NTERA-2细胞中人类CDCA8基因的转录因子谱的芯片分析

为了研究细胞周期相关基因8（CDCA8）的转录调控机制,首先克隆了人类CDCA8基因5’端上游的1071 bp转录调控区。生物信息学预测发现,此区域存在一系列已知转录因子的可能结合位点。联合运用DNA pull-down和转录因子芯片技术分析发现共有114种转录因子在人恶性多发性畸胎瘤细胞（NTERA-2）中与该区域结合, 其中某些转录因子有预测的结合位点,其他没有预测结合位点的转录因子可能是以复合物的形式结合到CDCA8基因的转录调控区。     

Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models

DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA. Recent experimental results and theoretical analyses revealed that the proteins show a rotation-coupled sliding along DNA helical pitch. Here, we performed Brownian dynamics simulations using newly developed coarse-grained protein and DNA models for evaluating how hydrodynamic interactions between the protein and DNA molecules, binding affinity of the protein to DNA, and DNA fluctuations affect the one dimensional diffusion of the protein on the DNA. Our results indicate that intermolecular hydrodynamic interactions reduce 1D diffusivity by 30%. On the other hand, structural fluctuations of DNA give rise to steric collisions between the CG-proteins and DNA, resulting in faster 1D sliding of the protein. Proteins with low binding affinities consistent with experimental estimates of non-specific DNA binding show hopping along the CG-DNA. This hopping significantly increases sliding speed. These simulation studies provide additional insights into the mechanism of how DNA binding proteins find their target sites on the genome.