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https://www.readbyqxmd.com/read/28102005/blind-prediction-of-deleterious-amino-acid-variations-with-snps-go
#1
Emidio Capriotti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
: SNPs&GO is a machine learning method for predicting the association of single amino acid variations (SAVs) to disease, considering protein functional annotation. The method is a binary classifier that implements a Support Vector Machine algorithm to discriminate between disease-related and neutral SAVs. SNPs&GO combines information from protein sequence with functional annotation encoded by Gene Ontology terms. Tested in sequence mode on more than 38,000 SAVs from the SwissVar dataset, our method reached 81% overall accuracy and an area under the receiving operating characteristic curve (AUC) of 0...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28076792/the-mre11-nbs1-interface-is-essential-for-viability-and-tumor-suppression
#2
Jun Hyun Kim, Malgorzata Grosbart, Roopesh Anand, Claire Wyman, Petr Cejka, John H J Petrini
The Mre11 complex (Mre11, Rad50, and Nbs1) is integral to both DNA repair and ataxia telangiectasia mutated (ATM)-dependent DNA damage signaling. All three Mre11 complex components are essential for viability at the cellular and organismal levels. To delineate essential and non-essential Mre11 complex functions that are mediated by Nbs1, we used TALEN-based genome editing to derive Nbs1 mutant mice (Nbs1(mid) mice), which harbor mutations in the Mre11 interaction domain of Nbs1. Nbs1(mid) alleles that abolished interaction were incompatible with viability...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28073364/lack-of-mre11-rad50-nbs1-mrn-complex-detection-occurs-frequently-in-low-grade-epithelial-ovarian-cancer
#3
Simone Brandt, Eleftherios P Samartzis, Anne-Katrin Zimmermann, Daniel Fink, Holger Moch, Aurelia Noske, Konstantin J Dedes
BACKGROUND: BRCA1/2-deficient ovarian carcinomas are recognized as target for Poly (ADP-ribose) polymerase (PARP) inhibitors. BRCA1 and BRCA2 proteins are involved in homologous recombination repair of double-strand DNA breaks. The relevance of other homologous recombination repair proteins, e.g. MRE11, RAD50, NBS1 (MRN complex) in ovarian carcinomas is unclear. The objective of this study was to investigate the prevalence of lack of MRE11, RAD50, NBS1 protein detection in epithelial ovarian cancer (EOC)...
January 10, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28031358/association-of-human-papillomavirus-type-16-e2-with-rad50-interacting-protein-1-enhances-viral-dna-replication
#4
Karen Campos León, Kalpanee Wijendra, Abida Siddiqa, Ieisha Pentland, Katherine M Feeney, Alison Knapman, Rachel Davies, Elliot J Androphy, Joanna L Parish
: Rad50-interacting protein 1 (Rint1) associates with the DNA damage response protein Rad50 during the S phase to G2/M transition and functions in radiation-induced G2 checkpoint control. It has also been demonstrated that Rint1 is essential in vesicle trafficking from the Golgi to the endoplasmic reticulum (ER) through interaction with Zeste-White 10 (ZW10). We have isolated a novel interaction between Rint1 and the human papillomavirus type 16 (HPV16) transcription and replication factor E2...
December 28, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27997699/chromatin-remodelling-and-dna-repair-genes-are-frequently-mutated-in-endometrioid-endometrial-carcinoma
#5
Pablo García-Sanz, Juan Carlos Triviño, Alba Mota, María Pérez López, Eva Colás, Alejandro Rojo-Sebastián, Ángel García, Sonia Gatius, María Ruiz, Jaime Prat, Rafael López-López, Miguel Abal, Antonio Gil-Moreno, Jaume Reventós, Xavier Matias-Guiu, Gema Moreno-Bueno
In developed countries, endometrial carcinoma is the most common cancer that affects the female genital tract. Endometrial carcinoma is divided into two main histological types, type I or endometrioid and type II or non-endometrioid, each of which have characteristic, although not exclusive, molecular alterations and mutational profiles. Nevertheless, information about the implication and relevance of some of these genes in this disease is lacking. We sought here to identify new recurrently mutated genes in endometrioid cancers that play a role in tumourigenesis and that influence the clinical outcome...
December 20, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27966484/genetic-and-biochemical-evidences-reveal-novel-insights-into-the-mechanism-underlying-saccharomyces-cerevisiae-sae2-mediated-abrogation-of-dna-replication-stress
#6
Indrajeet Ghodke, K Muniyappa
In Saccharomyces cerevisiae, the Mre11-Rad50-Xrs2 (MRX) protein complex plays pivotal roles in double-strand break (DSB) repair, replication stress and telomere length maintenance. Another protein linked to DSB repair is Sae2, which regulates MRX persistence at DSBs. However, very little is known about its role in DNA replication stress and repair. Here, we reveal a crucial role for Sae2 in DNA replication stress. We show that different mutant alleles of SAE2 cause hypersensitivity to genotoxic agents, and when combined with Δmre11 or nuclease-defective mre11 mutant alleles, the double mutants are considerably more sensitive suggesting that the sae2 mutations synergize with mre11 mutations...
December 2016: Journal of Biosciences
https://www.readbyqxmd.com/read/27932484/role-of-mdm2-and-mdmx-in-dna-repair
#7
REVIEW
Christine M Eischen
Mdm2 and Mdmx are critical regulators of the p53 tumour suppressor and are overexpressed in many human malignancies. However, in recent years, their impact on genome instability was shown to be at least, in part, independent of p53. Both Mdm2 and Mdmx inhibit DNA break repair through their association with the Mre11/Rad50/Nbs1 DNA repair complex. Recent evidence indicates that harnessing Mdm2 and/or Mdmx-mediated inhibition of DNA break repair in cancer cells could provide a therapeutic opportunity, particularly for those malignancies that have lost functional p53...
December 8, 2016: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/27915381/regulation-of-non-homologous-end-joining-via-post-translational-modifications-of-components-of-the-ligation-step
#8
REVIEW
Kristína Durdíková, Miroslav Chovanec
DNA double-strand breaks are the most serious type of DNA damage and non-homologous end joining (NHEJ) is an important pathway for their repair. In Saccharomyces cerevisiae, three complexes mediate the canonical NHEJ pathway, Ku (Ku70/Ku80), MRX (Mre11/Rad50/Xrs2) and DNA ligase IV (Dnl4/Lif1). Mammalian NHEJ is more complex, primarily as a consequence of the fact that more factors are involved in the process, and also because higher chromatin organization and more complex regulatory networks exist in mammals...
December 3, 2016: Current Genetics
https://www.readbyqxmd.com/read/27889450/rpa-mediates-recruitment-of-mrx-to-forks-and-double-strand-breaks-to-hold-sister-chromatids-together
#9
Andrew Seeber, Anna Maria Hegnauer, Nicole Hustedt, Ishan Deshpande, Jérôme Poli, Jan Eglinger, Philippe Pasero, Heinz Gut, Miki Shinohara, Karl-Peter Hopfner, Kenji Shimada, Susan M Gasser
The Mre11-Rad50-Xrs2 (MRX) complex is related to SMC complexes that form rings capable of holding two distinct DNA strands together. MRX functions at stalled replication forks and double-strand breaks (DSBs). A mutation in the N-terminal OB fold of the 70 kDa subunit of yeast replication protein A, rfa1-t11, abrogates MRX recruitment to both types of DNA damage. The rfa1 mutation is functionally epistatic with loss of any of the MRX subunits for survival of replication fork stress or DSB recovery, although it does not compromise end-resection...
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27889449/phosphorylated-ctip-functions-as-a-co-factor-of-the-mre11-rad50-nbs1-endonuclease-in-dna-end-resection
#10
Roopesh Anand, Lepakshi Ranjha, Elda Cannavo, Petr Cejka
To repair a DNA double-strand break (DSB) by homologous recombination (HR), the 5'-terminated strand of the DSB must be resected. The human MRE11-RAD50-NBS1 (MRN) and CtIP proteins were implicated in the initiation of DNA end resection, but the underlying mechanism remained undefined. Here, we show that CtIP is a co-factor of the MRE11 endonuclease activity within the MRN complex. This function is absolutely dependent on CtIP phosphorylation that includes the key cyclin-dependent kinase target motif at Thr-847...
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27878828/rhs6-coordinately-regulates-the-th2-cytokine-genes-by-recruiting-gata3-satb1-and-irf4
#11
S S Hwang, S W Jang, K O Lee, H S Kim, G R Lee
BACKGROUND: Asthma is a Th2 cell-driven inflammatory disease and a major public health concern. The cis-acting element Rad50 hypersensitive site 6 (RHS6) in the Th2 locus control region is essential for regulation of the Th2 cytokine genes; however, its role in allergic airway inflammation and underlying molecular mechanisms of the regulation by RHS6 are poorly understood. OBJECTIVE: We sought to understand the role of RHS6 in the development of allergic airway inflammation and its molecular mechanism for Th2 cytokine expression...
November 5, 2016: Allergy
https://www.readbyqxmd.com/read/27844240/identification-of-a-rare-germline-nbn-gene-mutation-by-whole-exome-sequencing-in-a-lung-cancer-survivor-from-a-large-family-with-various-types-of-cancer
#12
Makia J Marafie, Mohammed Dashti, Fahd Al-Mulla
Nijmegen breakage syndrome is an autosomal recessive disorder caused by biallelic mutation in NBN gene. It is characterized by microcephaly, growth retardation, immuno-deficiency and cancer predisposition. The monoallelic carriers of NBN gene are also reported to be at increased risk of developing various types of malignancy. We have investigated an individual with lung cancer from an extended family segregating different types of hereditary cancer over several generations, including lung, breast, ovarian, colon, prostate and renal cancers...
November 14, 2016: Familial Cancer
https://www.readbyqxmd.com/read/27821299/biomarkers-related-with-seizure-risk-in-glioma-patients-a-systematic-review
#13
REVIEW
Xing-Wang Zhou, Xiang Wang, Yuan Yang, Jie-Wen Luo, Hui Dong, Yan-Hui Liu, Qing Mao
Increasing evidence indicates that genetic biomarkers play important roles in the development of glioma-associated seizures. Thus, we performed a systematic review to summarise biomarkers that are associated with seizures in glioma patients. An electronic literature search of public databases (PubMed, Embase and Medline) was performed using the keywords glioma, seizure and epilepsy. A totall of 26 eligible studies with 2224 cases were included in this systematic review of publications to 20 June, 2016. Genetic biomarkers such as isocitrate dehydrogenase 1 (IDH1) mutations, low expression of excitatory amino acid transporter 2 (EAAT2), high xCT expression, overexpression of adenosine kinase (ADK) and low expression of very large G-protein-coupled receptor-1 (VLGR1) are primarily involved in synaptic transmission, whereas BRAF mutations, epidermal growth factor receptor (EGFR) amplification, miR-196b expression and low ki-67 expression are associated with regulation of cell proliferation...
December 2016: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/27814491/nbs1-converts-the-human-mre11-rad50-nuclease-complex-into-an-endo-exonuclease-machine-specific-for-protein-dna-adducts
#14
Rajashree A Deshpande, Ji-Hoon Lee, Sucheta Arora, Tanya T Paull
The human Mre11/Rad50/Nbs1 (hMRN) complex is critical for the sensing, processing, and signaling of DNA double-strand breaks. The nuclease activity of Mre11 is essential for mammalian development and cell viability, although the regulation and substrate specificity of Mre11 have been difficult to define. Here we show that hMRN catalyzes sequential endonucleolytic and exonucleolytic activities on both 5' and 3' strands of DNA ends containing protein adducts, and that Nbs1, ATP, and adducts are essential for this function...
November 3, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27814490/mre11-is-essential-for-the-removal-of-lethal-topoisomerase-2-covalent-cleavage-complexes
#15
Nguyen Ngoc Hoa, Tsubasa Shimizu, Zhong Wei Zhou, Zhao-Qi Wang, Rajashree A Deshpande, Tanya T Paull, Salma Akter, Masataka Tsuda, Ryohei Furuta, Ken Tsusui, Shunichi Takeda, Hiroyuki Sasanuma
The Mre11/Rad50/Nbs1 complex initiates double-strand break repair by homologous recombination (HR). Loss of Mre11 or its nuclease activity in mouse cells is known to cause genome aberrations and cellular senescence, although the molecular basis for this phenotype is not clear. To identify the origin of these defects, we characterized Mre11-deficient (MRE11(-/-)) and nuclease-deficient Mre11 (MRE11(-/H129N)) chicken DT40 and human lymphoblast cell lines. These cells exhibit increased spontaneous chromosomal DSBs and extreme sensitivity to topoisomerase 2 poisons...
November 3, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27808280/metal-coupled-folding-as-the-driving-force-for-the-extreme-stability-of-rad50-zinc-hook-dimer-assembly
#16
Tomasz Kochańczyk, Michał Nowakowski, Dominika Wojewska, Anna Kocyła, Andrzej Ejchart, Wiktor Koźmiński, Artur Krężel
The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn(2+)-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27798884/high-expression-of-mre11-rad50-nbs1-is-associated-with-poor-prognosis-and-chemoresistance-in-gastric-cancer
#17
Bolag Altan, Takehiko Yokobori, Munenori Ide, Tuya Bai, Toru Yanoma, Akiharu Kimura, Norimichi Kogure, Masaki Suzuki, Pinjie Bao, Erito Mochiki, Kyoichi Ogata, Tadashi Handa, Kyoichi Kaira, Masahiko Nishiyama, Takayuki Asao, Tetsunari Oyama, Hiroyuki Kuwano
BACKGROUND: The MRN complex of meiotic recombination 11 (MRE11), DNA repair protein Rad50 (RAD50) and Nijmegen breakage syndrome 1 (NBS1) proteins coordinate the detection and repair of DNA double-strand breaks (DSBs). DNA DSB repair-dependent chemoresistance likely has an effect on the treatment of human cancer. MATERIALS AND METHODS: We investigated the expression of MRN complex in human gastric cancer (GC) tissues using immunohistochemistry and analyzed its clinical significance and prognostic relevance...
2016: Anticancer Research
https://www.readbyqxmd.com/read/27798167/batf-modulates-the-th2-locus-control-region-and-regulates-cd4-t-cell-fate-during-antihelminth-immunity
#18
Katherine Bao, Tiffany Carr, Jianxuan Wu, William Barclay, Jingxiao Jin, Maria Ciofani, R Lee Reinhardt
The AP-1 factor basic leucine zipper transcription factor, ATF-like (BATF) is important for CD4(+) Th17, Th9, and follicular Th cell development. However, its precise role in Th2 differentiation and function remains unclear, and the requirement for BATF in nonallergic settings of type-2 immunity has not been explored. In this article, we show that, in response to parasitic helminths, Batf(-/-) mice are unable to generate follicular Th and Th2 cells. As a consequence, they fail to establish productive type-2 immunity during primary and secondary infection...
December 1, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27783279/frequency-of-pathogenic-germline-mutation-in-chek2-palb2-mre11-and-rad50-in-patients-at-high-risk-for-hereditary-breast-cancer
#19
Haeyoung Kim, Dae-Yeon Cho, Doo Ho Choi, Mijin Oh, Inkyung Shin, Won Park, Seung Jae Huh, Seok Jin Nam, Jeong Eon Lee, Seok Won Kim
PURPOSE: This study was performed to evaluate the frequency of mutations in CHEK2, PALB2, MRE11, and RAD50 among Korean patients at high risk for hereditary breast cancer. METHODS: A total of 235 Korean patients with hereditary breast cancer who tested negative for BRCA1/2 mutation were enrolled to this study. Entire coding regions of CHEK2, PALB2, MRE11, and RAD50 were analyzed using massively parallel sequencing (MPS). Sequence variants detected by MPS were confirmed by Sanger sequencing...
October 25, 2016: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/27782108/whole-exome-sequencing-of-finnish-hereditary-breast-cancer-families
#20
Kirsi Määttä, Tommi Rantapero, Anna Lindström, Matti Nykter, Minna Kankuri-Tammilehto, Satu-Leena Laasanen, Johanna Schleutker
A remarkable proportion of factors causing genetic predisposition to breast cancer (BC) are unknown in non-BRCA1/2 families. Exome sequencing was performed for 13 high-risk Finnish hereditary breast and/or ovarian cancer (HBOC) families to detect variants contributing to BC susceptibility. After filtering, 18 candidate variants in DNA damage response (DDR) pathway genes were screened in 129 female HBOC patients, up to 989 female controls, and 31 breast tumours by Sanger sequencing/TaqMan assays. In addition, two variants were further studied in 49 male BC patients and 909 male controls...
January 2016: European Journal of Human Genetics: EJHG
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