Nuclear Receptors

SANAULLAH IQBAL
 Transcription factor glossary
 gene expression – the process by which information from a gene is used in the
synthesis of a functional gene product such as a protein
 transcription – the process of making RNA from a DNA template by RNA
polymerase
 transcription factor – a protein that binds to DNA and regulates gene expression by
promoting or suppressing transcription
 upregulation, activation, or promotion – increase the rate of gene transcription
 downregulation, repression, or suppression – decrease the rate of gene
transcription
 coactivator – a protein that works with transcription factors to increase the rate of
gene transcription
 corepressor – a protein that works with transcription factors to decreasethe rate of
gene transcription
 response element – a specific sequence of DNA that a transcription factor binds to
 Transcription Factors
 TF are proteins that are required to initiate or regulate gene transcription in
eukaryotic cells.
 General transcription factors are required for basal transcription of genes and
participate in formation of the transcription-initiation complex.
 Many interact directly with RNA polymerase.
 Specific TF stimulate or repress transcription of particular genes by binding to their
coordinate regulatory sequence which promotes or blocks RNA
polymerase binding respectively.
 TF is that they contain one or more DNA-binding domains (DBDs), which attach to
specific sequences of DNA adjacent to the genes that they regulate.
 Additional proteins such as coactivators, chromatin remodelers, histone
acetylases, deacetylases, kinases, and methylases, while also playing crucial roles
in gene regulation, lack DNA-binding domains, and, therefore, are not classified as
transcription factors.
 Transcription Factors-Mechanism

 stabilize or block the binding of RNA polymerase to DNA

 catalyze the acetylation or deacetylation of histone
 The transcription factor can either do this directly or recruit other
proteins with this catalytic activity. Many transcription factors use one
or the other of two opposing mechanisms to regulate transcription:
 histone acetyltransferase (HAT) activity – acetylates histone proteins, which
weakens the association of DNA with histones, which make the DNA more
accessible to transcription, thereby up-regulating transcription
 histone deacetylase (HDAC) activity – deacetylates histone proteins, which
strengthens the association of DNA with histones, which make the DNA less
accessible to transcription, thereby down-regulating transcription
 recruit coactivator or corepressor proteins to the transcription factor
DNA complex
 Nuclear Receptors
 Nuclear receptors (also known as nuclear hormone receptors) are a
large family of TF that bind directly to DNA to regulate the expression of
target genes.
 Small lipophilic molecules, such as fat-soluble hormones, vitamins, and
intermediary metabolites, play an important role in the growth,
differentiation, metabolism, reproduction, and morphogenesis of
higher organisms and humans.
 Unlike polypeptide hormones that act on membrane-bound receptors
and activate signaling pathways that lead to gene regulation, most
cellular actions of the lipophilic hormones are mediated through direct
binding to nuclear receptors, which act as ligand-inducible
transcription factors to activate or repress many target genes
 Nuclear Receptors

 Nuclear receptors (NRs) are a family of highly conserved TF

that regulate transcription in response to small lipophilic
compounds
 Nuclear receptors (NRs) are proteins that share
considerable amino acid sequence similarity in two highly
conserved domains – the DNA binding (DBD) and the
ligand binding domains (LBD)
Nuclear Receptor Parts
Nuclear Receptors
 Most NRs have molecular masses b/w 50 and 100 Kda
 (A-B) N-terminal regulatory domain: Contains the activation function 1 (AF-1)
whose action is independent of the presence of ligand. It is highly variable in
sequence b/w various NRs.
 (C) DNA-binding domain (DBD): Highly conserved domain containing two zinc
fingers that binds to specific sequences of DNA called hormone response
elements (HRE).
 (D) Hinge region: a flexible domain that connects the DBD with the LBD
 (E) Ligand binding domain (LBD): Moderately conserved in sequence and
highly conserved in structure b/w the various NRs. The LBD also contains the
activation function 2 (AF-2) whose action is dependent on the presence of
bound ligand.
 (F) C-terminal domain: Highly variable in sequence b/w various NRs
 Ligands

 Ligands for NRs are as varied as the proteins themselves.

 Although the structures of these compounds is varied, a few
generalized comments can be made.
 All ligands are lipophilic and can easily transverse the plasma
membrane as well as the nuclear membrane, if required.
 The affinity (Kd) of the ligand-receptor complex is generally in
the nM range, but can vary from pM to mM.
 the concentrations of each natural ligand should approach
their Kd to be considered a physiologically-relevant ligand.
What could be a Ligand?
What could be a Ligand?
Subfamilies of nuclear receptors
 Nuclear Receptors classification
The nuclear receptor superfamily are classified by sequence alignment and
phylogenetic tree construction into six main subfamilies:
 Thyroid Hormone Receptor-like: includes thyroid receptor, retinoic acid
receptor, PPAR, LXR, FXR, VDR, PXR and CAR
 Retinoid X Receptor-like: includes RXR
 Estrogen Receptor-like (also known as steroid hormone receptors): includes
receptors for estrogen (ER), androgen, glucocorticoid, mineralocorticoid and
progesterone
 Nerve Growth Factor IB-like
 Steroidogenic Factor-like
 Germ Cell Nuclear Factor-like
 Nuclear Receptors Mechanism

 Many unliganded non-steroid receptors are located in the nucleus

and can interact directly with chromatin.

 Once in the nucleus the receptors regulate transcription by

binding, generally as dimers, to DNA sequences termed positive or
negative hormone response elements (HREs), normally located in
regulatory regions of target genes
 Nuclear Receptors Mechanism
 The effects of NRs on transcription are mediated through recruitment
of co-regulators.
 A subset of receptors binds co-repressors and actively represses target
gene expression in the absence of ligand.
 Upon ligand binding the receptors undergo a conformational change
that causes co-repressor release and the recruitment of co-activator
complexes and transcriptional activation of genes containing HREs.
 NRs can also regulate expression of genes that do not contain HREs by
modulation of the activity of signaling pathways and transcription
factors that bind to the target promoter.
Nuclear Receptors Mechanism

 Hydrophylic activators
 Alternative ligand-independent pathways for activation of nuclear
receptors exist.
 For example, some receptors can be activated by phosphorylation
mediated by hormones and growth factors that stimulate diverse
signal transduction pathways.
 These signaling pathways can also affect hormone-mediated
transcription by modification of co-activators and co-repressors
 Nuclear Receptors Mechanism

Once in the nucleus the receptors regulate transcription by binding, generally as dimers,
to HREs located in regulatory regions of target genes, Activity is regulated by an
exchange of co-repressor (CoR) and coactivator (CoA) complexes.
Receptors Mechanism
Mechanism I of nuclear receptor action
NR, in the absence of ligand, is located in the cytosol. Hormone binding to the NR triggers dissociation
of heat shock proteins (HSP), dimerization, and translocation to the nucleus, where the NR binds to HRE.
The NR DNA complex in turn recruits other proteins that are responsible for transcription of downstream
DNA into mRNA, which is eventually translated into protein, which results in a change in cell function.
 Mechanism II nuclear receptor action
NR, regardless of ligand-binding status, is located in the nucleus bound to DNA. E.g. the nuclear receptor
shown here is the thyroid hormone receptor (TR). In the absence of ligand, the TR is bound to corepressor
protein. Ligand binding to TR causes a dissociation of corepressor and recruitment of coactivator protein,
which, in turn, recruits additional proteins such as RNA polymerase that are responsible for transcription of
downstream DNA into RNA and eventually protein.
Nuclear Receptors Mechanism

Intracellular receptors Signal transduction