The chromatin structure in the coding region of genes: in vivo studies with a model yeast gene

真核基因组紧凑成染色质，才能使DNA与有限的核体积相适应。因此，这种紧凑的结构天生就抑制了需要访问DNA序列的过程，如转录调控。染色质在转录起始控制中的作用已经引起了人们的极大兴趣，因为许多转录激活因子招募了在基因调控区进行染色质重塑的特殊酶。这些事件是转录机制随后的预启动复合体组装所必需的。现在很清楚，转录延长是转录过程中一个高度受调控的步骤。RNA聚合酶需要穿过核小体，这是转录延长的主要障碍。因此，近年来，人们投入了大量的努力来了解RNA聚合酶是如何通过染色质模板伸长的。虽然已经取得了重要的进展，但目前的大部分知识都来自于体外研究。更好地了解体内基因编码区的染色质结构仍然是一个挑战。包括我自己在内的许多研究表明，高转录的核糖体基因的编码区缺乏规范的核小体。然而，组蛋白蛋白是否以修饰和(或)未折叠的形式存在仍在很大程度上是未知的。此外，是否需要RNA聚合酶的存在来保持核糖体基因的编码区不受规范核小体的影响，目前还不清楚。为了研究基因编码区的染色质结构，我们提出了酵母核糖体基因作为生物模型。我们已经开发了在体内进行这些研究所需的生化方法。结合在酵母中如此成功地使用的强大的遗传分析工具，我们希望帮助定义染色质中转录延伸的过程。

Compaction of eukaryotic genomes into chromatin is required to fit the DNA within the limited volume of the nucleus. Consequently, this compacted structure is inherently repressive to processes that require access to the DNA sequence, such as the regulation of transcription. The role of chromatin in the control of transcription initiation has received a great share of interest with the discovery that a number of transcriptional activators recruit specialized enzymes that carry out chromatin remodeling at regulatory regions of genes. These events are required for the subsequent pre-initiation complex assembly of the transcription machinery. It is now clear that transcript elongation is a highly regulated step of the transcription process. The requirement of RNA polymerases to traverse a nucleosome represents a major block to transcriptional elongation. Thus, in recent years a great deal of effort has been invested to understand how RNA polymerases elongate through chromatin templates. Although important progress has been made, most of the current knowledge derives from in vitro studies. Challenges remain to better understand what is the structure of chromatin in the coding regions of genes in vivo. A number of studies, including my own, have shown that the coding regions of the highly transcribed ribosomal genes are depleted of canonical nucleosomes. However, it is still largely unknown if histone proteins are present in a modified and (or) unfolded form. Also, it remains elusive whether the presence of RNA polymerases is needed to keep the coding region of ribosomal genes free of canonical nucleosomes. To study the structure of chromatin in the coding region of genes, we propose the yeast ribosomal genes as a biological model. We have developed the biochemical methods needed to carry out these studies in vivo. In combination with the powerful tools of genetic analysis used so successfully in yeast, we hope to help define the process of transcription elongation in chromatin.