当前位置: X-MOL 学术IUBMB Life › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Hypoxia‐induced alterations of transcriptome and chromatin accessibility in HL ‐1 cells
IUBMB Life ( IF 4.6 ) Pub Date : 2020-04-29 , DOI: 10.1002/iub.2297
Jingru Wang 1 , Yang Wang 1 , Zhiying Duan 1 , Weina Hu 1
Affiliation  

Cardiac hypoxia plays a significant role in various types of heart disease, and improper treatment of hypoxia often leads to myocardial cell damage or even death. Transcriptome profiling and open chromatin mapping have been used as powerful tools to understand the development of heart disease, but the interplay between gene expression and chromatin accessibility has not been extensively investigated in hypoxia‐induced cardiac damage. In this study, with HL‐1 cardiomyocytes as a model, we performed temporal profiling of transcriptome and chromatin accessibility to show the cardiac responses to hypoxia (for 4 and 8 hr) and reoxygenation (for 24 hr). With RNA‐seq and ATAC‐seq, we identified a total of 2,912 differentially expressed genes and 3,004 differential peaks across the whole genome and showed that these data were in good agreement with each other. For hypoxia‐related genes, we also discovered high correlations between their ATAC‐seq signals and mRNA levels, such as VEGF, Angpt1, Slc2a1, Bnip3, and Casp3 with Pearson correlations >0.7. Interestingly, after 24 hr reoxygenation, the expression levels of 235 genes were still significantly different from the counterparts in the control, suggesting that these genes need a longer recovery time after reoxygenation. In conclusion, our study shows the close relationship between alterations of transcriptome and chromatin accessibility after hypoxia exposure and reoxygenation, emphasizing the importance of open chromatin profiling in related studies. In addition, the profiled molecular responses here will be valuable resources for better understanding of the mechanisms responsible for hypoxia‐induced heart disease in future.

中文翻译:

缺氧诱导的 HL-1 细胞转录组和染色质可及性的改变

心脏缺氧在各类心脏病中起重要作用,缺氧治疗不当常导致心肌细胞损伤甚至死亡。转录组分析和开放染色质图谱已被用作了解心脏病发展的有力工具,但基因表达和染色质可及性之间的相互作用尚未在缺氧诱导的心脏损伤中得到广泛研究。在这项研究中,以 HL-1 心肌细胞为模型,我们对转录组和染色质可及性进行了时间分析,以显示心脏对缺氧(4 小时和 8 小时)和复氧(24 小时)的反应。使用 RNA-seq 和 ATAC-seq,我们共鉴定了 2,912 个差异表达基因和 3, 004 整个基因组的差异峰,表明这些数据彼此非常吻合。对于缺氧相关基因,我们还发现它们的 ATAC-seq 信号与 mRNA 水平之间存在高度相关性,例如 VEGF、Angpt1、Slc2a1、Bnip3 和 Casp3,Pearson 相关性 >0.7。有趣的是,再充氧 24 小时后,235 个基因的表达水平仍与对照中的对应基因显着不同,表明这些基因在再充氧后需要更长的恢复时间。总之,我们的研究表明,缺氧暴露和复氧后转录组的改变与染色质可及性之间存在密切关系,强调开放染色质分析在相关研究中的重要性。此外,
更新日期:2020-04-29
down
wechat
bug