Dynamic regulation of nucleosome positioning in the human genome

The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription. However, nucleosome mapping has been performed for only limited genomic regions in humans. We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique. We find that nucleosome phasing relative to the transcription start sites (TSSs) is directly correlated to RNA polymerase II binding. Furthermore, the first nucleosome downstream of TSSs exhibits differential positioning in active and silent genes. TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression. Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome. This microarray dataset is the gene expression data from resting and activated CD4+ T cells. We used this data to look at nucleosome positioning, Pol II and a few chromatin modifications at genes that are silent and activated in both resting and activated T cells as well as genes that are induced or repressed with T cell activation. Keywords: nucleosome mapping, expression data complementary to Solexa ChIP-Seq data Overall design: Gene expression data from resting (M0 and T0) and activated (M18 and T18) T cells.

核小体与DNA的相对定位在转录调控中发挥关键作用。然而，当前人类基因组中仅对有限的基因组区域完成了核小体定位图谱绘制。
本研究利用Solexa高通量测序技术对核小体末端进行直接测序，构建了静息态与活化态人CD4+ T细胞全基因组范围内的核小体定位图谱。
我们发现，相对于转录起始位点（Transcription Start Sites, TSSs）的核小体相位排布与RNA聚合酶II（RNA polymerase II）的结合直接相关。
此外，转录起始位点下游的首个核小体在活跃基因与沉默基因中呈现出差异化的定位模式。
T细胞受体（T cell receptor, TCR）信号传导可诱导启动子与增强子区域发生大规模核小体重排布，以实现转录的激活或抑制。
本研究结果显示，携带H2A.Z组蛋白的核小体与修饰型核小体更易从-1核小体位点处丢失。
本研究数据全面展现了人类基因组中的核小体分布图谱及其动态调控机制。
本微阵列数据集包含静息态与活化态CD4+ T细胞的基因表达数据。
我们利用该数据集分析了静息态与活化态T细胞中沉默基因、活化基因，以及随T细胞活化被诱导或抑制的基因的核小体定位、RNA聚合酶II结合情况与部分染色质修饰状态。
关键词：核小体定位图谱绘制、与Solexa平台染色质免疫共沉淀测序（Chromatin Immunoprecipitation Sequencing, ChIP-Seq）数据互补的表达谱数据
实验设计：包含静息态（M0、T0组）与活化态（M18、T18组）T细胞的基因表达数据。