6.6.3.2.6 Chromatin Structure and Gene Expression. Nucleosomesmodulate the accessibility
of genes to the transcription machinery in at least two different ways. First, the exact position of individ-
ual nucleosomes in promoter regions can change, allowing or denying access of promoter elements to their
transcription factors. Second, the overall density of nucleosomes in a genomic region can alter, leading to
chromatin packingor unpacking, which can have global effects on promoter accessibility.
Transcribed genes in a cell nucleus are more susceptible to digestion by the nuclease DNAse I than those
not undergoing transcription. This demonstrates that the chromatin structure must loosen on transcription.
Sometimes, this ‘active’ chromatinstructure persists in a gene that is no longer being transcribed. This
shows that active chromatin may be a prerequisite for transcriptional activation but it is not sufficient. The
regions of DNase I sensitivity can extend a thousand base pairs or more away from the transcribed region,
suggesting that there are active domains within chromosomes. These domains may be determined by
where they are attached to a nuclear scaffold, also called nuclear matrix,^41 which are comprised mainly of
histone H1 and topoisomerase proteins (Section 2.6.2).
Certain sites within the transcribed regions are even more susceptible to cleavage by DNase I and are there-
fore termed nuclease hypersensitive sites.^42 This hypersensitivity is presumably a consequence of the
nucleosome–DNA interactions. These sites often correspond to promoter regions. For example, in a develop-
ing chick embryo, the adult globin gene becomes nuclease hypersensitive before transcription begins,
which implies that a change in chromatin structure must have already occurred. Such hypersensitivity is
not seen in tissues that never express the gene. For example, no globin genes ever become hypersensi-
tive in developing brain tissue.
A key factor that affects chromatin packing is histone acetylation.^43 The histone components of the nucleo-
some are basic proteins that have many lysine amino acids which bind the phosphate backbone of the DNA
double helix. Some of these lysine residues can become acetylated by nuclear histone acetyltransferase
enzymes, which leads to a reduced affinity of the histones both for the DNA and also each other. Intriguingly,
some proteins known to affect transcriptional initiation have turned out also to be histone acetyltransferases.
6.6.3.2.7 DNA Methylation and Gene Expression. Many of the CG dinucleotides in animals
and CNG trinucleotides (where N can be any nucleotide) in plants carry methyl groups at position 5 of the
cytosine residues.^44 This position lies in the major groove of the double helix and does not disturb either
the helix structure or the base pairing within it (Section 2.2.1). Normally, both C residues of each strand
of the duplex are methylated. It is the only common covalent modification to DNA in eukaryotes and is
found less in lower than in higher eukaryotes. For example, Drosophilahas nearly no DNA methylation
and yeast has none. DNA methylationis detected by the inability of some restriction endonucleases
(Section 5.3.1) to cleave methylated DNA when a cleavage recognition site is present. For example, HpaII
cleaves CCGG but cannot digest CmCGG. Other enzymes that recognise the same site (isoschizomers)
may be unaffected by methylation, or example MspI cuts CmCGG. Unfortunately, not all methylated sites
can be detected in this way, because many are not within restriction sites.
Many constitutively active genes (i.e., those whose expression are never switched off) possess many
more CG dinucleotides than do inducible genes. These ‘CpG-rich islands’ are generally undermethylated
throughout the life of the organism. When methylated DNA is replicated in the cell, the newly synthesised
DNA strands are unmethylated. A DNA methylation complex scans DNA and, if it finds such hemi-
methylated sites in the DNA duplex, it methylates the other strand at the appropriate site.
DNA methylation can have a dramatic effect on gene expression. In general, DNA methylation is asso-
ciated with non-expressed regions of the genome. For example, the majority of detectable methylation
sites for the embryonic -like globin genes become unmethylated in expressing tissue. In adult tissues,
after the switch from embryonic gene expression to adult, the embryonic genes become partially methylated,
and in tissues not expressing globin they are fully methylated.
Thus if an unmethylated segment of the mouse globin locus, containing both the foetal and adult
genes (Figure 6.23), is introduced into cultured mouse cells, both genes are expressed. If instead a meth-
ylated -globin gene is introduced next to an unmethylated globin gene, the gene is no longer active
230 Chapter 6