Shahed Al Massri 250 572 285 Dr. Torchia Take Home Exam November 4th, 2014 Question 1 Epigenetic inheritance is defined as the regulatory information passed down from parent to offspring without any changes in the underlying DNA sequence. This process can involve various modifications of histones as well as DNA itself. These types of alterations include acetylation, methylation and phosphorylation. Such changes can regulate expression through a variety of different mechanisms, including controlling how accessible the DNA is to transcription factors (1). Epigenetic regulation is a highly prevalent method of controlling gene expression, and a vast number of diseases involve disturbances in the epigenome (2). It has been shown …show more content…
A transcription factor can be converted from active to inactive form (and vice versa) through either a ligand dependent or independent method. A ligand independent activation of transcription factors can happen through phosphorylation by a kinase protein. For example, estrogen receptor is inactivated through phosphorylation of serine 236 by Protein Kinase A (20). S236 lies within the DNA binding domain of ER, which is also important for functional heterodimerization of ERα and ERβ. It was observed that overexpression of PKA inhibited ER activity in the absence of ligand. An immunoprecipitation assay revealed that phosphorylation of S236 prevented heterdimerization. This helped conclude that phosphorylation of S236 by PKA regulates ER activity. Another way a transcription factor can be activated is through binding of a specific ligand. This ligand is termed an agonist or antagonist depending on whether it is resulting in activation or inactivation of the gene being regulated. For example, ER is activated upon binding of 17β estradiol (21). Crystallographic analysis showed a conformational change that occurs upon binding of estradiol, which stabilizes the ligand binding domain. FRET analysis revealed that this agonist binding promotes heterodimerization and subsequent activation of ER …show more content…
DNA methylation is usually responsible for transcription silencing, and can do so through three different mechanisms (2). First, the presence of methylcytosines can directly interfere with transcription factor binding by physically hindering their association with DNA. An example of this can be seen in the downstream enhancer region shared by Igf2 and H19, where only one of these two genes is expressed depending on gender (23). The transcription factor CTCF normally binds a CpG-rich imprint control region (ICR) upstream of H19, repressing Igf2 expression restricting the enhancer to act only on H19 . However, when this ICR region is methylated, CTCF can no longer bind the DNA at that site. This lifts the restricting boundary on the enhancer region, allowing it to promote Igf2 transcription instead of H19. When CTCF binding sites were mutated, restriction on the enhancer was lifted, supporting CTCF’s important role for suppression of Igf2 (24).The direct effect of methylation on CTCF binding was determined through an in vitro essay with probes methylated at CpG sites, showing that methylation blocked CTCF binding without other requiring other factors to do so. The second manner that CpG methylation silences transcription is by recruiting proteins which possess a methylCpG binding domain (MBD), which in turn recruit chromatin modifiers that promote chromatin
Takahashi, Y., et al. “Analysis of Promoter binding by the E2F and pRB Families In Vivo: Distinct E2F Proteins Mediate Activation and Repression.” Genes 14 (2000): 804-816.
The underlying purpose of the experiments performed in the study, Promoter Hypermethylation of KLF4 Inactivates its Tumor Suppressor Function in Cervical Carcinogenesis, is to investigate the mechanism by which the KLF4 gene is silenced in cervical carcinomas. Cervical cancer accounts for 250,000 female deaths every year. Developing therapies for cervical cancer has been limited due to the lack of genetic and epigenetic data of the mechanism causing the cancer. The KLF4 gene is a transcriptional regulator of cell growth and differentiation. It functions as a tumor suppressor in cervical cancer, but is found to be inactivated in cervical cancer. The overexpression of KLF4 protein is known to inhibit cervical cancer cell growth and tumor formation by activating a cell cycle suppressor. Promoter CpG island hypermethylation can result in transcriptional silencing of many tumor suppressing genes. Two CpG regions, BSQ1 and BSQ3, were examined in this experiment.
...plicates the identification of the loss of tumor suppressor gene (TSG) is epigenetic changes in the gene promoter. Hypomethylation of DNA and hyperacetylation of histones in the promoter region leads to successful transcription of the DNA. Therefore, any alteration in either of the two will disrupt the gene transcription.
The human genome was mapped for RNA transcribed regions (functional RNA’s other than protein coding), protein coding regions, transcription factor binding sites, chromatin structure and DNA methylation sites (including histone modifications). (The ENCODE Project Consortium)
DNA methylation is catalyzed by the enzyme: DNA methyl trasnferase (DNMTs). Methylation of DNA segments leads to the silencing of transposable elements. Hence this mechanism is repressive to transcription, by that enhancing genomic stability. However, there exist “CpG” islands that are associated with gene promoters that escape methylation hence stability.
A major mechanism in epigenetics is DNA methylation. DNA methylation occurs in two mechanisms and is the addition of a methyl (-CH₃) group through a covalent bond to a cytosine side chain. DNA methylation is catalysed by a group of enzymes called DNA methyltransferases (DNMTs). DNMT adds methyl groups to cytosine residues. Cytosines have to be immediately followed by a Guanine In order to be methylated, these are called CpG dinucleotides. Around 70% of these dinucleotides get methylated whilst the rest are in clusters called CpG islands. There are two typ...
Epigenetics is the word that is used for genes that are modified in order to assist certain genome sequences that lead to diseases and disorders. Epigenetics has come a long way since the first genome sequence had its draft breakthrough in the year 2000 (NOVA 2012). From depression to cancer, epigenetics has made its way through to provide families with the appropriate knowledge and perhaps medication in order to avoid these diseases and disorders in the future.
Precise chromosomal DNA replication during S phase of the cell cycle is a crucial factor in the proper maintenance of the genome from generation to generation. The current “once-per-cell-cycle” model of eukaryotic chromosome duplication describes a highly coordinated process by which temporally regulated replicon clusters are sequentially activated and subsequently united to form two semi-conserved copies of the genome. Replicon clusters, or replication domains, are comprised of individual replication units that are synchronously activated at predetermined points during S phase. Bi-directional replication within each replicon is initiated at periodic AT-rich origins along each chromosome. Origins are not characterized by any specific nucleotide sequence, but rather the spatial arrangement of origin replication complexes (ORCs). Given the duration of the S phase and replication fork rate, adjacent origins must be appropriately spaced to ensure the complete replication of each replicon. Chromatin arrangement by the nuclear matrix may be the underpinning factor responsible for ORC positioning. The six subunit ORC binds to origins of replication in an ATP-dependent manner during late telophase and early G1. In yeast, each replication domain simply contains a single ORC binding site. However, more complex origins are characterized by an initiation zone where DNA synthesis may begin at numerous locations. A single round of DNA synthesis at each activated origin is achieved by “lic...
Epigenetics, which also means “above genetics”, is defined as the study of chemical reactions that take place in the organism as this one grows and develop. This chemical reaction activate and deactivate at certain time and location some parts of the genome. The video resulted extremely interesting because it shows how our body react to the epigenomes and how important is our lifestyle to our health and for the health of our next generations.
Another easily identifiable factor in increasing the onset of DM are the epigenetic risk factors. The genetic susceptibility, caused by the missing genomic information, can be accounted by additional variants like histone posttranslational modifications, which remove or rearrange the histones bound with the DNA. DNA methylation alters the methylation levels of INS gene promoters and has been discovered in patients with TD1 that altered methylation of histones upstream of HLA-DRB1 and HLA-DQB1. Noncoding RNAs give rise to altered expression of miRNAs in regulatory T cells of T1D.
Epigenetics is the study of both heritable and non-heritable changes in gene translation, which do not stem from mutation. Epigenetic alterations to DNA may occur in several different ways; histone modification, DNA methylations, expression of microRNAs, and changes of the chromatin structure (Ntanasis-Stathopoulos et al). Depending on their presentation, they may be passed on to offspring. The exact mechanism of heritable epigenetic modification has not been discovered, but all of these alterations may have some impact on a wide range of disorders and have far reaching implications in the medical field. The study of epigenetics seeks to answer the age old question of whether nature or nurture is responsible for our phenotype, and it has arrived at the answer that in fact, both are. The discovery of epigenetic changes may lead us to cure many disorders, and even personality problems.
Campbell N. A., Reece L. A., Cain M. L., Wasserman S. A., Minorsky P. V. and Jackson R. B. (2008). Regulation of Gene Expression
The background information began providing clear explanation for hematopoiesis whereby hematopoiesis is the process of cell differentiation to blood and immune cells from multipotent hematopoietic stem cells and progenitor cells. It carried on by explaining the processes which are regulated by general RNA polymerase II transcriptional machinery and lineage specific transcriptional factors that specify the diverse cell type’s development. Then information started to come together in the direction of this study giving an overview of what this study will focus on which is Med 12 mediator. Mediators are an essential component regulating RNA polymerase II with enhancer bound regulatory factors and it exists in two major forms, the core complex and Med12-mediator. The core complex is a strong co-activator of transcription made up of 25 subunits with Med26 while Med12-mediator is able to positively and negatively control transcription. Med12 mediator has the same 25 subunits but with the addition of Med12 module that consists of Med12, Med13, CDK8 and Cyclin C. The Med12 module negatively affects transcription by inhibiting RNAP II re-initiation while Med12 positively affect transcription by interacting with SOX9 and Rta. There was an extremely detailed explanation of those individual subunits of the complex interacting specifically with different activators and repressors to regulate specific signaling pathways for example nuclear receptors interacts with Med1, MAP kinase pathway requires Med23, CDK8 interacts with myc and Med15 is required for TGFb signaling however the molecular mechanism of mediator regulatory function is not well understood. It carries on explaining the importance of Med12 in vivo pro...
It is likely that gene regulation is affected by certain enzymes after initial hormone binding. Genes may be altered by secondary and tertiary messengers of a cellular cascade as well. Hormones may indirectly control gene expression through these enzymes and messengers at a number of control sites such as transcription, mRNA processing, mRNA stability, translation, and post-translation