Zeng Jia, Cao Xiao-Qin, Zhao Hongya, Yan Hong
Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Oct;80(4 Pt 1):041917. doi: 10.1103/PhysRevE.80.041917. Epub 2009 Oct 13.
DNA rigidity is an important physical property originating from the DNA three-dimensional structure. Although the general DNA rigidity patterns in human promoters have been investigated, their distinct roles in transcription are largely unknown. In this paper, we discover four highly distinct human promoter groups based on similarity of their rigidity profiles. First, we find that all promoter groups conserve relatively rigid DNAs at the canonical TATA box [a consensus TATA(A/T)A(A/T) sequence] position, which are important physical signals in binding transcription factors. Second, we find that the genes activated by each group of promoters share significant biological functions based on their gene ontology annotations. Finally, we find that these human promoter groups correlate with the tissue-specific gene expression.
DNA刚性是源自DNA三维结构的一项重要物理特性。尽管人类启动子中一般的DNA刚性模式已得到研究，但其在转录过程中的独特作用在很大程度上仍不为人知。在本文中，我们基于其刚性图谱的相似性发现了四个高度不同的人类启动子组。首先，我们发现所有启动子组在典型的TATA框[一致的TATA(A/T)A(A/T)序列]位置保留相对刚性的DNA，这些是结合转录因子时重要的物理信号。其次，我们发现基于基因本体注释，每组启动子激活的基因具有显著的生物学功能。最后，我们发现这些人类启动子组与组织特异性基因表达相关。
