The molecular basis of chromatin dynamics during nucleotide excision repair

Anthocyanins from black peanut skin protect against UV-B induced keratinocyte cell and skin oxidative damage through activating Nrf 2 signaling

Excessive Ultraviolet (UV) irradiation induces skin damage. In the present study, the potential protective activity of anthocyanins (cyanidin-3-O-sophoroside and cyanidin-3-O-sambubioside) from black peanut against skin damage induced by UV-B was evaluated in vitro and in vivo. Treatment with anthocyanins significantly reversed UV-B induced oxidative damage and following apoptotic death in human HaCaT cells. Nuclear-factor-E2-related factor 2 (Nrf 2) was activated by anthocyanins through Nrf 2 protein stabilization and nuclear translocation, along with the expressions of antioxidant responsive element (ARE)- related genes (HO1, GCLC and NOQ1). Nrf 2 knockdown in HaCaT cells by targeted-shRNA plasmid markedly abolished the protective activity of anthocyanins against UV-B irradiation. Additionally, topical application of anthocyanins (5 mg cm-2) inhibited UV-B induced oxidative stress and cell apoptosis in BALB/c mouse skin tissues. The protective effect of anthocyanins can be explained by the regulation of oxidative-stress and the suppression of cell apoptosis through the activation of Nrf-2 by interaction with the MAPK and NF-κB signaling pathways. Our results suggested that anthocyanins from black peanut skin might be used as a potential photochemo-protective agent against UV-B induced skin damage.

The Uve1 endonuclease is regulated by the white collar complex to protect cryptococcus neoformans from UV damage

The pathogenic fungus Cryptococcus neoformans uses the Bwc1-Bwc2 photoreceptor complex to regulate mating in response to light, virulence and ultraviolet radiation tolerance. How the complex controls these functions is unclear. Here, we identify and characterize a gene in Cryptococcus, UVE1, whose mutation leads to a UV hypersensitive phenotype. The homologous gene in fission yeast Schizosaccharomyces pombe encodes an apurinic/apyrimidinic endonuclease acting in the UVDE-dependent excision repair (UVER) pathway. C. neoformans UVE1 complements a S. pombe uvde knockout strain. UVE1 is photoregulated in a Bwc1-dependent manner in Cryptococcus, and in Neurospora crassa and Phycomyces blakesleeanus that are species that represent two other major lineages in the fungi. Overexpression of UVE1 in bwc1 mutants rescues their UV sensitivity phenotype and gel mobility shift experiments show binding of Bwc2 to the UVE1 promoter, indicating that UVE1 is a direct downstream target for the Bwc1-Bwc2 complex. Uve1-GFP fusions localize to the mitochondria. Repair of UV-induced damage to the mitochondria is delayed in the uve1 mutant strain. Thus, in C. neoformans UVE1 is a key gene regulated in response to light that is responsible for tolerance to UV stress for protection of the mitochondrial genome.

The majority of fungi sense light using the White Collar complex (WCC), a two-protein combination of a photoreceptor and a transcription factor. The WCC regulates circadian rhythms, sexual development, sporulation, metabolism, and virulence. As such, the exposure to light controls properties of fungi that are beneficial and detrimental to people, depending on the species and its interaction with humans. Despite the importance of light on fungal biology, the underlying evolutionary benefit of light-sensing in fungi has remained a mystery. Here we identify a DNA damage repair endonuclease, Uve1, required for UV stress tolerance in the human pathogen Cryptococcus neoformans. UVE1 is a direct target of the WCC in C. neoformans, and UVE1 homologs are also regulated by WCC in two other major lineages of fungi, the Ascomycota and Mucoromycotina. The divergence of the three groups indicates that for about a billion years the same transcription factor complex has regulated a common gene to protect fungal genomes from deleterious effects of light. Curiously, in C. neoformans Uve1 localizes to mitochondria and contributes to mitochondrial DNA repair, implicating its importance in genome repair of this organelle. Thus, light-sensing in fungi exists to protect them against harmful light, and likely all other responses to light relate to or are a secondary consequence of this selective pressure.

Functional architecture of the nuclear pore complex

The nuclear pore complex (NPC) is the sole gateway between the nucleus and the cytoplasm. NPCs fuse the inner and outer nuclear membranes to form aqueous translocation channels that allow the free diffusion of small molecules and ions, as well as receptor-mediated transport of large macromolecules. The NPC regulates nucleocytoplasmic transport of macromolecules, utilizing soluble receptors that identify and present cargo to the NPC, in a highly selective manner to maintain cellular functions. The NPC is composed of multiple copies of approximately 30 different proteins, termed nucleoporins, which assemble to form one of the largest multiprotein assemblies in the cell. In this review, we address structural and functional aspects of this fundamental cellular machinery.

Downregulation of SWI/SNF chromatin remodeling factor subunits modulates cisplatin cytotoxicity

Chromatin remodeling complex SWI/SNF plays important roles in many cellular processes including transcription, proliferation, differentiation and DNA repair. In this report, we investigated the role of SWI/SNF catalytic subunits Brg1 and Brm in the cellular response to cisplatin in lung cancer and head/neck cancer cells. Stable knockdown of Brg1 and Brm enhanced cellular sensitivity to cisplatin. Repair kinetics of cisplatin DNA adducts revealed that downregulation of Brg1 and Brm impeded the repair of both intrastrand adducts and interstrand crosslinks (ICLs). Cisplatin ICL-induced DNA double strand break repair was also decreased in Brg1 and Brm depleted cells. Altered checkpoint activation with enhanced apoptosis as well as impaired chromatin relaxation was observed in Brg1 and Brm deficient cells. Downregulation of Brg1 and Brm did not affect the recruitment of DNA damage recognition factor XPC to cisplatin DNA lesions, but affected ERCC1 recruitment, which is involved in the later stages of DNA repair. Based on these results, we propose that SWI/SNF chromatin remodeling complex modulates cisplatin cytotoxicity by facilitating efficient repair of the cisplatin DNA lesions.

Implication of posttranslational histone modifications in nucleotide excision repair

Histones are highly alkaline proteins that package and order the DNA into chromatin in eukaryotic cells. Nucleotide excision repair (NER) is a conserved multistep reaction that removes a wide range of generally bulky and/or helix-distorting DNA lesions. Although the core biochemical mechanism of NER is relatively well known, how cells detect and repair lesions in diverse chromatin environments is still under intensive research. As with all DNA-related processes, the NER machinery must deal with the presence of organized chromatin and the physical obstacles it presents. A huge catalogue of posttranslational histone modifications has been documented. Although a comprehensive understanding of most of these modifications is still lacking, they are believed to be important regulatory elements for many biological processes, including DNA replication and repair, transcription and cell cycle control. Some of these modifications, including acetylation, methylation, phosphorylation and ubiquitination on the four core histones (H2A, H2B, H3 and H4) or the histone H2A variant H2AX, have been found to be implicated in different stages of the NER process. This review will summarize our recent understanding in this area.

The emerging roles of ATP-dependent chromatin remodeling enzymes in nucleotide excision repair

DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon the overall rate of DNA repair. Chromatin is highly responsive to DNA damage and undergoes specific remodeling to facilitate DNA repair. How damaged DNA is accessed, repaired and restored to the original chromatin state, and how chromatin remodeling coordinates these processes in vivo, remains largely unknown. ATP-dependent chromatin remodelers (ACRs) are the master regulators of chromatin structure and dynamics. Conserved from yeast to humans, ACRs utilize the energy of ATP to reorganize packing of chromatin and control DNA accessibility by sliding, ejecting or restructuring nucleosomes. Several studies have demonstrated that ATP-dependent remodeling activity of ACRs plays important roles in coordination of spatio-temporal steps of different DNA repair pathways in chromatin. This review focuses on the role of ACRs in regulation of various aspects of nucleotide excision repair (NER) in the context of chromatin. We discuss current understanding of ATP-dependent chromatin remodeling by various subfamilies of remodelers and regulation of the NER pathway in vivo.

Factors influencing heterogeneity of radiation-induced DNA-damage measured by the alkaline comet assay

Background

To investigate whether different conditions of DNA structure and radiation treatment could modify heterogeneity of response. Additionally to study variance as a potential parameter of heterogeneity for radiosensitivity testing.

Methods

Two-hundred leukocytes per sample of healthy donors were split into four groups. I: Intact chromatin structure; II: Nucleoids of histone-depleted DNA; III: Nucleoids of histone-depleted DNA with 90 mM DMSO as antioxidant. Response to single (I-III) and twice (IV) irradiation with 4 Gy and repair kinetics were evaluated using %Tail-DNA. Heterogeneity of DNA damage was determined by calculation of variance of DNA-damage (V) and mean variance (Mvar), mutual comparisons were done by one-way analysis of variance (ANOVA).

Results

Heterogeneity of initial DNA-damage (I, 0 min repair) increased without histones (II). Absence of histones was balanced by addition of antioxidants (III). Repair reduced heterogeneity of all samples (with and without irradiation). However double irradiation plus repair led to a higher level of heterogeneity distinguishable from single irradiation and repair in intact cells. Increase of mean DNA damage was associated with a similarly elevated variance of DNA damage (r = +0.88).

Conclusions

Heterogeneity of DNA-damage can be modified by histone level, antioxidant concentration, repair and radiation dose and was positively correlated with DNA damage. Experimental conditions might be optimized by reducing scatter of comet assay data by repair and antioxidants, potentially allowing better discrimination of small differences. Amount of heterogeneity measured by variance might be an additional useful parameter to characterize radiosensitivity.

Identification of residues in chromodomain helicase DNA-binding protein 1 (Chd1) required for coupling ATP hydrolysis to nucleosome sliding

Chromatin remodelers are ATP-dependent machines responsible for directionally shifting nucleosomes along DNA. We are interested in defining which elements of the chromodomain helicase DNA-binding protein 1 (Chd1) remodeler are necessary and sufficient for sliding nucleosomes. This work focuses on the polypeptide segment that joins the ATPase motor to the C-terminal DNA-binding domain. We identify amino acid positions outside the ATPase motor that, when altered, dramatically reduce nucleosome sliding ability and yet have only ∼3-fold reduction in ATPase stimulation by nucleosomes. These residues therefore appear to play a role in functionally coupling ATP hydrolysis to nucleosome sliding, and suggest that the ATPase motor requires cooperation with external elements to slide DNA past the histone core.

Nucleotide excision repair in chromatin: damage removal at the drop of a HAT

In an earlier review of our understanding of the mechanism of nucleotide excision repair (NER) we examined the process with respect to how it occurs in chromatin [1]. We described how much of our mechanistic understanding of NER was derived from biochemical studies that analysed the repair reaction in DNA substrates not representative of that which exists in the living cell. We pointed out that our efforts to understand how NER operates in chromatin had been hampered in part because of the well-known inhibition of NER that occurs when DNA is assembled into nucleosomes and used as the substrate to examine the repair reaction in vitro. Despite this technical bottleneck, we summarized the biochemical, genetic and cell-based studies which have provided insights into the molecular mechanism of NER in the cellular context. More recently, we revisited the topic of how UV induced DNA damage is repaired in chromatin. In this review we examined the commonly held view that depicts a struggle in which the DNA repair machinery battles to overcome the inhibitory effect of chromatin during the repair process. We suggested that in this interpretation of events, the DNA repair mechanisms might be described as 'tilting at windmills': fighting an imaginary foe [2]. We surmised that this scenario was overly simplistic, and we described an emerging picture in which the DNA repair process and chromatin remodeling were mechanistically linked and were in fact functioning cooperatively to organize the efficient removal of DNA damage from the genome. Here we discuss the latest findings, which contribute to the idea that DNA damage induced changes to chromatin represent an important way in which the DNA repair process is initiated and organized throughout the genome to promote the efficient removal of damage in response to UV radiation.

Stem cell protein Piwil2 modulates chromatin modifications upon cisplatin treatment

Piwil2 (mili in mouse or hili in humans), a member of the PIWI/Argonaute gene family, plays important roles in stem cell self-renewal, RNA silencing, and translational regulation in various organisms. Recent demonstration of stable Piwil2 expression in pre-cancerous stem cells and in various human and animal tumor cell lines suggests its association in tumorigenesis. Here, we show that cisplatin induces chromatin relaxation in Mili-wild type (WT) mouse embryonic fibroblasts (MEFs), but not in Mili-knockout (KO) MEFs. Moreover, in contrast to Mili-WT MEFs, Mili-KO MEFs showed a discernable H3 hypoacetylation response upon cisplatin treatment. Levels of the histone acetyltransferase (HAT), p300, were dramatically different due to a consistent cisplatin post-treatment decrease in Mili-WT and an increase in Mili-KO MEFs. Concomitant reduction of specific HAT activity of p300 could explain the decrease of H3 acetylation in Mili-KO MEFs. Our data also shows Mili is required for maintaining the euchromatic marks in MEFs upon cisplatin treatment. In addition, Mili-KO MEFs exhibited a significant deficiency in repairing cisplatin-induced DNA damage and displayed higher sensitivity to cisplatin. Further analysis revealed that Piwil2 was also enhanced in two completely different cisplatin-resistant ovarian cancer cell lines. Interestingly, knockdown of Piwil2 expression in these two cell lines also resulted in their enhanced sensitivity to cisplatin and decreased their efficiency for removing cisplatin-induced DNA intrastrand crosslinks (Pt-GG). The overall data showed that Piwil2 is a key factor in regulating chromatin modifications especially in response to cisplatin. To conclude, the overexpression of Piwil2 in some cancers could lead to cellular cisplatin resistance, possibly due to enhanced chromatin condensation affecting normal DNA repair.

UV damage in DNA promotes nucleosome unwrapping

The association of DNA with histones in chromatin impedes DNA repair enzymes from accessing DNA lesions. Nucleosomes exist in a dynamic equilibrium in which portions of the DNA molecule spontaneously unwrap, transiently exposing buried DNA sites. Thus, nucleosome dynamics in certain regions of chromatin may provide the exposure time and space needed for efficient repair of buried DNA lesions. We have used FRET and restriction enzyme accessibility to study nucleosome dynamics following DNA damage by UV radiation. We find that FRET efficiency is reduced in a dose-dependent manner, showing that the presence of UV photoproducts enhances spontaneous unwrapping of DNA from histones. Furthermore, this UV-induced shift in unwrapping dynamics is associated with increased restriction enzyme accessibility of histone-bound DNA after UV treatment. Surprisingly, the increased unwrapping dynamics is even observed in nucleosome core particles containing a single UV lesion at a specific site. These results highlight the potential for increased “intrinsic exposure” of nucleosome-associated DNA lesions in chromatin to repair proteins.

HMGNs, DNA repair and cancer

DNA lesions threaten the integrity of the genome and are a major factor in cancer formation and progression. Eukaryotic DNA is organized in nucleosome-based higher order structures, which form the chromatin fiber. In recent years, considerable knowledge has been gained on the importance of chromatin dynamics for the cellular response to DNA damage and for the ability to repair DNA lesions. High Mobility Group N1 (HMGN1) protein is an emerging factor that is important for chromatin alterations in response to DNA damage originated from both ultra violet light (UV) and ionizing irradiation (IR). HMGN1 is a member in the HMGN family of chromatin architectural proteins. HMGNs bind directly to nucleosomes and modulate the structure of the chromatin fiber in a highly dynamic manner. This review focuses mainly on the roles of HMGN1 in the cellular response pathways to different types of DNA lesions and in transcriptional regulation of cancer-related genes. In addition, emerging roles for HMGN5 in cancer progression and for HMGN2 as a potential tool in cancer therapy will be discussed.

Modulation of nucleotide excision repair by mammalian SWI/SNF chromatin-remodeling complex

Accessibility within chromatin is an important factor in the prompt removal of UV-induced DNA damage by nucleotide excision repair (NER). Chromatin remodeling by the SWI/SNF complex has been shown to play an important modulating role in NER in vitro and yeast in vivo. Nevertheless, the molecular basis of cross-talk between SWI/SNF and NER in mammalian cells is not fully understood. Here, we show that knockdown of Brg1, the ATPase subunit of SWI/SNF, negatively affects the elimination of cyclobutane pyrimidine dimers (CPD), but not of pyrimidine (6, 4)pyrimidone photoproducts (6-4PP) following UV irradiation of mammalian cells. Brg1-deficient cells exhibit a lower chromatin relaxation as well as impaired recruitment of downstream NER factors, XPG and PCNA, to UV lesions. However, the assembly of upstream NER factors, DDB2 and XPC, at the damage site was unaffected by Brg1 knockdown. Interestingly, Brg1 interacts with XPC within chromatin and is recruited to UV-damaged sites in a DDB2- and XPC-dependent manner. Also, postirradiation decrease of XPC levels occurred more rapidly in Brg1-deficient than normal cells. Conversely, XPC transcription remained unaltered upon Brg1 knockdown indicating that Brg1 affects the stability of XPC protein following irradiation. Thus, Brg1 facilitates different stages of NER by initially modulating UV-induced chromatin relaxation and stabilizing XPC at the damage sites, and subsequently stimulating the recruitment of XPG and PCNA to successfully culminate the repair.

Assays for chromatin remodeling during nucleotide excision repair in Saccharomyces cerevisiae

How DNA repair proteins interact with the dynamic structure of chromatin is an emerging question. Chromatin structure impedes the access of repair proteins to sites of DNA damage. Several recent studies have implicated chromatin remodeling complexes in DNA repair. In this report we summarize the methods we used to investigate chromatin remodeling during nucleotide excision repair (NER) in vivo. We describe a procedure to analyze UV-induced chromatin remodeling at the silent mating-type locus HML using isolated nuclei from UV-treated yeast cells. In addition, a method to capture transient protein-protein associations in chromatin is outlined. We have used the methods described here to demonstrate that the SWI/SNF chromatin remodeling complex is involved in chromatin rearrangement during NER.