Histone Deacetylation Of Sirtuids

histone – these are a type of protein that help to organize the DNA. There are 8 histones that make up one group. Each have tails that are covered with chemical tags and stick out of the protein grouping. The chemical tags on the tails affect how they interact with DNA.

The gene that we are interested in for this project and for the duration of this semester is DMAP1. Not a lot is known about this is a gene, however in other organisms, it is involved in the methylation of DNA. DMAP1 is responsible for encoding a protein that associates with another protein that methylates DNA. The methylation of DNA alters the DNA structure and makes it unavailable to transcription factors, so the mutation of DMAP1 could lead to changes in transcription and gene regulation. For example, if DMAP1 were mutated, less DNA methylation might occur and more areas of DNA could be accessible to transcription factors and ‘active’, making more genes transcribed than should be. Gene alterations are important as they can lead

The team carefully picked through their massive list of 2000 genes related to HDAC2. Based on their extensive knowledge of gene functions, they zeroed in on three genes of interest. They subjected these 3 genes to

Hssb1 is a protein which is critical for genome stability. It detects and promotes repair to damaged DNA and signals for other proteins to repair the cell, and if it is unsuccessful, it essentially tells the cell to commit suicide. Hssb1 ensures that the strands repairs properly however, if there is a mutation on the hssb1, the damage goes unrepaired. Cancer is a disease of bodily cells. Where cells normally divide and multiply in a controlled way through mitosis and controlled by cyclins, there can be mutations in these cells that cause control of the growth and multiplication of these cells to be lost. Cancer is a collection of these out-of-control cells which are known as malignant tumours. Mutations are random changes in the base sequence of the genes and in the cells can be caused by genes that can become

The writer subunit of the protein adds a modification to the next histone when it is activated by the binding of the reader portion. This initiates a chain of chromatin modifications that alter a gene’s expression by either condensing or de-condensing the chromatin. The condensing of the chromatin can block transcriptional proteins from accessing the gene site, thereby inhibiting transcription. Modifications to the histone tails can also be removed by histone deacetylases and histone demethylases, which function in a similar manner. The modifications can also be prevented from being added to the chromatin in the first place by barrier sequences.

One of the main conclusions drawn from this experiment was that the cis memory system is the one used to inherit modified histones because they concluded that epigenetic memory is stored locally in FLC gene. One of the main pieces of evidence to support this is in Figure 3 of this paper. This figure describes heritable expression states, and it is concluded that the cis memory system is used because mitotic stability of all four possible combinations (ON/ON, ON/OFF, OFF/ON, and OFF/OFF) are observed. ‘Mixed’ ON/OFF and OFF/ON states are only seen in cis systems, thus the trans system cannot be implemented. Using this they were also able to show that two identical DNA sequences can have different transcriptional states in the same nucleus, which is only demonstrated by cis memory. Another conclusion they were able to make was that PRC2 is necessary for histone

At the ZPA, a specific gradient of SHH determines anterior digits, and the length of time that cells are exposed to direct SHH signaling in the posterior region determines the posterior digits. This is possible thanks to the dual function of GLI3 as a transcriptional activator (GLI3A, full length) or as a repressor (GLI3R, truncated) depending on the SHH protein gradient. At the posterior end, a high SHH concentration at the ZPA suppresses conversion of GLI3A to GLI3R, whereas at the anterior end (opposite to the ZPA) GLI3A is truncated to GLI3R. An appropriate balance between the levels of GLI3A and GLI3R determines the number of digits and their identity.

Clearly, it performs a significant role in the development of the organism on multiple levels. Chromatin directs the course of a cell’s specialization from the time the zygote divides, resulting in the physical structure of a multicellular organism. Evolutionary development is also impacted when an altered form of the chromatin is inherited by the offspring of an organism. Regulation of the chromatin at the level of transcription also provides much insight to the maintenance of the genetic materials, which determines its expression during growth and

The nuclear periphery is fundamental to maintaining the structural and functional integrity of the nucleus (Van de Vosse et al., 2011). It has long been known to participate in various nuclear processes and contribute to cytoplasmic trafficking (Van de Vosse et al., 2011). In recent decades, researchers have uncovered a new role for the nuclear periphery - the silencing of genes (Shaklai et al., 2007). Since then, many have come to appreciate the extent by which it modulates the spatiotemporal expression of a gene.

RNA interference pathways play an integral role in the silencing of gene expressions, predominately by destroying specific targeted molecules of messenger RNA (mRNA). Messenger RNA are single- stranded RNA molecules which move from the nucleus of the cell to the cytoplasm, while sending and receiving genetic information from DNA via ribosomes, to where the specific amino acid sequence of the protein involved in gene expression is located, as the article, “Messenger RNA - Glossary Entry” explains. The RNA interference pathway (RNAi) breaks double- stranded (dsRNA) molecules which match a specified targeted gene into short single- stranded RNA (ssRNA), which triggers the deterioration of the mRNA in its corresponding sequence. According to Cartel,

Scientists have known for several decades that cancer may be caused by mutations in the DNA of cells. These mutations may result from exposure to certain substances (e.g. radiation, benzene) or they may occur spontaneously in the process of cell division, especially in the context of aging. Recently, researchers have discovered another level of inherited cellular information separate from the genes themselves. Epigenetics is the study of modifications to genes that change their patterns of expression. Epigenetic processes can silence a gene or even an entire chromosome. They can cause normally silent genes to be expressed, and can change the process of transcription so that the nucleotides are transcribed in a different order. Normally, epigenetic information is stabilized early in development and is maintained as cells divide. However, over time, mutations or epigenetic drift may change the inherited pattern. This type of event often results in disease such as cancer (Jones & Baylin 2002).

The seven transcription factors studied were: ESR1, TP53, MYC, RELA, POU5f1-SOX2 (mouse), and CTCF (mouse). They were chosen because of their crucial genome regulating roles in numerous different organisms. The binding sequences where these transcription factors bind were examined with whole-genome occupancy data sets; the conserved bound

(2009), who showed that EYA family members are tyrosine phosphatases that remove the Tyr142 mark from H2AX, and that knockout of EYA genes leads to increased apoptosis. Phosphatase activity of EYA members may play a novel role in mammalian organogenesis, in order to block an improper apoptotic response to normal levels of genotoxic stress, by dephosphorylating H2AX on the tyrosine residue (Cook et al., 2009). This group also showed that MDC1 - promoting repair - binds specifically to mono-γH2AX (pSer139 only) and not to di-γH2AX, while activated JNK - promoting apoptosis - seems to bind to the di-phosphorylated form. The precise recognition of the phosphorylated residues of the tetrapeptide C-terminal H2AX is key to the ability of MDC1 to facilitate and control interactions with H2AX through phosphophorylation of H2AX at Tyr142. pTyr142 is believed to be an important H2AX mark in undamaged chromatin, where one of its roles is to likely block binding of MDC1 (Campbell et al., 2010). Also, it was shown that blocking the tyrosine phosphorylation by mutating the tyrosine to phenylalanine significantly reduced apoptosis. Studies have indicated that phosphorylation of tyrosine 142 prevents recruitment of repair protein complexes to phosphoserine 139 of H2AX, although it is likely that there are many additional and not well-understood aspects that lie beneath the full molecular philosophy of

The siRNA molecule is the product of the RNA interference (RNAi) pathway. The starting molecule in the pathway is a long “triggering” double stranded RNA (dsRNA). The dsRNA is formed from either an RNAi molecule inserted into the cell or a siRNA which complexes with a specific strand of messenger RNA

Pretreatment with hypoxia has been shown to lead to long lasting changes, such as increased metastatic aggressiveness in cancer (52), and some of these changes have been linked to lasting changes in epigenetic landscape (53). My preliminary studies demonstrate that pretreatment of OPCs with hypoxia mimetic drugs leads to lasting inhibition of differentiation. In subaims 2.1 and 2.2, I seek to determine whether there are changes in histone modifications at the MyRF promoter that could lead to transcriptional silencing. Here I propose to assess whether histone modifications discovered in these first two subaims remain following return to normoxia. In order to test this, I will pretreat OPCs with either DMOG or CoCl2 to induce HIFs and then wash out the drugs and plate into normal media for either 48 hours or 96 hours. I will perform chIP-qPCR at the MyRF promoter at both of these timepoints to assess for lasting loss of activation histone marks (aim 2.1) or gain of repressive histone marks (aim 2.2). As an additional method for validation, I plan to test whether histone modifications noted in aims 2.1 and 2.2 remain at the MyRF promoter even after VHL is restored in the VHL knockout OPCs using a VHL ORF construct (71, 72).