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

真核生物基因组压缩成染色质是在细胞核有限体积内容纳DNA所必需的。因此，这种紧凑的结构固有地抑制了需要访问DNA序列的过程，例如转录调节。染色质在控制转录起始中的作用已经引起了人们的极大兴趣，因为人们发现许多转录激活因子招募专门的酶，这些酶在基因的调控区域进行染色质重塑。这些事件是转录机制的后续起始前复合体组装所必需的。现在很清楚，转录延伸是转录过程中一个高度调控的步骤。RNA聚合酶穿越核小体的要求是转录延伸的主要障碍。因此，近年来已经投入了大量的努力来了解RNA聚合酶如何通过染色质模板延长。尽管已经取得了重要进展，但目前的大多数知识都来自体外研究。更好地了解体内基因编码区染色质的结构仍然是一个挑战。包括我自己的研究在内的许多研究表明，高度转录的核糖体基因的编码区域缺少典型核小体。然而，如果组蛋白以修饰和（或）未折叠的形式存在，它仍然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典型核小体的影响仍然是难以捉摸的。为了研究基因编码区染色质的结构，我们提出酵母核糖体基因作为生物学模型。我们已经开发了在体内进行这些研究所需的生化方法。结合在酵母中成功使用的强大的遗传分析工具，我们希望能够帮助定义染色质中转录伸长的过程。

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.