Delphine Balaramane, Yannick G Spill, Michaël Weber, Anaïs Flore Bardet
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引用次数: 0
Abstract
DNA methylation is an epigenetic mark involved in the regulation of gene expression, and patterns of DNA methylation anticorrelate with chromatin accessibility and transcription factor binding. DNA methylation can be profiled at the single cytosine resolution in the whole genome and has been performed in many cell types and conditions. Computational approaches are then essential to study DNA methylation patterns in a single condition or capture dynamic changes of DNA methylation levels across conditions. Toward this goal, we developed MethyLasso, a new approach to segment DNA methylation data. We use it as an all-in-one tool to perform the identification of low-methylated regions, unmethylated regions, DNA methylation valleys and partially methylated domains in a single condition as well as differentially methylated regions between two conditions. We performed a rigorous benchmarking comparing existing approaches by evaluating the agreement of the regions across tools, their number, size, level of DNA methylation, boundaries, cytosine–guanine content and coverage using several real datasets as well as the sensitivity and precision of the approaches using simulated data and show that MethyLasso performs best overall. MethyLasso is freely available at https://github.com/bardetlab/methylasso.
DNA 甲基化是一种参与基因表达调控的表观遗传标记,DNA 甲基化模式与染色质可及性和转录因子结合反相关。DNA 甲基化可在全基因组中以单胞嘧啶为分辨率进行分析,并已在多种细胞类型和条件下进行了研究。因此,计算方法对于研究单一条件下的 DNA 甲基化模式或捕捉不同条件下 DNA 甲基化水平的动态变化至关重要。为了实现这一目标,我们开发了 MethyLasso,这是一种分割 DNA 甲基化数据的新方法。我们将其作为一种一体化工具,用于识别单一条件下的低甲基化区域、未甲基化区域、DNA 甲基化谷和部分甲基化域,以及两种条件下的差异甲基化区域。我们对现有方法进行了严格的基准比较,使用多个真实数据集评估了不同工具的区域一致性、区域数量、大小、DNA 甲基化水平、边界、胞嘧啶-鸟嘌呤含量和覆盖率,并使用模拟数据评估了各种方法的灵敏度和精确度,结果表明 MethyLasso 的总体性能最佳。MethyLasso 可在 https://github.com/bardetlab/methylasso 免费获取。
期刊介绍:
Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.