplification. RESULTS A single molecule approach is presented for the discernment of methylation profiles, based on optical mapping. We report results from a series of pilot studies demonstrating the capabilities of optical mapping as a platform for methylation profiling of whole genomes. Optical mapping was used to discern the methylation profile from both an engineered and wild type Escherichia coli. Furthermore, the methylation status of selected loci within the genome of human embryonic stem cells was profiled using optical mapping. CONCLUSION The optical mapping platform effectively detects DNA methylation patterns. Due to single molecule detection, optical mapping offers significant advantages over other technologies. This advantage stems from obviation of DNA modification steps, such as bisulfite treatment, and the ability of the platform to assay repeat dense regions within mammalian genomes inaccessible to techniques using array-hybridization technologies.

中文翻译:

光学作图识别全基因组 DNA 甲基化谱。

背景CpG二核苷酸的甲基化是真核基因组中表观遗传调控的基本机制。开发快速全基因组甲基化分析方法将极大地促进表观遗传学领域的假设和发现驱动研究。在这方面,甲基化分析的单分子方法提供了几个独特的优势,包括消除化学 DNA 修饰步骤和 PCR 扩增。结果 基于光学作图,提出了一种用于识别甲基化图谱的单分子方法。我们报告了一系列试点研究的结果,这些研究证明了光学作图作为全基因组甲基化分析平台的能力。光学作图用于从工程大肠杆菌和野生型大肠杆菌中辨别甲基化图谱。此外,使用光学作图分析了人类胚胎干细胞基因组内选定基因座的甲基化状态。结论 光学映射平台有效地检测 DNA 甲基化模式。由于单分子检测,光学映射提供了优于其他技术的显着优势。这一优势源于避免了 DNA 修饰步骤,例如亚硫酸氢盐处理,以及该平台能够分析哺乳动物基因组中使用阵列杂交技术无法访问的重复密集区域。结论 光学映射平台有效地检测 DNA 甲基化模式。由于单分子检测,光学映射提供了优于其他技术的显着优势。这一优势源于避免了 DNA 修饰步骤,例如亚硫酸氢盐处理,以及该平台能够分析哺乳动物基因组内重复密集区域的能力,这些区域是使用阵列杂交技术的技术无法获得的。结论 光学映射平台有效地检测 DNA 甲基化模式。由于单分子检测,光学映射提供了优于其他技术的显着优势。这一优势源于避免了 DNA 修饰步骤,例如亚硫酸氢盐处理,以及该平台能够分析哺乳动物基因组中使用阵列杂交技术无法访问的重复密集区域。
更新日期:2019-11-01
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