Transcription Factors

Author: simona torriano
Date: 11/09/2012



The transcription factor REST, an RE1-silencing transcription factor, also known as neuron-restrictive silencer factor NRSF blocks transcription of its target genes by binding to a specific consensus 21 bp RE1 binding site/neuron-restrictive silencer element (RE1/NRSE) that is present in the target genes’ regulatory regions. REST/NRSF functions very effectively as a transcriptional repressor at a distance and is able to repress transcription despite location or orientation of the binding site within a gene.
No rest for REST: REST/NRSF regulation of neurogenesis.

Consensus RE1 and relative frequency of occurrence of individual bases at each position of the RE1.

Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes.

From its sequence, fulllength REST has a predicted molecular weight of approximately 121 kDa. However, there are discrepancies in the literature concerning the apparent molecular weight of REST as detected by western blotting. Some studies show REST at about 120 kDa, while most report a higher molecular weight of 190–210 kDa. The anomalous molecular weight of REST is thought to be caused by O-linked glycosylation.
A role for the transcriptional repressor REST in maintaining the phenotype of neurosecretory-deficient PC12 cells.


Your Favorite Gene SigmaREST


The sequence of the longest human clone obtained, XHZ4 (2.04 kb), has a continuous open reading frame that encodes a protein containing eight zinc fingers of the C2H2c class with interfinger sequences that place REST/NRSF in the GLI-Krùppel family of zinc finger proteins.
REST harbors three functional domains: a DNA binding domain containing eight zinc-finger motifs that binds to the RE1 motif, and two independent repressor domains one located at the amino- and one at the carboxy- terminus of the protein.
However, these zinc fingers contain a conserved tyrosine residue absent from the canonical finger sequence. COOH-terminal to the zinc fingers is a 174-amino acid domain rich in lysine (26%; 46 of 174) and serine or threonine (21 percent; 37 of 174).
The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes.

A- Schematic diagram of the predicted amino acid sequence from the NRSF XHZ4 cDNA clone. Stippled boxes indicate the position of zinc fingers, cross-hatched region a domain rich in basic amino acids. B- Alignment of NRSF zinc finger and interfinger sequences. The eight zinc fingers of human NRSF were aligned beginning with the conserved aromatic residue and including the interfinger sequences of fingers z2-7. The consensus (Cons) for GLI-Kruppel zinc fingers and interfinger sequences is shown for comparison.

Tertiary structure: Solution structure of the NRSF/REST-mSin3B PAH1 complex.

Protein Aminoacids Percentage (Width 700 px)


It was originally thought that the REST/NRSF-RE-1/ NRSE system served as a molecular switch that helped distinguish neural from non-neural cell types. Although REST/NRSF is expressed mainly in non-neural cells, the expression of REST/NRSF in neuronal progenitor cells, neurons, and neuronal cell lines has been a matter of controversy.
REST/NRSF expression is regulated on the post-translational level, and although
REST/NRSF mRNA levels stay relatively constant, its protein level is down-regulated via a proteosomal pathway when cells progress on their way to lineage restricted neural progenitors.
No rest for REST: REST/NRSF regulation of neurogenesis.

The transition from stem or progenitor cell to a postmitotic neuron requires disarming REST. During cortical differentiation, post-translational degradation of the REST protein precedes both its dismissal from RE1 sites and transcriptional inactivation of the REST gene itself at terminal differentiation. In contrast to differentiation during embryogenesis, the differentiation of adult hippocampal stem cells to neurons occurs via a small non-coding double stranded RNA (dsRNA) containing RE1 motif that converts REST from a repressor to an activator of neuronal genes. Whether this dsRNA plays a role in differentiation of neural stem and progenitor cells during development has yet to be determined. If so, it must act through a different mechanism that does not depend upon the persistent presence of REST.
A small modulatory dsRNA specifies the fate of adult neural stem cells.


Expression during embryonic stem (ES) cell differentiation into neurons. A- REST, in red, is expressed in both nuclei and cytoplasm of ES cells before differentiation. B- REST, in red, continues to be expressed in ES-derived neural stem cells.. C-D- REST is down-regulated in differentiated early and mature neurons.

The amino terminal repressor domain interacts with mSin3, a corepressor found in all eukaryotes that recruits histone deacetylases (HDACs). The mSin3–HDAC complex, however, is associated primarily with a dynamic mode of repression that can alternate between repression and activation and, therefore, by itself, would probably be inadequate for long-term silencing of neuronal genes. This conundrum was solved by the discovery of the corepressor CoREST, which interacts directly with the carboxy terminal repressor domain of REST and, similar to mSin3, exists stably in complexes with HDACs. Interestingly, unlike mSin3, CoREST is present only in organisms with a nervous system, pointing to CoREST as a more specialized corepressor. Several recent studies indicate that the REST–CoREST complex recruits chromatin modifiers for long-term silencing of neuronal genes. Specifically, CoREST can form immuno-complexes not only with HDACs but also with the histone H3 lysine 9 (H3–K9) methyltransferase G9a and with the histone H3 lysine 4 (H3–K4) demethylase LSD1, both of which mediate modifications associated with gene silencing. These histone-modifying enzymes are required for REST–CoREST silencing in non-neuronal cells. CoREST recruits to the REST–RE1 site other silencing machinery, including the methyl DNA-binding protein MeCP2 and the histone H3–K9 methyltransferase SUV39H1. Heterochromatin protein 1 (HP1), which causes compaction of chromatin and is associated with histone H3–K9 methyltransferases, is also present on the neuronal gene chromatin, specifically on the RE1 region. The effects of these modifications are manifested in histone deacetylation, an absence of H3–K4 methylation, and presence of H3–K9 methylation, which creates binding sites for HP1 and condensation of the targeted chromatin. Additionally, the recruitment of silencing machinery by REST–CoREST might result in the propagation of silencing across a large chromosomal interval
containing several neuronal genes that do not have their own REST binding sites, suggesting a relationship between higher order chromatin structure and patterns of gene expression.
The REST binding site (RE1) contains a CpG dinucleotide and recent studies reveal that the RE1 and surrounding region of neuronal genes is methylated in differentiated non-neuronal cells.
The many faces of REST oversee epigenetic programming of neuronal genes.

Many REST target genes involved in regulating core aspects of neuronal phenotype such as vesicular transport and release, signaling, and neurite outgrowth. Several known REST target genes are involved in neurite outgrowth and/or axonal guidance through regulation of intercellular and cell matrix interactions and of the intracellular cytoskeleton and include L1cam, Cdh4, Adam23, Catnd2, Ppp2r2c, and Unc5d. This list can now be expanded by the addition of a further four REST target genes, Cspg3, Shank2, Extl3, and Arc, all of which are involved in regulation of cell adhesion or modulation of the cytoskeleton. This cohort of target genes lends mechanistic insight into the axon pathfinding errors resulting from constitutive expression of REST. Two new targets regulating vesicular trafficking and release include Rab4a and Apba2.These add to the known REST targets, Snap25, Syt2, Syt7, synapsin 1, and synaptophysin and illustrate the ability of REST to regulate every step of neurosecretion from trafficking, through docking to fusion and release.
Distinct profiles of REST interactions with its target genes at different stages of neuronal development.

Target Gene

Assignment of putative REST target genes within the RE1 can be assigned to 1 of 10 functional groups.

Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes.


REST is expressed in many adult postmitotic neurons, most notably those of the hippocampus, where both REST and its target genes are modulated in the adult hippocampus in response to ischemic or epileptic insults. REST is also up-regulated in stress-induced neurones.
Neuronal expression of zinc finger transcription factor REST/NRSF/XBR gene.
Ischemic insults derepress the gene silencer REST in neurons destined to die.

During ES cell differentiation ,the expression profile of REST declines as neuronal differentiation proceeds. Most target genes are transcribed at high levels in the hippocampus compared with ES and NS cells.
Distinct profiles of REST interactions with its target genes at different stages of neuronal development.


Recently, the wild-type huntingtin protein was found to bind to REST/NRSF and thereby sequester REST/NRSF in the cytoplasm. It was postulated that in the pathology of Huntington’s disease, the REST/NRSF-huntingtin protein interaction is lost, causing REST/NRSF to enter the nucleus and repress its target genes.
Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes.

In Huntington's Disease, REST/NRSF enters pathologically into the nucleus of affected cells, leading to the activation of the RE1/NRSE sites and causing decreased transcription of several important neuronal genes. New approaches aimed to identifying or designing small molecules able to impact REST/NRSF nuclear translocation, its DNA binding or, more generally, the formation of the REST/NRSF transcriptional complex, in the attempt to restore neuronal gene transcription in pathological conditions of the brain.
Turning REST/NRSF dysfunction in Huntington's disease into a pharmaceutical target.

The demonstration that REST target genes are required for insulin secretion in pancreatic b-cells suggests that the function of REST in this process is not confined to cells of the neural lineage.
Neuronal traits are required for glucose-induced insulin secretion.

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