Influence of catalytic and non-catalytic functions of class I HDACs on the cellular transcriptome

We generated a cellular class I HDAC toolbox allowing to discriminate between catalytic and non-catalytic roles of class I HDACs. Our study reveals a comprehensive, functional analysis of class I HDACs. Overall design: HAP1 cell lines lacking individual HDACs or expressing catalytically inactive, transgenic isoforms were used for gene expression analysis. We demonstrate that HDAC1 and HDAC2 have crucial, partially overlapping functions in the regulation of gene expression. Disrupting HDAC3 caused major changes in the transcriptome, indicating that this enzyme has unique regulatory roles. Furthermore, cells expressing inactive HDAC1, HDAC2 and HDAC8 better mimicked HDAC inhibitor treated cells compared to their respective knockouts. 3 biological replica were analyzed of each cell line or treatment condition, including: 1) control cell line (untreated), 2) cells with knockout of individual class I HDACs, 3) cells expressing inactive transgenic HDAC from the AAVS1 locus in the control background, 4) cells expressing either active or inactive transgenic HDAC from the AAVS1 locus in the corresponding knockout background, 4) cells treated with MS-275, 5) cells treated with JQ12

我们构建了一套可区分I类组蛋白去乙酰化酶（class I HDAC）催化与非催化功能的细胞工具库。本研究实现了对I类HDAC的全面功能分析。整体实验设计：本研究采用缺失单个HDAC或表达催化失活转基因亚型的HAP1细胞系开展基因表达分析。研究表明，HDAC1与HDAC2在基因表达调控中发挥关键且部分重叠的功能。敲除HDAC3会导致转录组发生显著变化，提示该酶具有独特的调控作用。此外，相较于对应的HDAC敲除细胞系，表达失活HDAC1、HDAC2与HDAC8的细胞能更好地模拟HDAC抑制剂处理后的细胞表型。每个细胞系或处理条件均设置3次生物学重复，分析样本包括：1) 未处理的对照细胞系；2) 单个I类HDAC敲除细胞系；3) 在对照背景中从AAVS1位点表达失活转基因HDAC的细胞；4) 在对应敲除背景中从AAVS1位点表达活性或失活转基因HDAC的细胞；4) 经MS-275处理的细胞；5) 经JQ12处理的细胞。