Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA.
Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA.
Free Radic Biol Med. 2021 Aug 1;171:319-331. doi: 10.1016/j.freeradbiomed.2021.05.016. Epub 2021 May 13.
Reactive oxygen species (ROS) are important signaling molecules in many physiological processes, yet excess ROS leads to cell damage and can lead to pathology. Accordingly, cells need to maintain tight regulation of ROS levels, and ROS-responsive transcriptional reprogramming is central to this process. Although it has long been recognized that oxidative stress leads to rapid, significant changes in gene expression, the impact of oxidative stress on the underlying chromatin accessibility landscape remained unclear. Here, we asked whether ROS-responsive transcriptional reprogramming is accompanied by reprogramming of the chromatin environment in MCF7 human breast cancer cells. Using a time-course exposure to multiple inducers of oxidative stress, we determined that the widespread ROS-responsive changes in gene expression induced by ROS occur with minimal changes to the chromatin environment. While we did observe changes in chromatin accessibility, these changes were: (1) far less numerous than gene expression changes after oxidative stress, and (2) occur within pre-existing regions of accessible chromatin. Transcription factor (TF) footprinting analysis of our ATAC-seq experiments identified 5 TFs or TF families with evidence for ROS-responsive changes in DNA binding: NRF2, AP-1, p53, NFY, and SP/KLF. Importantly, several of these (AP-1, NF-Y, and SP/KLF factors) have not been previously implicated as widespread regulators in the response to ROS. In summary, we have characterized genome-wide changes in gene expression and chromatin accessibility in response to ROS treatment of MCF7 cells, and we have found that regulation of the large-scale transcriptional response to excess ROS is primarily constrained by the cell's pre-existing chromatin landscape.
活性氧（ROS）是许多生理过程中重要的信号分子，但过量的 ROS 会导致细胞损伤，并可能导致病理学。因此，细胞需要对 ROS 水平进行严格的调节，ROS 响应的转录重编程是这个过程的核心。尽管人们早就认识到氧化应激会导致基因表达的快速、显著变化，但氧化应激对潜在染色质可及性景观的影响仍不清楚。在这里，我们询问 ROS 响应的转录重编程是否伴随着 MCF7 人乳腺癌细胞染色质环境的重编程。通过对多种氧化应激诱导剂进行时间过程暴露，我们确定 ROS 诱导的基因表达的广泛 ROS 响应变化伴随着染色质环境的最小变化。虽然我们确实观察到染色质可及性的变化，但这些变化是：（1）在氧化应激后，远远少于基因表达变化的数量，并且（2）发生在预先存在的可及染色质区域内。我们的 ATAC-seq 实验的转录因子（TF）足迹分析确定了 5 个具有 ROS 响应 DNA 结合证据的 TF 或 TF 家族：NRF2、AP-1、p53、NFY 和 SP/KLF。重要的是，其中一些（AP-1、NF-Y 和 SP/KLF 因子）以前没有被认为是对 ROS 反应的广泛调节因子。总之，我们已经描述了 MCF7 细胞对 ROS 处理的全基因组基因表达和染色质可及性变化，并且我们发现，对过量 ROS 的大规模转录反应的调节主要受到细胞预先存在的染色质景观的限制。
