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

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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.