[16] Nuclease digestion of transcriptionally active chromatin

This chapter discusses the various nuclease digestion of transcriptionally active chromatin. Active chromatin is less compact than bulk chromatin, and this is reflected in its increased accessibility to enzymes. This can be seen at several levels. First, it compare the structure surrounding a specific gene in terms of its nuclease sensitivity in a cell type where there can be no expression to a cell type where there has been, is, or will be expression of that gene. In general, the structure will be more sensitive in the latter case, even when gene expression is not evident. Second, further changes are associated with gene activity and expression during cell development that are due to modifications in chromatin structure of flanking sequences and increased sensitivity in coding sequences, probably reflecting changes in nucleosomal structure during the passage of polymerase. A number of different situations have been described when filters are probed with DNA from regions of active chromatin. In general, there is an important increase in the general sensitivity to micrococcal nuclease. In certain cases, the regular ladder is disrupted and bands of novel size are detected. In other cases, a repeat structure is found but displaced when compared with that of the bulk chromatin.