Regulation of Gene Expression in Eukaryotes:- Transcriptionally Active Chromatin Is Structurally Distinct from Inactive Chromatin
The effects of chromosome structure on gene regulation in eukaryotes have no clear parallel in prokaryotes. In the eukaryotic cell cycle, interphase chromosomes appear, at first viewing, to be dispersed and amorphous . Nevertheless, several forms of chromatin can be found along these chromosomes. About 10% of the chromatin in a typical eukaryotic cell is in a more condensed form than the rest of the chromatin. This form, heterochromatin, is transcription ally inactive. Heterochromatin is generally associated with particular chromosome structures—the centromeres, for example. The remaining, less condensed chromatin is called euchromatin. Transcription of a eukaryotic gene is strongly re pressed when its DNA is condensed within heterochromatin. Some, but not all, of the euchromatin is transcriptionally active. Transcriptionally active chromosomal regions can be detected based on their increased sensitivity to nuclease-mediated degradation. Nucleases such as DNase I tend to cleave the DNA of carefully isolated chromatin into fragments of multiples of about 200 bp, reflecting the regular repeating structure of the nucleosome . In actively tran scribed regions, the fragments produced by nuclease activity are smaller and more heterogeneous in size. These regions contain hypersensitive sites, sequences especially sensitive to DNase I, which consist of about 100 to 200 bp within the 1,000 bp flanking the 5 ends of transcribed genes. In some genes, hypersensitive sites are found farther from the 5end, near the 3end, or even within the gene itself. Many hypersensitive sites correspond to binding sites for known regulatory proteins, and the relative absence of nucleosomes in these regions may allow the binding of these proteins. Nucleosomes are entirely ab sent in some regions that are very active in transcription, such as the rRNA genes. Transcriptionally active chromatin tends to be deficient in histone H1, which binds to the linker DNA between nucleosome particles. Histones within transcriptionally active chromatin and heterochromatin also differ in their patterns of co valent modification. The core histones of nucleosome particles (H2A, H2B, H3, H4; see Fig. 24–27) are modified by irreversible methylation of Lys residues, phos phorylation of Ser or Thr residues, acetylation (see below), or attachment of ubiquitin . Each of the core histones has two distinct structural domains. A central domain is involved in histone-histone interaction and the wrapping of DNA around the nucleosome. A second, lysine-rich amino-terminal domain is generally positioned near the exterior of the assembled nucleosome particle; the covalent modifications occur at specific residues concentrated in this amino-terminal domain. The patterns of modification have led some re searchers to propose the existence of a histone code, in which modification patterns are recognized by enzymes that alter the structure of chromatin. Modifications as sociated with transcriptional activation would be recognized by enzymes that make the chromatin more accessible to the transcription machinery. 5-Methylation of cytosine residues of CpG sequences is common in eukaryotic DNA (p. 296), but DNA in transcriptionally active chromatin tends to be undermethylated. Furthermore, CpG sites in particular genes are more often undermethylated in cells from tis sues where the genes are expressed than in those where the genes are not expressed. The overall pattern suggests that active chromatin is prepared for transcription by the removal of potential structural barriers.
