Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
Bioinformatics. 2011 Jan 15;27(2):147-52. doi: 10.1093/bioinformatics/btq637. Epub 2010 Nov 11.
Chromatin regulators (CR) and transcription factors (TF) are important trans-acting factors regulating transcription process, and many efforts have been devoted to understand their underlying mechanisms in gene regulation. However, the influences of CR and TF regulation effects on nucleosomes during transcription are still minimally understood, and it remains to be determined the extent to which CR and TF regulatory effect shape the organization of nucleosomes in the genome. In this article we attempted to address this problem and examine the patterns of CR and TF regulation effects from the nucleosome perspective.
Our results show that the CR and TF regulatory effects exhibit different paradigms of transcriptional control in Saccharomyces cerevisiae. We grouped yeast genes into two categories, 'CR-sensitive' genes and 'TF-sensitive' genes, based on how their expression profiles change upon deletion of CRs or TFs. We found that genes in these two groups have very different patterns of nucleosome organization. The promoters of CR-sensitive genes tend to have higher nucleosome occupancy, whereas the promoters of TF-sensitive genes are depleted of nucleosomes. Furthermore, the nucleosome profiles of CR-sensitive genes tend to show more dynamic characteristics than TF-sensitive genes. These results reveal that the nucleosome organizations of yeast genes have a strong impact on their mode of regulation, and there are differential regulation effects on nucleosomes between CRs and TFs.
染色质调节因子 (CR) 和转录因子 (TF) 是调节转录过程的重要反式作用因子，许多努力都致力于理解它们在基因调控中的潜在机制。然而，CR 和 TF 调节效应在转录过程中对核小体的影响仍知之甚少，并且仍需要确定 CR 和 TF 调节效应在多大程度上塑造了基因组中核小体的组织。在本文中，我们试图解决这个问题，并从核小体的角度研究 CR 和 TF 调节效应的模式。
我们的结果表明，CR 和 TF 的调节效应在酿酒酵母中表现出不同的转录控制模式。我们根据 CR 或 TF 缺失时其表达谱的变化，将酵母基因分为两类，即“CR 敏感基因”和“TF 敏感基因”。我们发现这两组基因的核小体组织模式非常不同。CR 敏感基因的启动子往往具有更高的核小体占有率，而 TF 敏感基因的启动子则缺乏核小体。此外，CR 敏感基因的核小体谱往往比 TF 敏感基因表现出更多的动态特征。这些结果表明，酵母基因的核小体组织对其调节模式有很强的影响，并且 CR 和 TF 对核小体的调节作用存在差异。
