Transcriptional elongation is a crucial step in eukaryotic gene regulation whose mis-regulation leads to cellular pathologies. This makes it quite imperative to aim for a better understanding of the processes regulating transcriptional elongation. An important process promoting the association of RNA Polymerase II (RNAPII) with the coding region of the active gene and hence transcriptional elongation is the monoubiquitination of histone H2B at lysine 123. A complex of an E2 conjugase, Rad6p, and an E3 ligase, Bre1p, is essential for this process. Consistent with the role of histone H2B monoubiquitination in promoting the association of RNAPII with the active gene, this process was found to be impaired in the absence of Rad6p or point mutation of lysine 123 to arginine (H2B-K123R). Intriguingly, the association of RNAPII with the coding region of the active gene was not impaired in the absence of Bre1p, even though Bre1p is essential for histone H2B monoubiquitination. However, deletion of Bre1p’s RING domain that is essential for histone H2B monoubiquitination led to an impaired RNAPII association with the active gene. This observation indicates a role of the non-RING domain of Bre1p in repressing the association of RNAPII with the active gene, resulting in no net decrease in RNAPII occupancy in the absence of Bre1p. Taken together, my results implicated both the stimulatory and repressive roles of the histone H2B ubiquitin ligase Bre1p in regulation of RNAPII association with the coding regions of active genes and hence transcriptional elongation. Interestingly, my work also revealed that for efficient transcriptional elongation by histone H2B monoubiquitination, its optimum level needs to be maintained by a proper balance between Rad6p-Bre1p-mediated ubiquitination and de-ubiquitination (DUB) by the DUB module of SAGA. It was found that Sus1p, a subunit of the DUB module, promotes transcriptional elongation, DNA repair and replication via regulation of histone H2B DUB. In addition to Rad6p- Bre1p and the DUB module, global level of histone H2B monoubiquitination is also critically regulated by Cdk9, a kinase essential for phosphorylation of the serine 2 residue in the C-terminal domain (CTD) of RNAPII, which promotes transcriptional elongation. Apart from serine phosphorylation, proline residues at RNAPII-CTD undergo isomerization by proline isomerases, which also regulate transcription. One of the proline isomerases, Rrd1p, has been previously implicated in transcription in response to rapamycin treatment. Based on this fact and Rrd1p’s known interaction with RNAPII-CTD, we predicted that Rrd1p might regulate transcription independently of rapamycin treatment. In agreement with this hypothesis, our work revealed Rrd1p’s role in facilitating transcription of both rapamycin responsive and non-responsive genes in the absence of rapamycin treatment. Consistently, the absence of Rrd1p led to an impaired nucleosomal disassembly at the active gene, which correlates with the role of Rrd1p in promoting transcription. This is because maintenance of proper nucleosomal dynamics is essential for efficient transcription. It is known that transcriptional elongation is facilitated by the regulation of nucleosomal dynamics via the histone chaperone, FACT. Efficient chromatin reassembly in the wake of elongating RNAPII contributing to the fidelity of transcription is promoted by FACT. Being evolutionarily conserved among eukaryotes, FACT is also known to regulate DNA replication and repair, apart from transcription. Intriguingly, FACT has been found to be upregulated in cancers while its downregulation leads to tumor cell death. However, the mechanism which fine-tunes FACT for normal cellular functions remained unknown. My studies revealed a novel mechanism of regulation of FACT by the ubiquitin-proteasome system in yeast. San1p, an E3 ligase involved in nuclear protein quality control, was found to associate with the active gene and regulate transcriptional elongation through its E3 ligase activity- mediated turnover of Spt16p component of FACT. This regulation was found to maintain optimum level of Spt16p/FACT to engage with the active gene for proper transcriptional elongation, DNA repair and replication. In spite of playing such crucial roles in gene regulation, it was not known how FACT is targeted to the active gene. We discovered that a direct physical interaction between FACT and Cet1p, the mRNA capping enzyme, targets FACT to the active gene independently of Cet1p’s mRNA capping activity. Such targeting of FACT to the active gene leads to the release of promoter proximally paused-RNAPII into transcriptional elongation. However, the progress of RNAPII along the active gene during transcriptional elongation is frequently impeded by various kinds of damages along the underlying template DNA. Even though some of these lesions are co-transcriptionally repaired, it was not known whether the repair of extremely toxic DNA double-strand breaks (DSBs) was coupled to transcription. My results showed that DSBs at the transcriptionally active state of a gene are repaired faster than at the inactive state but such repair was not mediated by a co-transcriptional recruitment of DSB repair factors. This observation is in contrast to other DNA repair pathways such as nucleotide excision repair (NER) where repair factors are co-transcriptionally recruited to the lesion containing DNA. In this regard, we found that an NER factor, Rad14p, co-transcriptionally associates with the active gene in the absence of DNA damage to promote transcription, which unraveled a new role of Rad14p in transcription in addition its established role in NER. In summary, my results provide significant novel insights into the regulation of transcriptional elongation and associated processes leading to better understanding of eukaryotic gene expression.

No description available.

An attempt has been made to demonstrate an association between the carcinogenic activity of a chemical compound and its capacity to induce DNA damage and chromosome aberrations which may result in mutations and/or neoplastic transformation. Twenty-five 4-nitroquinoline 1-oxide (4NQO) derivatives and five related compounds of 4-nitropyridine 1-oxide (4NPO) of varying carcinogenicity were examined. [Formulae omitted] The induction of DNA damage, chromosome aberrations and clone forming capacity were used as end points. Monolayer cultures of embryonal Syrian-hamster cells and an established line of baby hamster kidney cells (BHK-21) were employed in this study. DNA damage, as measured by the unscheduled incorporation of tritiated thymidine (³H-TdR), was assayed by the autoradiographic procedure. To distinguish DNA repair synthesis from DNA replication synthesis at S-phase, cultured embryonal hamster cells were arrested at G₁ by growing them in an arginine deficient medium (ADM) prior to the application of the various carcinogens. The unscheduled uptake of radioisotope was estimated by counting the number of grains per diploid nucleus of carcinogen treated cells. The highly oncogenic derivatives of 4NQO and 4NPO elicited an elevated level of unscheduled ³H-TdR incorporation in treated cells, while the weakly oncogenic compounds induced only a smaller amount of DNA repair synthesis. The non-oncogenic N-oxides failed to provoke any detectable ³H-TdR uptake. Chromosome aberrations were studied in ADM-arrested cells which were exposed to the various compounds and then triggered into division by transferring them into the regular growth medium. A direct proportionality was observed between the degree of carcinogenicity of a compound and the frequency of induced chromosome aberrations. The clone forming ability of treated cells was employed as a means to compare the cytotoxicity of the 4NQO and 4NPO derivatives. Potent carcinogens were highly cytotoxic; weakly carcinogenic compounds showed only a slight lethal effect and non-oncogenic derivatives did not affect cell survival. This study demonstrated the capacity of carcinogens to induce alterations at the chromosome and DNA level. The possible role of DNA repair and chromosome aberrations in neoplastic transformation was discussed. The use of DNA repair synthes as an economic and relevant tool for identifying mutagens and/or carcinogens has been suggested. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

Several short-term assays are in use to assess the carcinogenic hazard of chemicals. While the ability to induce initiating events that may lead to carcinogenesis is measured, compounds and conditions that might modify the ability of chemicals to cause those initiating events are not assessed by such tests. In addition, compounds that affect the ability of cells to react in a normal fashion to the damaging action of carcinogens are not detected by these methods. Shifts in alkaline sucrose gradient profiles of centrifuged DNA (as an indication of DNA fragmentation) and formation of aryl and alkyl DNA adducts (as an indication of DNA modification) have been used as short-term assays for carcinogenic and mutagenic potential. Repair of DNA damage has been measured by restoration of near-control sedimentation profiles of DNA and the loss of aryl and alkyl adducts over time after damage or modification of DNA by carcinogens and mutagens. In this study, the ability of sodium ascorbate to modify the DNA fragmenting and adduct-forming action of the carcinogens N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and benzo(a)pyrene (BP) was investigated. In addition, the ability of cells In vivo and In vitro to repair DNA in the presence of sodium ascorbate was assessed by the two methods described above. It was found that sodium ascorbate inhibited repair in vivo and in vitro. In addition, sodium ascorbate was found to fragment DNA in vivo and in vitro in the presence of copper, and to inhibit the action of carcinogens _in vivo and in vitro by nucleophilic scavenging of electrophilic carcinogens. Sodium ascorbate was also found to inhibit the binding of BP to DNA jLn vivo and In vitro. On the other hand, other reducing agents had other effects. Propyl gallate (a sulphydryl reducing compound) inhibited binding of BP to DNA in vitro, but enhanced binding of BP to DNA in vivo. The sulphydryl reducing agent glutathione enhanced binding of BP to DNA in vivo and in vitro. Alkaline sucrose gradient analysis of DNA damage and recovery from that damage, and BP adduct formation in DNA and disappearance over time, appear to be suitable methods for assessment of the modifying properties of compounds and conditions on the initiating events that may lead to mutation or carcinogenesis. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

Genomic DNA is under constant assault by environmental factors that introduce a variety of DNA lesions. Cells evolved several DNA repair and recombination mechanisms to remove these damages and ensure the integrity of the DNA material. A variety of specific proteins, called nucleases, processes toxic DNA structures that deviate from the heritable duplex DNA as common pathway intermediates. DNA-induced protein ordering is a common feature in all DNA repair nucleases. Still, the conformational requirement of the DNA and the protein and how they control the catalytic selectivity of the nuclease remain largely unknown. This study focus on the bases of catalytic activity of a protein belongs to the 5’ nuclease super-family called the human Flap endonuclease 1 (FEN1); it removes excess 5’ flaps that are generated during DNA replication. hFEN1 mutations and over-expression had been linked to a variety of cancers. This thesis aims to study the structural and dynamic properties of free hFEN1 and the catalytic activity of DNA-bound hFEN1 in solution utilizing the modern high-resolution multidimensional Nuclear Magnetic Resonance (NMR) spectroscopy. It was possible to depict the secondary structure and backbone conformation in solution of wild type (WT) hFEN1 by the usage of the improved list of assigned resonances, derived from the NMR 2D and 3D ¹⁵N-detected experiments and compared to the assignment with the previously published resonance assignment (BMRB id: 27160). I was successfully assigned the new spectrum and enhanced it by assigning seven more residues. Moreover, we tested the interaction of 1:10 ratio of hFEN1-Ca2+ with DNA by the ¹³C-detected 2D CACO experiment. The results indicate hFEN1:DNA interaction. Furthermore, parts of hFEN1 get more ordered/structured once DNA appears, thus we recorded the protein flexibly by 2D ¹H-¹⁵N TROSY-HSQC using the relaxation rate parameters: longitudinal R1, transverse R2 complemented with ¹⁵N-{¹H} NOEs (heteronuclear Overhauser enhancement). It was found that the overall molecular architecture is rigid, and the highest flexibility lies in the α2-α3 loop and arch (α4-α5) regions. Further analysis is needed to understand more profoundly the activity of hFEN1 in an atomic level by inducing mutations and testing the protein in various environmental conditions.

Chromosomal translocation is a characteristic feature of human lymphoid malignancies and a driver of the initiation and progression of the disease. They arise from the mis-repair of physiological DNA double-strand breaks (DSBs) generated during the assembly and subsequent modifications of the antigen receptor gene loci, namely V(D)J recombination and class switch recombination (CSR). Mammalian cells have three DSB repair pathways –classical non-homologous end-joining (cNHEJ), alternative end-joining (A-EJ), and homologous recombination. DNA end-resection that generates a single-strand 3’ overhang is a critical regulator for the repair pathway choice. Specifically, localized end-resection prevents cNHEJ and exposes flanking microhomology (MH) to promote error-prone A-EJ. In addition to DNA repair, DNA end-resection generates extended single-strand DNA, which activates the ATR-mediated cell cycle checkpoint and indirectly contributes to genomic integrity. The central goal of my thesis research is to investigate the physiological role of DNA end-resection initiation in lymphocyte development and lymphomagenesis. DNA end-resection in mammalian cells is mostly initiated by the endonuclease activity of MRE11-RAD50-NBS1 (MRN) complex aided by CtIP. In addition, MRN protein also recruits EXO1 and DNA2 nucleases in combination with Top3 helicase complex for more extensive resection. The CtIP protein is essential for the endonuclease activity of the MRN complex that initiates DNA end-resection. CtIP is essential for embryonic development. Here I utilized B cell-specific conditional deletion models and loss-of-function mutations to investigate the role and regulation of CtIP and CtIP-mediated DNA end-resection in lymphocyte development and tumorigenesis. The level and extent of CtIP-mediated resection are tightly regulated. For the first aim, we applied the ATAC-Seq and EndSeq methods to test whether chromatin accessibility determines the level of DNA end-resection. Specially, we found that chromatin-bound DNA damage response factors – H2AX and 53BP1- reduced the accessibility of the DNA around the DSBs and antagonized end-resection. Our data also suggest that during DNA damage response, the nucleosome-free or accessible regions are more prone to secondary DNA breakages. Mechanistically, the preferential vulnerability is correlated with the availability of chromatin-bound DNA damage response factor 53BP1, which protects the nucleosome covered region at the price of the nucleosome-free regions. The work provides one explanation for tissue and cell type-specific translocations in transcriptionally active regions and super-enhancers. For the second and third aims, I investigated the role of CtIP and CtIP-mediated end-resection in lymphocyte development and lymphomagenesis in vivo using the conditional deletional CtIP allele and a phosphorylation-deficient CtIP-T855A mutant. T855 phosphorylation promotes end-resection but is not essential for cellular viability. I identified a sequence-context-dependent role of CtIP and end-resection in A-EJ mediated repair. We found that the reduced level of end-resection did not alter the frequency of the A-EJ mediated joining during B cell CSR, nor the levels of micro-homology at the junction, a defining feature of A-EJ mediated repair. These findings, for the first time, showed that DNA end-resection is not essential for A-EJ-mediated chromosomal DSBs repair nor for the generation of MH at the junction in vivo. This unexpected observation also highlights a tissue- and cell type-specific regulation of A-EJ and the importance of sequence context for A-EJ. Moreover, we found that ATM kinase suppresses A-EJ mediated translocation and reported the very first cell cycle-dependent analyses of CSR junctions. In cNHEJ-deficient B cells (e.g., Xrcc4- or DNA-PKcs- deficient), the A-EJ pathway is responsible for both the residual CSR events and the generation of the oncogenic IgH-Myc chromosomal translocations. In the last chapter, I determined how CtIP contributes to oncogenesis using the CtIP-T855A phospho-deficient mouse model. The result showed that CtIP T855 phosphorylation is critical for the neonatal development of Xrcc4-/-p53-/- mice and IgH-Myc translocation driven lymphomagenesis in DNA-PKcs-/-Tp53-/- mice. Mechanistically, phospho-deficient CtIP compromises the extent of end-resection without affecting the initiation. Reduced end-resection in CtIP-T855A mice and cells attenuated G2/M checkpoints and reduced the tolerance to the oncogene-induced replication stress, thereby limit lymphomagenesis. Collectively, our data provided the first in vivo characterization for the role of CtIP and its related end-resection pathway in lymphocyte development and lymphomagenesis. The results highlight the importance of end-resection for checkpoint maintenance (§ 4) and the context-dependent regulation of A-EJ and DNA repair pathway choice in vivo (§ 3), explaining why A-EJ is more robust at the repetitive switch regions. Finally, the application of HTGTS, EndSeq, and ATAC-Seq technologies in lymphocyte-specific gene rearrangements markedly improved the analysis depth and sensitivity while reducing the cost of repair-junction sequencing, allowing the quantitative detection of subtle changes and additional mechanistic insights. Specifically, we showed that end-resection could be regulated at the level of chromatin accessibility, which is determined by both baseline chromatin occupancy and DNA damage-induced changes (§ 2). These findings provide one explanation for the tissue and cell type-specificity of translocation targeting. These techniques can be used to analyze the impact of other DNA repair factors during lymphocyte development and lymphomagenesis and in translocation in general.

No description available.

In many DNA processes, action at a distance is required for signaling across long distances on DNA. These pathways, generally have an initiation site (site 1) that signals an event at a second location (site 2). Such a paradigm is found in processes such as transcription, replication, and DNA repair. To overcome long distances on DNA, proteins can utilize translocation, oligomerization, and DNA looping to bridge the distance between the initiating signal at site 1 and the site of action at site 2. The utilization of these mechanisms for action at a distance is crucial in eukaryotic mismatch repair. In this pathway, MutS homologs scan DNA and recognize mis-paired bases. The MutS protein then recruits the endonuclease MutLα, which nicks the nascent strand of DNA containing a mis-incorporated DNA base. The MutLα-generated nick leads to downstream mis-pair removal through excision by an exonuclease or strand displacement activities of a DNA polymerase working together with a flap endonuclease. Although, previous models have suggested that MutL homolog endonucleases can form oligomeric complexes on DNA, the role of a MutLα oligomeric complex and how it might facilitate action at a distance has been unclear. Here, I present evidence that the mismatch repair MutLα endonuclease is activated by DNA-DNA associations, and it can use this activity to overcome DNA torsional barriers. Using DNA ligation and pull-down experiments, I determined that a MutLα oligomer associates two DNA duplexes and that this activity can stimulate MutLα’s endonuclease function. I also show evidence that MutLα enhances a topoisomerase without nicking the DNA itself. These behaviors of MutLα could localize nicking on DNA near a mismatch and help overcome barriers that could inhibit additional repair proteins from activating MutLα and facilitating efficient DNA repair. The endonuclease activity of MutLα is critical for efficient mismatch repair, but in addition to this activity, MutLα is also an ATPase, although the crosstalk between the two enzymatic functions has been largely unexplored. It has been shown previously that the ATPase activity of MutLα allows the protein to undergo conformational changes and in vivo is necessary for efficient mismatch repair. Mechanistically, how this activity supports MutLα’s functions in the mismatch repair pathway remains unclear. Using DNA binding and photo-crosslinking experiments, I provide evidence that MutLα recognizes and localizes itself to a nick. Additionally, through DNA protection assays and photo-crosslinking I provide evidence of a signaling mechanism initiated at the nick for a MutLα oligomer to undergo its ATP cycle. These data provide insight into how MutLα uses ATP to signal events for mismatch removal. These data also provide a mechanistic explanation for how MutL proteins interact with DNA during mismatch repair and send signals for additional repair processes after the protein nicks DNA that help explain new models for action at a distance. / Chemistry

No description available.

The entire epidermis of patients with vitiligo exhibits accumulation of up to 10-3M concentrations of hydrogen peroxide (H2O2) (Schallreuter, Moore et al. 1999). Over the last decade our group and others have focused on the effect of H2O2-mediated oxidative stress on the function of many proteins and peptides due to oxidation of target amino acid residues in their structure including L-methionine, L-tryptophan, L-cysteine and seleno cysteine (Rokos, Beazley et al. 2002; Gillbro, Marles et al. 2004; Hasse, Kothari et al. 2005; Schallreuter, Chavan et al. 2005; Spencer, Chavan et al. 2005; Chavan, Gillbro et al. 2006; Elwary, Chavan et al. 2006; Gibbons, Wood et al. 2006; Schallreuter, Bahadoran et al. 2008; Shalbaf, Gibbons et al. 2008; Wood, Decker et al. 2009). Moreover, it was shown that patients with vitiligo possess up regulated wild type functioning p53 protein in their skin (Schallreuter, Behrens- Williams et al. 2003). The reason behind this up regulation has remained unclear (Schallreuter, Behrens-Williams et al. 2003). Therefore the aim of this thesis was to get a better understanding of these puzzling data. Along this project different techniques have been used including Western blot, dot blot, immuno precipitation, immuno fluorescence, EMSA and computer modelling. In this thesis we confirmed the previous result on up regulation of p53 in vitiligo and we showed that p90MDM2, the master regulator for p53 protein is not different in patients and healthy controls. Therefore we decided to test for expression of p76MDM2 which mediates the inhibition of p90MDM2-p53 binding. Our results show for the first time the presence and over expression of p76MDM2 protein in vitiligo compared to 3 healthy individuals. This result could provide an explanation, why up regulated p53 is not degraded in this disease. Since epidermal H2O2 accumulation has been extensively documented in vitiligo, we wanted to know whether other ROS could also contribute to the overall oxidative stress in this scenario. Therefore we turned our interest to nitric oxide (NO) and its possible effects on p53 protein. In order to elucidate this role in more detail, the expression levels of epidermal nitric oxide synthesase (iNOS) and the oxidation product of NO and O2 - i.e peroxynitrite (ONOO-) were investigated. Our data revealed over expression of iNOS and nitrated tyrosine residues, the foot print for ONOO-. Moreover, we show for the first time the presence of abundant nitration of p53 protein in vitiligo. In addition using purified p53 from E. coli strain (BL21/DE3) and mutant p53 protein from HT-29 cells (colon cancer cells), we show that nitration takes place in a dose and time dependent manner. On this basis we investigated the effect of both H2O2 and ONOO- on p53-DNA binding capacity employing EMSA, since this is the most acceptable technique to follow the binding between proteins and DNA. Our results revealed that ONOO- abrogated p53-DNA binding capacity at concentrations >300 ¿M, meanwhile oxidation of p53 protein with H2O2 at the same concentrations does not affect binding capacity. Importantly, a much higher p53- DNA binding capacity was observed after exposure to both ONOO- and H2O2. Taken together, p53 is regulated by both ROS (H2O2) and RNS (ONOO-). Next we identified the presence of phosphorylated and acetylated p53 in vitiligo. Phosphorylation of ser 9 and ser 15 residues of the protein are associated with over expressed ATM protein kinase, while acetylation of lys 373, 382 residues correlates with increased PCAF expression. We show that up regulated p53 is associated with over expressed p21 (cyclin dependent kinase inhibitor 1) and induced PCNA 4 expression. Hence, we can conclude that p53 in patients with vitiligo is up regulated, activated and functional. Finally we show up regulated BCL-2 supporting the long voiced absence of increased apoptosis in vitiligo. Given that patients with vitiligo have no increased risk for solar induced skin cancer and increased photo damage (Calanchini-Postizzi and Frenk 1987; Westerhof and Schallreuter 1997; Schallreuter, Tobin et al. 2002), despite the presence of increased DNA damage as evidenced by increased 8-oxoG levels in the skin and in the plasma, our findings suggest that both p53 and PCNA provide a powerful machinery to mediate DNA repair via hOgg1, APE1 and DNA polymerase ß (Shalbaf 2009). On this basis it is tempting to conclude that DNArepair is the overriding mechanism to combat oxidative stress in this disease. / Egyptian government; Institute for Pigmentary Disorders in association with the EM Arndt University of Greifswald, Germany.