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"Genomic integration"

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https://www.readbyqxmd.com/read/29779017/-xpg-rs17655-g-c-polymorphism-associated-with-cancer-risk-evidence-from-60-studies
#1
Jie Zhao, Shanshan Chen, Haixia Zhou, Ting Zhang, Yang Liu, Jing He, Jinhong Zhu, Jichen Ruan
Xeroderma pigmentosum group G (XPG), a key component in nucleotide excision repair pathway, functions to cut DNA lesions during DNA repair. Genetic variations that alter DNA repair gene expression or function may decrease DNA repair ability and impair genome integrity, thereby predisposing to cancer. The association between XPG rs17655 G>C polymorphism and cancer risk has been investigated extensively, but the results remain contradictory. To get a more accurate conclusion, we performed a comprehensive meta-analysis of 60 case-control studies, involving 27,098 cancer cases and 30,535 healthy controls...
May 20, 2018: Aging
https://www.readbyqxmd.com/read/29777171/mll-fusion-driven-leukemia-requires-setd2-to-safeguard-genomic-integrity
#2
Anna Skucha, Jessica Ebner, Johannes Schmöllerl, Mareike Roth, Thomas Eder, Adrián César-Razquin, Alexey Stukalov, Sarah Vittori, Matthias Muhar, Bin Lu, Martin Aichinger, Julian Jude, André C Müller, Balázs Győrffy, Christopher R Vakoc, Peter Valent, Keiryn L Bennett, Johannes Zuber, Giulio Superti-Furga, Florian Grebien
MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL. While studies of selected MLL-fusions have revealed critical molecular pathways, unifying mechanisms across all MLL-fusions remain poorly understood. We present the first comprehensive survey of protein-protein interactions of seven distantly related MLL-fusion proteins. Functional investigation of 128 conserved MLL-fusion-interactors identifies a specific role for the lysine methyltransferase SETD2 in MLL-leukemia...
May 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29772801/ogt-o-glcnac-transferase-selectively-modifies-multiple-residues-unique-to-lamin-a
#3
Dan N Simon, Amanda Wriston, Qiong Fan, Jeffrey Shabanowitz, Alyssa Florwick, Tejas Dharmaraj, Sherket B Peterson, Yosef Gruenbaum, Cathrine R Carlson, Line M Grønning-Wang, Donald F Hunt, Katherine L Wilson
The LMNA gene encodes lamins A and C with key roles in nuclear structure, signaling, gene regulation, and genome integrity. Mutations in LMNA cause over 12 diseases ('laminopathies'). Lamins A and C are identical for their first 566 residues. However, they form separate filaments in vivo, with apparently distinct roles. We report that lamin A is β- O -linked N -acetylglucosamine- (O -GlcNAc)-modified in human hepatoma (Huh7) cells and in mouse liver. In vitro assays with purified O -GlcNAc transferase (OGT) enzyme showed robust O -GlcNAcylation of recombinant mature lamin A tails (residues 385⁻646), with no detectable modification of lamin B1, lamin C, or 'progerin' (Δ50) tails...
May 17, 2018: Cells
https://www.readbyqxmd.com/read/29762710/base-flipping-dynamics-from-an-intrahelical-to-an-extrahelical-state-exerted-by-thymine-dna-glycosylase-during-dna-repair-process
#4
Lin-Tai Da, Jin Yu
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive...
May 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29760432/microcephaly-short-stature-and-limb-abnormality-disorder-due-to-novel-autosomal-biallelic-donson-mutations-in-two-german-siblings
#5
Solveig Schulz, Martin A Mensah, Heike de Vries, Rosemarie Fröber, Bernd Romeike, Uwe Schneider, Stephan Borte, Detlev Schindler, Karim Kentouche
Recently, variants in DONSON have been reported to cause different disorders of the microcephalic primordial dwarfism spectrum. Using whole-exome sequencing, we identified two novel, compound heterozygous DONSON variants in a pair of siblings, one of whom was previously diagnosed with Fanconi anemia. This occurred because the present cases exhibited clinical findings in addition to those of the microcephalic primordial dwarfism disorder, including severe limb malformations. These findings suggest that the DONSON and Fanconi anemia proteins could have supplementary roles in developmental processes as they have in the maintenance of genomic integrity, resulting in related disease phenotypes...
May 14, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29754960/high-level-precise-knockin-of-ipscs-by-simultaneous-reprogramming-and-genome-editing-of-human-peripheral-blood-mononuclear-cells
#6
Wei Wen, Xinxin Cheng, Yawen Fu, Feiying Meng, Jian-Ping Zhang, Lu Zhang, Xiao-Lan Li, Zhixue Yang, Jing Xu, Feng Zhang, Gary D Botimer, Weiping Yuan, Changkai Sun, Tao Cheng, Xiao-Bing Zhang
We have developed an improved episomal vector system for efficient generation of integration-free induced pluripotent stem cells (iPSCs) from peripheral blood mononuclear cells. More recently, we reported that the use of an optimized CRISPR-Cas9 system together with a double-cut donor increases homology-directed repair-mediated precise gene knockin efficiency by 5- to 10-fold. Here, we report the integration of blood cell reprogramming and genome editing in a single step. We found that expression of Cas9 and KLF4 using a single vector significantly increases genome editing efficiency, and addition of SV40LT further enhances knockin efficiency...
May 4, 2018: Stem Cell Reports
https://www.readbyqxmd.com/read/29754818/dynamic-architecture-of-dna-repair-complexes-and-the-synaptonemal-complex-at-sites-of-meiotic-recombination
#7
Alexander Woglar, Anne M Villeneuve
Meiotic double-strand breaks (DSBs) are generated and repaired in a highly regulated manner to ensure formation of crossovers (COs) while also enabling efficient non-CO repair to restore genome integrity. We use structured-illumination microscopy to investigate the dynamic architecture of DSB repair complexes at meiotic recombination sites in relationship to the synaptonemal complex (SC). DSBs resected at both ends are converted into inter-homolog repair intermediates harboring two populations of BLM helicase and RPA, flanking a single population of MutSγ...
May 4, 2018: Cell
https://www.readbyqxmd.com/read/29754472/confirmation-of-drought-tolerance-of-ectopically-expressed-atabf3-gene-in-soybean
#8
Hye Jeong Kim, Hyun Suk Cho, Jung Hun Pak, Tackmin Kwon, Jai-Heon Lee, Doh-Hoon Kim, Dong Hee Lee, Chang-Gi Kim, Young-Soo Chung
Soybean transgenic plants with ectopically expressed AtABF3 were produced by Agrobacterium-mediated transformation and investigated the effects of AtABF3 expression on drought and salt tolerance. Stable Agrobacterium-mediated soybean transformation was carried based on the half-seed method (Paz et al. 2006). The integration of the transgene was confirmed from the genomic DNA of transformed soybean plants using PCR and the copy number of transgene was determined by Southern blotting using leaf samples from T2 seedlings...
May 10, 2018: Molecules and Cells
https://www.readbyqxmd.com/read/29748533/p53-attenuates-acetaminophen-induced-hepatotoxicity-by-regulating-drug-metabolizing-enzymes-and-transporter-expression
#9
Jiahong Sun, Yajie Wen, Yanying Zhou, Yiming Jiang, Yixin Chen, Huizheng Zhang, Lihuan Guan, Xinpeng Yao, Min Huang, Huichang Bi
Acetaminophen (APAP) overdose is the most frequent cause of drug-induced acute liver failure. Inhibition of APAP metabolic activation and promotion in APAP disposition are important to protect against APAP-induced liver injury. Tumor suppressor p53 is traditionally recognized as a surveillance molecule to preserve genome integrity. Recent studies have emerged on discovering its functions in metabolic regulation. Our previous study reported that p53 promoted bile acid disposition and alleviated cholestastic syndrome...
May 10, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29747023/assessment-of-dna-repair-susceptibility-genes-identified-by-whole-exome-sequencing-in-head-and-neck-cancer
#10
Raima Das, Sharbadeb Kundu, Shaheen Laskar, Yashmin Choudhury, Sankar Kumar Ghosh
Head and neck cancer (HNC), the sixth most common cancer globally, stands second in India. In Northeast (NE) India, it is the sixth most common cause of death in males and seventh in females. Prolonged tobacco and alcohol consumption constitute the major etiological factors for HNC development, which induce DNA damage. Therefore, DNA repair pathway is a crucial system in maintaining genomic integrity and preventing carcinogenesis. The present work was aimed to predict the consequence of significant germline variants of the DNA repair genes in disease predisposition...
April 26, 2018: DNA Repair
https://www.readbyqxmd.com/read/29744038/generating-and-repairing-genetically-programmed-dna-breaks-during-immunoglobulin-class-switch-recombination
#11
REVIEW
Laura Nicolas, Montserrat Cols, Jee Eun Choi, Jayanta Chaudhuri, Bao Vuong
Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR...
2018: F1000Research
https://www.readbyqxmd.com/read/29743367/a-screen-for-epstein-barr-virus-proteins-that-inhibit-the-dna-damage-response-reveals-a-novel-histone-binding-protein
#12
Ting-Hin Ho, Justine Sitz, Qingtang Shen, Ariane Leblanc-Lacroix, Eric I Campos, Ivan Borozan, Edyta Marcon, Jack Greenblatt, Amelie Fradet-Turcotte, Dong-Yan Jin, Lori Frappier
To replicate and persist in human cells, linear double-stranded (ds) DNA viruses, such as Epstein-Barr virus (EBV), must overcome the host DNA damage response (DDR) that is triggered by the viral genomes. Since this response is necessary to maintain cellular genome integrity, its inhibition by EBV is likely an important factor in the development of cancers associated with EBV infection, including gastric carcinoma. Here we present the first extensive screen of EBV proteins that inhibit dsDNA break signaling...
May 9, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29741662/physical-and-functional-interplay-between-pcna-dna-clamp-and-mre11-rad50-complex-from-the-archaeon-pyrococcus-furiosus
#13
Gaëlle Hogrel, Yang Lu, Sébastien Laurent, Etienne Henry, Clarisse Etienne, Duy Khanh Phung, Rémi Dulermo, Audrey Bossé, Pierre-François Pluchon, Béatrice Clouet-d'Orval, Didier Flament
Several archaeal species prevalent in extreme environments are particularly exposed to factors likely to cause DNA damages. These include hyperthermophilic archaea (HA), living at temperatures >70°C, which arguably have efficient strategies and robust genome guardians to repair DNA damage threatening their genome integrity. In contrast to Eukarya and other archaea, homologous recombination appears to be a vital pathway in HA, and the Mre11-Rad50 complex exerts a broad influence on the initiation of this DNA damage response process...
May 8, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29739872/chemical-compound-based-direct-reprogramming-for-future-clinical-applications
#14
REVIEW
Yukimasa Takeda, Yoshinori Harada, Toshikazu Yoshikawa, Ping Dai
Recent studies have revealed that a combination of chemical compounds enables direct reprogramming from one somatic cell type into another without the use of transgenes by regulating cellular signaling pathways and epigenetic modifications. The generation of induced pluripotent stem (iPS) cells generally requires virus vector-mediated expression of multiple transcription factors, which might disrupt genomic integrity and proper cell functions. The direct reprogramming is a promising alternative to rapidly prepare different cell types by bypassing the pluripotent state...
June 29, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29739311/transcriptome-analysis-reveals-new-micrornas-mediated-pathway-involved-in-anther-development-in-male-sterile-wheat
#15
Longqing Sun, Genlou Sun, Chenxia Shi, Dongfa Sun
BACKGROUND: 337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory function of MicroRNAs (miRNAs) in reproductive development has been increasingly studied, their roles in pre-meiotic and meiotic cells formation of plants have not been clearly explored. Here, we explored the roles of miRNAs in regulating male sterility of 337S at short day length/low temperature condition...
May 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29737433/report-of-a-bi-allelic-truncating-germline-mutation-in-tp53
#16
Natasha J Brown, Kanika Bhatia, Julie Teague, Susan M White, Patrick Lo, Jackie Challis, Victoria Beshay, Michael Sullivan, David Malkin, Jordan R Hansford
The TP53 gene is fundamental to genomic integrity, cell cycle regulation, and apoptosis; it is the most commonly mutated gene in human cancer. Heterozygous germline mutations cause the autosomal dominant cancer predisposition syndrome, Li-Fraumeni Syndrome. Homozygous germline TP53 mutations in humans are rare. We report an infant from a consanguineous family who presented with synchronous malignancies. Remarkably, he carries a homozygous germline TP53 mutation (NM_000546.4:c.52delA), predicted to cause protein truncation...
May 8, 2018: Familial Cancer
https://www.readbyqxmd.com/read/29735694/genomic-integration-of-err%C3%AE-hnf1%C3%AE-regulates-renal-bioenergetics-and-prevents-chronic-kidney-disease
#17
Juanjuan Zhao, Katherine Lupino, Benjamin J Wilkins, Chengxiang Qiu, Jian Liu, Yasuhiro Omura, Amanda L Allred, Caitlin McDonald, Katalin Susztak, Grant D Barish, Liming Pei
Mitochondrial dysfunction is increasingly recognized as a critical determinant of both hereditary and acquired kidney diseases. However, it remains poorly understood how mitochondrial metabolism is regulated to support normal kidney function and how its dysregulation contributes to kidney disease. Here, we show that the nuclear receptor estrogen-related receptor gamma (ERRγ) and hepatocyte nuclear factor 1 beta (HNF1β) link renal mitochondrial and reabsorptive functions through coordinated epigenomic programs...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29727725/dna-damage-and-tissue-repair-what-we-can-learn-from-planaria
#18
REVIEW
Paul G Barghouth, Manish Thiruvalluvan, Melanie LeGro, Néstor J Oviedo
Faithful renewal of aging and damaged tissues is central to organismal lifespan. Stem cells (SCs) generate the cellular progeny that replenish adult tissues across the body but this task becomes increasingly compromised over time. The age related decline in SC-mediated tissue maintenance is a multifactorial event that commonly affects genome integrity. The presence of DNA damage in SCs that are under continuous demand to divide poses a great risk for age-related disorders such as cancer. However, performing analysis of SCs with genomic instability and the DNA damage response during tissue renewal present significant challenges...
May 3, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29727616/the-bub3-bub1-complex-promotes-telomere-dna-replication
#19
Feng Li, Hyeung Kim, Zhejian Ji, Tianpeng Zhang, Bohong Chen, Yuanlong Ge, Yang Hu, Xuyang Feng, Xin Han, Huimin Xu, Youwei Zhang, Hongtao Yu, Dan Liu, Wenbin Ma, Zhou Songyang
Telomeres and telomere-binding proteins form complex secondary nucleoprotein structures that are critical for genome integrity but can present serious challenges during telomere DNA replication. It remains unclear how telomere replication stress is resolved during S phase. Here, we show that the BUB3-BUB1 complex, a component in spindle assembly checkpoint, binds to telomeres during S phase and promotes telomere DNA replication. Loss of the BUB3-BUB1 complex results in telomere replication defects, including fragile and shortened telomeres...
May 3, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29725014/clinical-and-genomic-landscape-of-gastric-cancer-with-a-mesenchymal-phenotype
#20
Sang Cheul Oh, Bo Hwa Sohn, Jae-Ho Cheong, Sang-Bae Kim, Jae Eun Lee, Ki Cheong Park, Sang Ho Lee, Jong-Lyul Park, Yun-Yong Park, Hyun-Sung Lee, Hee-Jin Jang, Eun Sung Park, Sang-Cheol Kim, Jeonghoon Heo, In-Sun Chu, You-Jin Jang, Young-Jae Mok, WonKyung Jung, Baek-Hui Kim, Aeree Kim, Jae Yong Cho, Jae Yun Lim, Yuki Hayashi, Shumei Song, Elena Elimova, Jeannelyn S Estralla, Jeffrey H Lee, Manoop S Bhutani, Yiling Lu, Wenbin Liu, Jeeyun Lee, Won Ki Kang, Sung Kim, Sung Hoon Noh, Gordon B Mills, Seon-Young Kim, Jaffer A Ajani, Ju-Seog Lee
Gastric cancer is a heterogeneous cancer, making treatment responses difficult to predict. Here we show that we identify two distinct molecular subtypes, mesenchymal phenotype (MP) and epithelial phenotype (EP), by analyzing genomic and proteomic data. Molecularly, MP subtype tumors show high genomic integrity characterized by low mutation rates and microsatellite stability, whereas EP subtype tumors show low genomic integrity. Clinically, the MP subtype is associated with markedly poor survival and resistance to standard chemotherapy, whereas the EP subtype is associated with better survival rates and sensitivity to chemotherapy...
May 3, 2018: Nature Communications
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