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nucleotide excision repair

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https://www.readbyqxmd.com/read/29328361/logistic-regression-analysis-for-the-identification-of-the-metastasis-associated-signaling-pathways-of-osteosarcoma
#1
Yang Liu, Wei Sun, Xiaojun Ma, Yuedong Hao, Gang Liu, Xiaohui Hu, Houlai Shang, Pengfei Wu, Zexue Zhao, Weidong Liu
Osteosarcoma (OS) is the most common histological type of primary bone cancer. The present study was designed to identify the key genes and signaling pathways involved in the metastasis of OS. Microarray data of GSE39055 were downloaded from the Gene Expression Omnibus database, which included 19 OS biopsy specimens before metastasis (control group) and 18 OS biopsy specimens after metastasis (case group). After the differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Analysis package, hierarchical clustering analysis and unsupervised clustering analysis were performed separately, using orange software and the self-organization map method...
January 2, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29323787/inhibition-of-uvssa-ubiquitination-suppresses-transcription-coupled-nucleotide-excision-repair-deficiency-caused-by-dissociation-from-usp7
#2
Mitsuru Higa, Kiyoji Tanaka, Masafumi Saijo
Transcription-coupled nucleotide excision repair (TC-NER) is a subpathway of nucleotide excision repair that efficiently removes transcription-blocking DNA damage from the transcribed strands of active genes. UVSSA is a causative gene for UV-sensitive syndrome (UVS S), which is an autosomal recessive disorder characterized by hypersensitivity to UV light and deficiency in TC-NER. UV-stimulated scaffold protein A (UVSSA), the product of UVSSA, forms a complex with ubiquitin-specific peptidase 7 (USP7) and is stabilized by interaction with USP7...
January 11, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29320546/rpa-and-xpa-interaction-with-dna-structures-mimicking-intermediates-of-the-late-stages-in-nucleotide-excision-repair
#3
Yuliya S Krasikova, Nadejda I Rechkunova, Ekaterina A Maltseva, Olga I Lavrik
Replication protein A (RPA) and the xeroderma pigmentosum group A (XPA) protein are indispensable for both pathways of nucleotide excision repair (NER). Here we analyze the interaction of RPA and XPA with DNA containing a flap and different size gaps that imitate intermediates of the late NER stages. Using gel mobility shift assays, we found that RPA affinity for DNA decreased when DNA contained both extended gap and similar sized flap in comparison with gapped-DNA structure. Moreover, crosslinking experiments with the flap-gap DNA revealed that RPA interacts mainly with the ssDNA platform within the long gap and contacts flap in DNA with a short gap...
2018: PloS One
https://www.readbyqxmd.com/read/29305302/actual-state-of-knowledge-in-the-field-of-diseases-related-with-defective-nucleotide-excision-repair
#4
REVIEW
Barbara Bukowska, Bolesław T Karwowski
Xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS) are rare genetic diseases characterized by a large range of clinical symptoms. However, they are all associated with defects in nucleotide excision repair (NER), the system responsible for removing bulky DNA lesions such as those generated by UV light: cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone photoproducts (6-4 PPs). Over the past years, detailed structural and biochemical information on NER-associated proteins has emerged...
January 2, 2018: Life Sciences
https://www.readbyqxmd.com/read/29296177/isg15-silencing-increases-cisplatin-resistance-via-activating-p53-mediated-cell-dna-repair
#5
Yi Huo, Zhaoyun Zong, Qingtao Wang, Zhenyu Zhang, Haiteng Deng
Tumor cells frequently evolved resistance to cisplatin that greatly compromises the efficacy of chemotherapy. Identification of the mechanisms underlying drug resistance is important for developing new therapeutic approaches. ISG15 is found to be elevated in many human carcinomas and cancer cell lines. Here, we identified that the expressions of ISG15 and ISG15-conjugating system were downregulated in drug resistant A549/DDP cells compared to drug sensitive A549 cells. Silencing of ISG15 robustly elevated the resistance to cisplatin, suggesting ISG15 plays an important role in cisplatin resistance...
December 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/29283557/%C3%AE-%C3%AE-unsaturated-aldehyde-induced-delays-in-nucleotide-excision-repair-and-the-contribution-of-reactive-oxygen-species
#6
Guang Yang, Yuko Ibuki
Aldehydes are widespread environmental and industrial compounds to which humans are frequently exposed. Despite their significant health risk, the mechanisms underlying aldehyde toxicity are poorly understand. We recently demonstrated that cigarette sidestream smoke (CSS) inhibited nucleotide excision repair (NER), and this was attributed to aldehydes in CSS. In the present study, we examined the influence of saturated and unsaturated aldehydes on NER. The human keratinocyte cell line, HaCaT was treated with aldehydes and then exposed to UVB...
December 28, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/29283431/rad4-and-rad23-hmr-contribute-to-arabidopsis-uv-tolerance
#7
Triparna Lahari, Janelle Lazaro, Dana F Schroeder
In plants, exposure to solar ultraviolet (UV) light is unavoidable, resulting in DNA damage. Damaged DNA causes mutations, replication arrest, and cell death, thus efficient repair of the damaged DNA is essential. A light-independent DNA repair pathway called nucleotide excision repair (NER) is conserved throughout evolution. For example, the damaged DNA-binding protein Radiation sensitive 4 (Rad4) in Saccharomyces cerevisiae is homologous to the mammalian NER protein Xeroderma Pigmentosum complementation group C (XPC)...
December 28, 2017: Genes
https://www.readbyqxmd.com/read/29247747/prognostic-values-of-excision-repair-cross-complementing-genes-mrna-expression-in-ovarian-cancer-patients
#8
Menghuang Zhao, Saisai Li, Lulu Zhou, Qi Shen, Haiyan Zhu, Xueqiong Zhu
Excision repair cross-complementing (ERCC) genes, key components of the nucleotide excision repair pathway, are regarded as crucial factors for DNA repair capacity. Previous studies have investigated prognostic values of ERCC genes in a number of malignancies. However, the relationship between ERCC genes and prognosis of ovarian cancer patients remains controversial. Therefore, in the current study, we systematically analyze the prognostic values of ERCC genes in ovarian cancer by the Kaplan-Meier plotter, which includes updated gene expression data and survival information of 1656 ovarian cancer patients...
December 13, 2017: Life Sciences
https://www.readbyqxmd.com/read/29240933/recruitment-of-uvrbc-complexes-to-uv-induced-damage-in-the-absence-of-uvra-increases-cell-survival
#9
Luke Springall, Craig D Hughes, Michelle Simons, Stavros Azinas, Bennett Van Houten, Neil M Kad
Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA2 and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA...
December 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29233865/dicer-and-mmset-catalyzed-h4k20me2-recruits-the-nucleotide-excision-repair-factor-xpa-to-dna-damage-sites
#10
Shalaka Chitale, Holger Richly
Ultraviolet (UV) irradiation triggers the recruitment of DNA repair factors to the lesion sites and the deposition of histone marks as part of the DNA damage response. The major DNA repair pathway removing DNA lesions caused by exposure to UV light is nucleotide excision repair (NER). We have previously demonstrated that the endoribonuclease DICER facilitates chromatin decondensation during lesion recognition in the global-genomic branch of NER. Here, we report that DICER mediates the recruitment of the methyltransferase MMSET to the DNA damage site...
December 12, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/29228550/regulation-of-xpc-deubiquitination-by-usp11-in-repair-of-uv-induced-dna-damage
#11
Palak Shah, Lei Qiang, Seungwon Yang, Keyoumars Soltani, Yu-Ying He
Nucleotide excision repair (NER) is the most versatile DNA repair pathway for removing DNA damage caused by UV radiation and many environmental carcinogens. NER is essential for suppressing tumorigenesis in the skin, lungs and brain. Although the core NER proteins have been identified and characterized, molecular regulation of NER remains poorly understood. Here we show that ubiquitin-specific peptidase 11 (USP11) positively regulates NER by deubiquitinating xeroderma pigmentosum complementation group C (XPC) and promoting its retention at the DNA damage sites...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29226731/pharmacogenetics-of-platinum-based-chemotherapy-in-non-small-cell-lung-cancer-predictive-validity-of-polymorphisms-of-ercc1
#12
Gerhard Hamilton, Barbara Rath
The efficacy of platinum based chemotherapy for patients with non-small cell lung cancer (NSCLC) is limited by chemoresistance. Platinum drugs damage DNA by introducing intrastrand and interstrand crosslinks which result in cell death. Excision repair cross-complementing 1 (ERCC1) is a member of the nucleotide excision repair (NER) pathway which erases such defects. Single nucleotide polymorphisms (SNPs) in ERCC1 impair this activity and have been suggested to predict the response to chemotherapy. Area covered...
December 11, 2017: Expert Opinion on Drug Metabolism & Toxicology
https://www.readbyqxmd.com/read/29225704/transcription-coupled-repair-and-biased-insertion-of-human-retrotransposon-l1-in-transcribed-genes
#13
Geraldine Servant, Vincent A Streva, Prescott L Deininger
Background: L1 retrotransposons inserted within genes in the human genome show a strong bias against sense orientation with respect to the gene. One suggested explanation for this observation was the possibility that L1 inserted randomly, but that there was negative selection against sense-oriented insertions. However, multiple studies have now found that de novo and polymorphic L1 insertions, which have little opportunity for selection to act, also show the same bias. Results: Here we show that the transcription-coupled sub-pathway of nucleotide excision repair does not affect the overall rate of insertion of L1 elements, which is in contrast with the regulation by the global sub-pathway of nucleotide excision repair...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29223826/modulation-effect-of-double-strand-dna-on-the-self-assembly-of-n-terminal-domain-of-euplotes-octocarinatus-centrin
#14
Wenlong Zhang, Enxian Shi, Yaqin Zhao, Binsheng Yang
Centrin is a member of the EF-hand super family of calcium-binding proteins, which can behave as a part of damage detector initiated the initiation of nucleotide excision repair (NER). Its self-assembly plays a causative role in fiber contraction associated with the cell division cycle and ciliogenesis. To explore the possible role of DNA in the process of centrin self-assembly, the aggregation properties of N-terminal domain of Euplotes octocarinatus centrin (N-EoCen) in the presence of DNA with or without metal ions are investigated...
December 5, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29223016/application-of-single-nucleotide-extension-and-maldi-tof-mass-spectrometry-in-proofreading-and-dna-repair-assay
#15
Kang-Yi Su, Hung-Ming Lai, Steven D Goodman, Wei-Yao Hu, Wern-Cherng Cheng, Liang-In Lin, Ya-Chien Yang, Woei-Horng Fang
Proofreading and DNA repair are important factors in maintaining the high fidelity of genetic information during DNA replication. Herein, we designed a non-labeled and non-radio-isotopic simple method to measure proofreading. An oligonucleotide primer is annealed to a template DNA forming a mismatched site and is proofread by Klenow fragment of Escherichia coli DNA polymerase I (pol I) in the presence of all four dideoxyribonucleotide triphosphates. The proofreading excision products and re-synthesis products of single nucleotide extension are subjected to MALDI-TOF mass spectrometry (MS)...
December 2, 2017: DNA Repair
https://www.readbyqxmd.com/read/29222335/single-cell-transcriptome-sequencing-reveals-that-cell-division-cycle-5-like-protein-is-essential-for-porcine-oocyte-maturation
#16
Xiao-Man Liu, Yan-Kui Wang, Yun-Hua Liu, Xiao-Xia Yu, Pei-Chao Wang, Xuan Li, Zhi-Qiang Du, Cai-Xia Yang
The brilliant cresyl blue (BCB) test is used in both basic biological research and assisted reproduction to identify oocytes likely to be developmentally competent. However, the underlying molecular mechanism targeted by the BCB test is still unclear. To explore this question, we first confirmed that BCB-positive porcine oocytes had higher rates of meiotic maturation, better rates of cleavage and development into blastocysts, and lower death rates. Subsequent single-cell transcriptome sequencing on porcine germinal vesicle (GV)-stage oocytes identified 155 genes that were significantly differentially expressed between BCB-negative and BCB-positive oocytes...
December 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29199611/association-of-ercc1-polymorphisms-with-the-risk-of-colorectal-cancer-a-meta-analysis
#17
Jianfeng Chen, Ningjie Sun, Gang Hu, Xiansheng Chen, Jiansong Jiang, Haiming Wu, Gaojian Luo
The ERCC1 enzyme in the nucleotide excision repair (NER) pathway plays a vital role in DNA repair. Numerous epidemiological studies have evaluated the association between ERCC1 polymorphisms and the risk of colorectal cancer (CRC), with conflicting results. To evaluate the potential associations, we conducted a meta-analysis. Eligible studies were identified by searching electronic databases. The odds ratio (OR) and 95% confidence interval (CI) were applied to assess the associations between ERCC1 polymorphisms and CRC risk...
2017: Critical Reviews in Eukaryotic Gene Expression
https://www.readbyqxmd.com/read/29180430/def1-interacts-with-tfiih-and-modulates-rna-polymerase-ii-transcription
#18
Nivedita Damodaren, Trevor Van Eeuwen, Joanna Zamel, Enrique Lin-Shiao, Nir Kalisman, Kenji Murakami
The DNA damage response is an essential process for the survival of living cells. In a subset of stress-responsive genes in humans, Elongin controls transcription in response to multiple stimuli, such as DNA damage, oxidative stress, and heat shock. Yeast Elongin (Ela1-Elc1), along with Def1, is known to facilitate ubiquitylation and degradation of RNA polymerase II (pol II) in response to multiple stimuli, yet transcription activity has not been examined. We have found that Def1 copurifies from yeast whole-cell extract with TFIIH, the largest general transcription factor required for transcription initiation and nucleotide excision repair...
November 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29171825/guardians-of-the-mycobacterial-genome-a-review-on-dna-repair-systems-in-mycobacterium-tuberculosis
#19
Amandeep Singh
The genomic integrity of Mycobacterium tuberculosis is continuously threatened by the harsh survival conditions inside host macrophages, due to immune and antibiotic stresses. Faithful genome maintenance and repair must be accomplished under stress for the bacillus to survive in the host, necessitating a robust DNA repair system. The importance of DNA repair systems in pathogenesis is well established. Previous examination of the M. tuberculosis genome revealed homologues of almost all the major DNA repair systems, i...
November 24, 2017: Microbiology
https://www.readbyqxmd.com/read/29170789/crebbp-and-p300-lysine-acetyl-transferases-in-the-dna-damage-response
#20
REVIEW
Ilaria Dutto, Claudia Scalera, Ennio Prosperi
The CREB-binding protein (CREBBP, or in short CBP) and p300 are lysine (K) acetyl transferases (KAT) belonging to the KAT3 family of proteins known to modify histones, as well as non-histone proteins, thereby regulating chromatin accessibility and transcription. Previous studies have indicated a tumor suppressor function for these enzymes. Recently, they have been found to acetylate key factors involved in DNA replication, and in different DNA repair processes, such as base excision repair, nucleotide excision repair, and non-homologous end joining...
November 23, 2017: Cellular and Molecular Life Sciences: CMLS
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