Stereotyped p53 binding tuned by chromatin accessibility. Homo sapiens

We accessed the cell type specificity of p53 by directly measuring DNA binding in twelve cell lines in response to ionizing radiation. We find that that vast majority of binding sites are occupied across all cells lines uniformly, in contrast to p53 regulated gene expression which shows great diversity in the same context. We further identify a subset of p53 binding sites that are more restricted, appearing in one or a few cell lines. We find that chromatin accessibility explains much of these differential binding events. Overall design: p53 DNA binding was measured in twelve cell lines after IR by ChIPseq. The transcriptional response of each of the twelve lines was also measured by mRNAseq. To explore the influence of chromatin accessability p53 binding was compared to ATAC-seq data from two cell lines.

本研究旨在解析p53的细胞类型特异性，通过直接检测12种细胞系受电离辐射（ionizing radiation）刺激后的DNA结合情况展开。我们发现，绝大多数结合位点在所有细胞系中均呈均匀占据状态；与之形成鲜明对比的是，同一刺激条件下p53调控的基因表达谱呈现出显著多样性。本研究进一步筛选得到一组受限性更强的p53结合位点，这类位点仅在一种或少数几种细胞系中出现。我们发现，染色质可及性（chromatin accessibility）可在很大程度上解释这些差异结合事件。实验设计总览：通过染色质免疫共沉淀测序（ChIP-seq）技术，检测了12种细胞系经电离辐射刺激后的p53 DNA结合情况；同时通过信使RNA测序（mRNA-seq）技术，检测了这12种细胞系的转录应答水平。为探究染色质可及性对p53结合的影响，本研究将p53结合数据与两种细胞系的转座酶可及性测序（ATAC-seq）数据进行了比对分析。