User:Richjoo/sandbox

Education Program:Boston College/Developmental Biology (Spring 2013)

Introduction
Members of the group will split the work evenly by researching respected subtopics: Tara will research the evolution and functionality of silencers, Richard will research mutations in silencers and their effects, and Chris will research the mechanism behind how silencers work in genomes.

Background Information on Silencers
Silencers are DNA sequences that are found in both eukaryotes and prokaryotes that are capable of binding transcription regulation factors called repressors. When repressors are bound to the silencers, RNA polymerase is prevented from allowing transcription and will decrease or fully suppress RNA synthesis. If transcription is prevented, proteins will not be translated from the RNA. Because silencers are so important to the accessibility of organisms to proteins, it is important to explain the purpose, functionality, diversity, and evolution of silencers. The best way to delve into this is to show the differences of silencers and functions across eukaryotes and prokaryotes. Comparing the different types of silencers and the genes they prevent the transcription of across both closely related and distantly related organisms would also show the evolution and diversity of silencers.

== Mutations and Diseases Mutations in Silencer and Transcription Factors that cause disease and abnormalitites. We will also be talking about the exact mechanism that the silencers undergo during the repression of an expressed gene. Also, we will go into detail the bonding of the repressor proteins to the silencer and the creation of heterochromatin. This then makes the gene inaccessible to transcriptional proteins.

1.	Huntington’s disease Huntington’s disease results from a mutation in the huntington protein. A wild-type huntingtin protein inhibits the activity of NRSE (neural restrictive silencer element), which allows the increased transcription of BDNF. By having a mutation in this protein, NRSE-containing genes lose expression and alter the neuronal phenotype of organisms. In summary, Huntington’s disease develops when the control in the availability of REST/NRSF to NRSE is lost. Sources: http://www.ncbi.nlm.nih.gov/pubmed/12881722 http://www.medicine.virginia.edu/basic-science/departments/neurosci/neurodiseasesjournclub/Zuccato-et-al-Huntingtin-interacts.pdf

2.	REST/NRSF (transcription factor that binds with RE1/NRSE silencer)mutation a.	A study made with mice presented that a mutation in the REST/NRSF and its consequent absence, resulted in the excessive expression of βIII tubulin gene. The lack of silencing in the gene led to morphological alterations “in the head mesenchyme and somites.” Furthermore, these modifications led to the death of the embryos. This shows that REST/NRSF have a role in regulating normal development and also in the expression of neuronal genes. b.	In Xenopus laevis, the mutation in the REST/NRSF presented abnormal eye development and perturbation in neural tube and cranial ganglia. These mutations were mainly due to an altering in the process of gastrulation. Moreover, if REST/NRSF functions are altered during late blastula stage, the neural plates expand, and the epidermal keratin and neural crest markers decrease in expression. Finally, modification in the function of REST/NRSF leads to deficiencies in neural cell development due to alterations in the expression of neuronal genes. Sources: http://www.jneurosci.org/content/26/10/2820.full.pdf+html

http://www.ncbi.nlm.nih.gov/pubmed/16525062?dopt=Abstract&holding=npg c.	NRSF also affects ventricular hypertrophy, which is the thickening of the ventricular walls. This is mostly due to the synthesis of atrial natriuretic peptide (ANP). Since NRSF controls the repression of the genes that synthesize this protein, a mutation in NRSF causes the overexpression of this protein, and causes this condition. NRSE is also involved in this process acting as a mediator that represses ANP promoter sites. Sources: http://www.ncbi.nlm.nih.gov/pubmed/11238943?dopt=Abstract&holding=npg

Subtopics

 * Background Information
 * Evolution and Functionality of Silencers
 * 1) Prokaryotes
 * 2) Eukaryotes
 * 3) Silencers on organismal levels
 * Mechanisms and Structures of Silencers
 * 1) Mechanisms
 * 2) Structure
 * 3) Signaling Pathways
 * Mutations and Diseases
 * 1) General Information
 * 2) Huntington's Disease
 * 3) REST/NRSF Mutation
 * 4) Ventricular hypertrophy
 * Further Implications
 * See Also
 * References

Mutated silencers, hereditary diseases, and their effects
Mutations lead to not only observable phenotypic influences in an individual but also alterations that are undetectable phenotypically. Silencers, being encoded in the genome, are susceptible to such alterations, which, in many cases, lead to severe phenotypical and functional abnormalities. In general terms, mutations in silencer elements or regions could lead to either the inhibition of the silencer’s action or to the persisting repression of a necessary gene. Thus, leading to the expression or suppression of an undesired phenotype, which then translates into impacts on the normal functionality of certain systems in the organism. Among the many silencer elements and proteins, REST/NSRF is an important silencer factor that has a variety of impacts not only in neural but also in other areas of development. In fact, in many cases, REST/NSRF acts in conjunction with RE-1/NRSE to repress and influence non-neuronal cells. Its effects range from humans to frogs, Xenopus laevis to be more specific, having innumerous repercussions not only in phenotype but also in development. In humans, a deficiency in the REST/NSRF silencer element has been correlated to Huntington’s disease, due to the decrease in the transcription of BDNF. Furthermore, ongoing studies indicate that NRSE is involved in the regulation of the ANP gene, which when overexpressed can lead to ventricular hypertrophy. Finally, in Xenopus laevis, REST/NRSF malfunction or damage has been associated to abnormal ectodermal patterning during development and significant consequences in neural tube, cranial ganglia, and eye development. Hence, modification in silencer elements and sequences can result in either devastating changes or unnoticeable ones.

REST/NSRF and Huntington’s Disease
Huntington’s disease (HD) is an inherited neurodegenerative disorder, which has the emergence of its symptoms during an individual’s mid-adulthood. The most noticeable symptoms of this progressive disease are cognitive and motor impairments as well as behavioral alterations. These impairments can develop into dementia, chorea, and eventually death. In the molecular level, HD results from a mutation in the huntingtin protein (Htt). More specifically, there is an abnormal repetition of a CAG sequence towards the 5’-end of the gene, which then leads to the development of a toxic polyglutamine (polyQ) stretch in the protein. The mutated Htt protein affects an individual’s proper neural functions by inhibiting the action of REST/NRSF.

REST/NRSF is an important silencer element that binds to regulatory regions to control the expression of certain proteins involved in neural functions. The mechanistic actions of huntingtin are still not fully understood, but a correlation between Htt and REST/NRSF exists in HD development. By attaching to the REST/NRSF, the mutated huntingtin protein inhibits the action of the silencer element, and retains it in the cytosol. Thus, REST/NRSF cannot enter the nucleus and bind to the 21 base-pair RE-1/NRSE regulatory element. An adequate repression of specific target genes are of fundamental importance, since many are involved in the proper development of neuronal receptors, neurotransmitters, synaptic vesicle proteins, and channel proteins. A deficiency in the proper development of these proteins can cause the neural dysfunctions seen in Huntington’s disease. In addition to the lack of repression due to the inactive REST/NRSF, mutated huntingtin protein can also decrease the transcription of the brain-derived neurotropic factor (BDNF) gene. BDNF influences the survival and development of neurons in the central nervous system as well as the peripheral nervous system. This abnormal repression occurs when the RE1/NRSE region within the BDNF promoter region is activated by the binding of REST/NRSF, which leads to the lack of transcription of the BDNF gene. Hence, the anomalous repression of the BDNF protein suggests a significant impact in Huntington’s disease.

REST/NRSF and Ventricular Hypertrophy in Mammals
REST/NRSF in conjunction with RE1/NRSE also acts outside the nervous system by acting as regulators and repressors. Researches have linked RE1/NRSE activity with the regulation of expression of the atrial natriuretic peptide (ANP) gene. A NRSE regulatory region is present in the 3’untranslated region of the ANP gene, and acts as a mediator for the appropriate expression of the gene. The protein encoded by the ANP gene is important during embryonic development for the maturation and development of cardiac myocytes. However, during early childhood and throughout adulthood, ANP expression is suppressed or kept to a minimum in the ventricle. Thus, an abnormal induction of the ANP gene can lead to ventricular hypertrophy, and severe cardiac consequences. In order to maintain the gene repressed, NRSF (neuron-restrictive silencer factor) or REST binds to the NRSE region in the 3’untranslated region of the ANP gene. Furthemore, the NRSF-NRSE complex recruits a transcriptional corepressor known as mSin3. Thus, leading to the activity of histone deacetylase in region, and the repression of gene expression. Therefore, studies have revealed the correlation between REST/NRSF and RE1/NRSE in regulating the ANP gene expression in ventricular myocytes. A mutation in either the NRSF or NRSE can lead to an undesirable development of ventricular myocytes, due to lack of repression, which can then cause ventricular hypertrophy. Left ventricular hypertrophy, for example, increases an individual’s chance of sudden death due to a ventricular arrhythmia resulting from the increased ventricular mass (8). In addition to the influence on the ANP gene, the NRSE sequence regulates other cardiac embryonic genes, such as BNP, skeletal α-actin, and Na, K – ATPase α3 subunit. Hence, the regulatory activity of both NRSE and NRSF in mammals prevents not only neural dysfunctions, but also physiological and phenotypical abnormalities in other non-neuronal regions of the body.

REST/NRSF in Xenopus laevis
[The effects and influences of RE1/NRSE and REST/NRSF are significant in non-neuronal cells that require the repression or silencing of neuronal genes. These silencer elements also regulate the expression of genes that do not induce neuron-specific proteins, and studies have shown the extensive impact these factors have in cellular processes. In Xenopus laevis, RE1/NRSE and REST/NRSF dysfunction or mutation demonstrated significant impact on neural tube, cranial ganglia, and eye development. All of these alterations can be traced to an improper patterning of the ectoderm during Xenopus development. Thus, a mutation or alteration in either the silencing region Re1/NRSE or silencer REST/NRSF factor can disrupt the proper differentiation and specification of the neuroepithelial domain, and also hinder the formation of skin or ectoderm. Furthermore, the lack of these factors result in a decreased production of bone morphogenetic protein (BMP), which translates into a deficient development of the neural crest. Hence, the effects of NRSE and NRSF are of fundamental importance for neurogenesis of the developing embryo, and also in the early stages of ectodermal patterning. Ultimately, inadequate functioning of these factors can result in aberrant neural tube, cranial ganglia, and eye development in Xenopus. Richjoo (talk) 00:26, 3 April 2013 (UTC)

REST/NRSF and Huntington's Disease
Huntington’s disease (HD) is an inherited neurodegenerative disorder, which has the emergence of its symptoms during an individual’s mid-adulthood. The most noticeable symptoms of this progressive disease are cognitive and motor impairments as well as behavioral alterations (4). These impairments can develop into dementia, chorea, and eventually death.

In the molecular level, HD results from a mutation in the huntingtin protein (Htt). More specifically, there is an abnormal repetition of a CAG sequence towards the 5’-end of the gene, which then leads to the development of a toxic polyglutamine (polyQ) stretch in the protein. The mutated Htt protein affects an individual’s proper neural functions by inhibiting the action of REST/NRSF.

REST/NRSF is an important silencer element that binds to regulatory regions to control the expression of certain proteins involved in neural functions. The mechanistic actions of huntingtin are still not fully understood, but a correlation between Htt and REST/NRSF exists in HD development. By attaching to the REST/NRSF, the mutated huntingtin protein inhibits the action of the silencer element, and retains it in the cytosol. Thus, REST/NRSF cannot enter the nucleus and bind to the 21 base-pair RE-1/NRSE regulatory element. An adequate repression of specific target genes are of fundamental importance, since many are involved in the proper development of neuronal receptors, neurotransmitters, synaptic vesicle proteins, and channel proteins. A deficiency in the proper development of these proteins can cause the neural dysfunctions seen in Huntington’s disease. In addition to the lack of repression due to the inactive REST/NRSF, mutated huntingtin protein can also decrease the transcription of the brain-derived neurotropic factor (BDNF) gene. BDNF influences the survival and development of neurons in the central nervous system as well as the peripheral nervous system. This abnormal repression occurs when the RE1/NRSE region within the BDNF promoter region is activated by the binding of REST/NRSF, which leads to the lack of transcription of the BDNF gene (6). Hence, the anomalous repression of the BDNF protein suggests a significant impact in Huntington’s disease. Richjoo (talk) 06:00, 2 April 2013 (UTC)