Hormone Binding to a Nuclear Receptor

Regulates Its Activity as a Transcription Factor

The mechanism whereby hormone binding controls the
activity of nuclear receptors differs between heterodimeric
and homodimeric receptors. Heterodimeric nuclear receptors
(e.g., RXR-VDR, RXR-TR, and RXR-RAR) are
located exclusively in the nucleus. In the absence of their
hormone ligand, they repress transcription when bound to
their cognate sites in DNA. They do so by directing histone
deacetylation at nearby nucleosomes by associating with histone
deacetylase complexes, as described earlier for other
repressors (see Figure 9-37a). When heterodimeric nuclear
receptors bind their ligand, they undergo a conformational
change, and as a consequence, they bind histone acetylase
complexes, thereby reversing their own repressing effects.
In the presence of ligand, the ligand-bound conformation of
the receptor also binds Mediator, stimulating preinitiation
complex assembly.
In contrast to heterodimeric nuclear receptors, homodimeric
receptors are found in the cytoplasm in the absence of
their ligands. Hormone binding to these receptors leads to
their translocation to the nucleus. The hormone-dependent
translocation of the homodimeric glucocorticoid receptor
(GR) was demonstrated in the transfection experiments shown
in Figure 9-45ac. The GR hormone-binding domain alone
mediates this transport. Subsequent studies showed that in
the absence of hormone, GR cannot be transported into the
nucleus because its ligand-binding domain is partially unfolded
by the major cellular chaperone Hsp70. As long as the receptor
is confined to the cytoplasm, it cannot interact with target
genes and hence cannot activate transcription. Hormone
binding promotes a handoff of GR from Hsp70 to Hsp90,
which, with coupled hydrolysis of ATP, refolds the GR ligandbinding
domain, increasing the affinity for hormone and releasing
GR from Hsp70 so that it can enter the nucleus. Once
in the nucleus in the conformation induced by ligand binding,
it can bind to response elements associated with target genes
(Figure 9-45d). Once the receptor with bound hormone binds
to a response element, it activates transcription by interacting
with chromatin-remodeling and histone acetylase complexes

Metazoans Regulate the RNA Polymerase II

Transition from Initiation to Elongation
A recent unexpected discovery that resulted from application
of the chromatin immunoprecipitation technique (see
Figure 9-18) is that a large fraction of genes in metazoans have
a paused elongating RNA polymerase II within about 100 bp
of the transcription start site. Thus expression of the encoded
protein is controlled not only by transcription initiation, but
also by transcription elongation early in the transcription
unit. The first genes discovered to be regulated by control of
transcription elongation were heat-shock genes (e.g., hsp70),
which encode molecular chaperones that help to refold denatured
proteins and other proteins that help the cell to deal
with the effects of heat shock. When heat shock occurs, the
heat-shock transcription factor (HSTF) is activated. Binding
of activated HSTF to specific sites in the promoter-proximal
region of heat-shock genes stimulates the paused polymerase
to continue chain elongation and promotes rapid reinitiation
by additional Pol II molecules, leading to many transcription
initiations per minute. This mechanism of transcriptional control
permits a rapid response: these genes are always paused
in a state of suspended transcription and therefore, when an
emergency arises, no time is required to remodel and acetylate
chromatin at the promoter and assemble a transcription preinitiation
complex.
Another transcription factor shown to regulate transcription
by controlling elongation by Pol II paused near the transcription
start site is MYC, which functions in the regulation
of cell growth and division. MYC is often expressed at high
levels in cancer cells and is a key transcription factor in the
reprogramming of somatic cells into pluripotent stem cells
capable of differentiation into any cell type. The ability to induce
differentiated cells to convert to pluripotent stem cells
has elicited enormous research interest because of its potential
for the development of therapeutic treatments for traumatic
injuries to the nervous system and degenerative diseases (see

Termination of Transcription Is Also Regulated

Once Pol II has transcribed about 200 nucleotides from
the transcription start site, elongation through most genes
is highly processive. Chromatin immunoprecipitation with
antibody to Pol II, however, indicates that the amount of
Pol II at various positions in a transcription unit in a population
of cells varies greatly (see Figure 9-18b, right). This
finding indicates that the enzyme can elongate through some
regions much more rapidly than others. In most cases, Pol
II does not terminate transcription until after a sequence is
transcribed that directs cleavage and polyadenylation of the
RNA at the sequence that forms the 3 end of the encoded
mRNA. Pol II can then terminate transcription at any of
multiple sites located 0.52 kb beyond this poly(A) addition
site. Experiments with mutant genes show that termination
is coupled to the process that cleaves and polyadenylates the
3 end of a transcript, which is discussed in the next chapter.