The Mechanical Basis Of Transcription Coupled Repair

The TP53 gene encodes a 53 kDa protein [18] that is involved in mediating cellular responses to various forms of stress signals [22]. Following these signals, the biological responses mediated by P53 can be attributed to its ability to act as a tetrameric transcription factor promoting the expression of genes involved in cell cycle arrest, apoptosis, DNA repair,

As our cells divide and our DNA replicates, our telomeres provide a start and an end point for the enzyme DNA polymerase to attach to our chromosomes and replicate our DNA. By using a repeated, non-coding section of DNA as the starting point for this replication, the telomeres allow our cells to replicate without damaging important genes at the attachment point of the replicating enzyme. As this occurs though, our telomere begin to lose base pairs

In this lab, we used two different strains of Saccharomyces cerevisiae (yeast) cells. One of them was, Saccharomyces cerevisiae, UV-Sensitive Strain, G948-1C/U, alpha, rad1 rad18 phr1 ura3 mutant in excision repair (Haploid), while the other was a wild type strain of this yeast. We chose to do this, because it is important to compare UV sensitive yeast cells, which have a mutation that yields them unable to repair themselves, to a wild type that is able to repair itself after UV radiation exposure. According to Conconi, “monitoring the formation of formazan in non-dividing yeast cells that are partially (rad7Δ) or totally (wt) proficient at DNA repair is a more accurate measure of cell survival after

On December 10, 2015, three profound individuals received the Nobel Prize in chemistry for their work on DNA repair systems. Paul Modrich, Thomas Lindahl, and Aziz Sancar studied how the cell repairs and protects the information held in its DNA; specifically, Paul Modrich focused on DNA mismatch repair. Since DNA constantly replicates, damage and incorrect pairings are expected, but enzymes watch over DNA as it replicates and repair any errors that occur. In the mismatch repair system, enzymes find the mismatch in the copy of DNA, cut the incorrect section out, and replace it with the correct sequence. Paul Modrich’s study of the mismatch repair system has provided the medical field with important information regarding cancer growth and the possibility of a cure.

On September 12, 1016, Belmont University graciously allowed Dr. Katherine Friedman from Vanderbilt University to come and talk to a crowd of students about the tendencies of how deoxyribose double stranded breaks can during cell replication and the elements required to hopefully repair this ordeal. She began the session by discussing what chromosomes are composed of and how they are produced, accompanied by visual and statistical representations. Moving on, she touched on how double strand breaks are a huge threat to a cell's, an organisms, stability. Correspondingly, she described what can cause these breaks; chemical factors, as well as inner cell disruptions during replication that are sometimes hard to remedy. However, she also stated that this breaks can occur on purpose, mostly in the immune system in efforts to make antibodies.

DNA topoisomerases are involved in many biological process, such as replication, transcription, recombination, and remodeling of chromatin (Champoux, 2001). The topoisomerase I is a monomeric protein (Fig. 1) that removes the negative superhelicity in DNA by changing the linking number of DNA in steps of 1, a reaction that does not need ATP (Burton and Kaguni, 1997). Topoisomerase I is composed by four domains

The damaged part of the DNA strand is nicked out by endonucleases that contain the dimer, which is then released from the DNA. After the fragment is released, DNA polymerase fills in the gap with a new strand and DNA ligase will close up the repaired strand.

We further wanted to determine the level of DNA damage in ATII cells isolated from emphysema patients compared to control non-smokers or smokers. We analyzed phosphorylation of H2AX (γH2AX), which is a sensitive indicator of DSBs (REF), by Western blotting and immunohistofluorescence. We found significantly higher γH2AX phosphorylation in ATII cells obtained from smokers in comparison with non-smokers (p<0.05; Figs. 2a, b). Interestingly, ATII cells isolated from emphysema patients have lower expression of γH2AX phosphorylation in comparison with smokers. We also determined γH2AX phosphorylation in lung tissue sections by immunohistofluorescence using SP-A as a marker of ATII cells. We obtained similar results showing higher γH2AX florescence intensity in ATII cells obtained from smokers in comparison with control non-smokers and emphysema (p< 0.05; Figs. 2c, d). Although, ATII cells isolated from emphysema patients have higher ROS levels (Figs. 1a, b), they don’t show a significant increase in γH2AX phosphorylation. This may suggest the impairment of DSBs repair signaling leading to lack of the DNA damage repair in these cells.

The RNA-induced-silencing complex is used for gene regulation and in defense against viral and bacterial infections. The RISC is loaded with small dsRNAs that will guide the complex through base-pairing interactions to specific messenger RNA targets, which the RISC will help degrade. Once degraded, no more protein can be made from these mRNAs. The RNA-induced silencing complex can silence targeted genes through several mechanisms. It can work to repress translation during protein synthesis, interfere with the transcript level through mRNA degradation, or work at the level of the genome itself and eliminate DNA/form degrading materials. Heterochromatin is a degrading material that can be created to modify or suppress genes in the RISC (MacRae

The integrated stress response (ISR) is characteristic of multicellular eukaryotes, and is triggered when cells experience any type of stress stimulus. Stress stimuli include misfolded proteins, oxidative damage, heat shock, and viral expression. ISR is initiated by phosphorylation of eukaryotic initiation factor 2 alpha (eIF2α) at the Ser51 residue, which promotes stronger binding to the regulatory subcomplex of eIF2B (Starck et al., 2016). This stronger binding inhibits eIF2B from catalyzing guanine nucleotide exchange of GDP for GTP, because it cannot release from eIF2 (Weaver, 2012). Several subunits of eIF2B are involved in guanine nucleotide exchange (Kashiwagi et al., 2016). The inhibition of guanine nucleotide exchange will limit the supply of initiator methionyl transfer RNA (Met-tRNAiMet), which plays a role in initiation at AUG start codons. Therefore, during IRS, eIF2α-phosphorylation blocks global translation of protein synthesis (Starck et al., 2016).

The exposure of skin to ultraviolet B (UVB) radiation has a destructive effect on keratinocytes by causing DNA damage that can subsequently lead to malignant transformation. Cellular defense mechanisms against this injury begin with the immediate UVB induced death of damaged cells. In less severely affected cells, cellcycle progression can be blocked and DNA damage can be repaired through nucleotideexcision repair (NER). If repair is successful and cells have not suffered irreversible damage, they will survive.

Once such break is generated, the inherent DNA repair machinery of the cell is activated, and during the repair process of double-strand break the genome is modified.

The best known function of mitochondria is the generation of ATP from food sources. Pyruvate, converted from glucose, is consumed by mitochondria to produce ATP. As mitochondria produce ATP, they release reactive oxygen species (ROS) locally that must be detoxified as they can induce oxidative damage to mitochondrial DNA (mtDNA). This damage results in mutations and deletions of mtDNA. The relative absence of repair enzymes for mtDNA may explain its sensitivity to oxidative stress-induced damage [8]. The 10- to 20-fold higher mutation rate in mitochondrial DNA compared with nuclear DNA is believed to be due to its proximity to ROS generation and the limited DNA repair capacity [9, 10]. As the organism, tissue, and cells age, exposure of the

Nucleotide excision repair genes are related to Xeroderma Pigmentosum. These are the genes that repair DNA damage caused by mutagenic agents such as UV. Previous studies have shown that mutations to these specific set of genes are highly related to clinical symptoms in XP patients. These genes are: DDB2, ERCC2, ERCC3, ERCC4, ERCC5, POLH, XPA and XPC.

Modification of damaged DNA seems to be an understudied subject, there is much to understand on the restoration of DNA damage, repair and DNA methylation. Genomic DNA can be modified by methylation but much of it is affected on a gene when silenced. When epigenetic modification has been implicated with cancer and aging it causes DNA methylation to also have an impact on the double strand of DNA analysis. Modification as such provoke deteriorating changes like aging found in multicellular organisms and DNA damage may magnify biochemical pathways that regulate a cells growth or control DNA replication with DNA repair. In the article “DNA Damage, Homology-Directed Repair, and DNA Methylation” written by Concetta Cuozzo, Antonio Porcellini, Tiziana Angrisano, et al. they hypothesize how DNA damage and gene silencing may induce a DNA double-strand break within a genome as well as when DNA methylation is induced by homologous recombination that it may somewhat mark its reparation through a DNA segment and protect its cells against any unregulated gene expression that may be followed by DNA damage. The experiments used to demonstration how gene conversion can modify methylation pattern of repaired DNA and when that occurs methylation is able to silence the recombined gene. When exploring the molecular mechanisms that link DNA damage and the silencing gene then there is an induced double strand break that can be found at a specific location or DNA sequence in where the