Applications of alignment-free methods in epigenomics
Applications of alignment-free methods in epigenomics
复制标题
DOI：
10.1093/bib/bbt078
复制
发表时间：
2014-05-01
影响因子：
9.5
通讯作者：
Yuan, Guo-Cheng
中科院分区：
文献类型：
--
作者：
Pinello, Luca;Lo Bosco, Giosue;Yuan, Guo-Cheng
表观遗传机制在调节细胞类型特异性基因活动中起着重要作用，但表观遗传模式如何建立和维持仍然知之甚少。最近的研究支持DNA序列在表观遗传调节因子的募集中的作用。无比对方法已被应用于鉴定与表观遗传模式相关的不同序列特征和预测表观基因组谱。本文综述了DNA序列到特征空间的映射方法、序列比较和预测模型等方面的研究进展。使用这些方法的计算研究提供了重要的见解表观遗传调控机制。
Epigenetic mechanisms play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators. Alignment-free methods have been applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles. Here, we review recent advances in such applications, including the methods to map DNA sequence to feature space, sequence comparison and prediction models. Computational studies using these methods have provided important insights into the epigenetic regulatory mechanisms.