Transcriptional landscape of Rag2 -/- thymocytes [Mnase-Seq]

We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene expression microarray analysis in CD4+ CD8+ DP thymocytes. Overall, we find a key role for the transcription factor Ets1, contributing towards alpha beta T cell lineage commitment via differential transactivation of stage-specific genes orchestrated by dynamic, co-association -mediated chromatin remodeling, as well as transcription dependent generation of a specialized chromatin structure at the TCR beta locus. Overall design: Genome-wide analysis via ChIP-Seq for Ets1, Runx1, total RNA Pol II binding, H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3, short RNA-Seq, Mnase-Seq in murine Rag2 -/- thymocytes, ChIP-Seq for E47, Mnase-Seq and gene expression microarray analysis in DP thymocytes This Series represents Mnase-Seq data.

本研究主要在小鼠Rag2缺陷型（Rag2 -/-）胸腺细胞中开展多项组学与分子实验：针对标志性转录因子（Transcription Factor, TF）Ets1、Runx1，组蛋白修饰标记H3K4me1、H3K4me2、H3K4me3、H3K27me3、H3K36me3，以及总RNA聚合酶II（RNA Polymerase II, RNA Pol II）进行染色质免疫共沉淀测序（ChIP-Seq）；同时完成短链RNA测序（short RNA-Seq）与核小体定位实验。此外，本研究还在CD4阳性CD8阳性双阳性（Double Positive, DP）胸腺细胞中，针对转录因子E47开展ChIP-Seq、核小体定位实验，并进行基因表达微阵列分析。综上，本研究揭示了转录因子Ets1的关键功能：其可通过动态共结合介导的染色质重塑调控阶段特异性基因的差异反式激活，并依赖转录过程在T细胞受体β（TCRβ）基因座生成特殊染色质结构，进而参与αβ T细胞谱系定向分化。整体实验设计：在小鼠Rag2 -/-胸腺细胞中，通过ChIP-Seq检测Ets1、Runx1、总RNA Pol II的结合情况，以及H3K4me1、H3K4me2、H3K4me3、H3K27me3、H3K36me3的修饰水平，同时开展short RNA-Seq与微球菌核酸酶测序（Mnase-Seq）；在DP胸腺细胞中开展E47的ChIP-Seq、Mnase-Seq及基因表达微阵列分析。本数据集对应Mnase-Seq数据。