Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden.
BMC Genomics. 2013 Jul 16;14:479. doi: 10.1186/1471-2164-14-479.
Gcn5 belongs to a family of histone acetyltransferases (HATs) that regulate protein function by acetylation. Gcn5 plays several different roles in gene transcription throughout the genome but their characterisation by classical mutation approaches is hampered by the high degree of apparent functional redundancy between HAT proteins.
Here we utilise the reduced redundancy associated with the transiently high levels of genomic reprogramming during stress adaptation as a complementary approach to understand the functions of redundant protein families like HATs. We show genome-wide evidence for two functionally distinct roles of Gcn5. First, Gcn5 transiently re-localises to the ORFs of long genes during stress adaptation. Taken together with earlier mechanistic studies, our data suggests that Gcn5 plays a genome- wide role in specifically increasing the transcriptional elongation of long genes, thus increasing the production efficiency of complete long transcripts. Second, we suggest that Gcn5 transiently interacts with histones close to the transcription start site of the many genes that it activates during stress adaptation by acetylation of histone H3K18, leading to histone depletion, probably as a result of nucleosome loss as has been described previously.
We show that stress adaptation can be used to elucidate the functions of otherwise redundant proteins, like Gcn5, in gene transcription. Further, we show that normalization of chromatin-associated protein levels in ChIP experiments in relation to the histone levels may provide a useful complement to standard approaches. In the present study analysis of data in this way provides an alternative explanation for previously indicated repressive role of Gcn5 in gene transcription.
Gcn5 属于组蛋白乙酰转移酶 (HATs) 家族，通过乙酰化调节蛋白质功能。Gcn5 在整个基因组中的基因转录中发挥着多种不同的作用，但由于 HAT 蛋白之间存在高度的表观功能冗余，经典的突变方法对其特征的描述受到了阻碍。
在这里，我们利用应激适应过程中基因组重编程水平暂时升高所带来的冗余度降低，作为理解 HAT 等冗余蛋白家族功能的补充方法。我们提供了 Gcn5 具有两种功能截然不同的作用的全基因组证据。首先，Gcn5 在应激适应期间短暂重新定位到长基因的 ORFs。结合早期的机制研究，我们的数据表明，Gcn5 在广泛的基因组范围内发挥作用，专门增加长基因的转录延伸，从而提高完整长转录本的生产效率。其次，我们认为，Gcn5 可能通过乙酰化组蛋白 H3K18 与应激适应过程中它激活的许多基因的转录起始位点附近的组蛋白短暂相互作用，导致组蛋白耗竭，可能是由于核小体丢失，如先前所述。
我们表明，应激适应可用于阐明其他冗余蛋白（如 Gcn5）在基因转录中的功能。此外，我们表明，与组蛋白水平相关的 ChIP 实验中染色质相关蛋白水平的归一化可能是标准方法的有用补充。在本研究中，以这种方式分析数据提供了对以前表明的 Gcn5 在基因转录中具有抑制作用的替代解释。
