Makeev Vsevolod J, Lifanov Alexander P, Nazina Anna G, Papatsenko Dmitri A
Scientific Center Genetika, Moscow 113545, Russia.
Nucleic Acids Res. 2003 Oct 15;31(20):6016-26. doi: 10.1093/nar/gkg799.
We explored distance preferences in the arrangement of binding motifs for five transcription factors (Bicoid, Krüppel, Hunchback, Knirps and Caudal) in a large set of Drosophila cis-regulatory modules (CRMs). Analysis of non-overlapping binding motifs revealed the presence of periodic signals specific to particular combinations of binding motifs. The most striking periodic signals (10 bp for Bicoid and 11 bp for Hunchback) suggest preferential positioning of some binding site combinations on the same side of the DNA helix. We also analyzed distance preferences in arrangements of highly correlated overlapping binding motifs, such as Bicoid and Krüppel. Based on the distance analysis, we extracted preferential binding site arrangements and proposed models for potential composite elements (CEs) and antagonistic motif pairs involved in the function of developmental CRMs. Our results suggest that there are distinct hierarchical levels in the organization of transcription regulatory information. We discuss the role of the hierarchy in understanding transcriptional regulation and in detection of transcription regulatory regions in genomes.
我们在大量果蝇顺式调控模块（CRM）中探究了5种转录因子（双胸、克鲁佩尔、驼背、克尼普斯和尾型）结合基序排列中的距离偏好。对非重叠结合基序的分析揭示了特定结合基序组合所特有的周期性信号的存在。最显著的周期性信号（双胸为10个碱基对，驼背为11个碱基对）表明某些结合位点组合在DNA螺旋的同一侧存在优先定位。我们还分析了高度相关的重叠结合基序（如双胸和克鲁佩尔）排列中的距离偏好。基于距离分析，我们提取了优先结合位点排列，并提出了参与发育CRM功能的潜在复合元件（CE）和拮抗基序对的模型。我们的结果表明，转录调控信息的组织存在不同的层次水平。我们讨论了这种层次结构在理解转录调控以及在基因组中转录调控区域检测中的作用。
