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Homologous recombination

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https://www.readbyqxmd.com/read/29912461/exploiting-crispr-cas9-technology-to-investigate-individual-histone-modifications
#1
Juan-José Vasquez, Carolin Wedel, Raul O Cosentino, T Nicolai Siegel
Despite their importance for most DNA-templated processes, the function of individual histone modifications has remained largely unknown because in vivo mutational analyses are lacking. The reason for this is that histone genes are encoded by multigene families and that tools to simultaneously edit multiple genomic loci with high efficiency are only now becoming available. To overcome these challenges, we have taken advantage of the power of CRISPR-Cas9 for precise genome editing and of the fact that most DNA repair in the protozoan parasite Trypanosoma brucei occurs via homologous recombination...
June 15, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29909066/characterization-of-a-plasmodium-falciparum-rrna-methyltransferase
#2
Kirti Gupta, Ankit Gupta, Saman Habib
The ribosomal RNA adenine dimethyltransferases (rAD) of KsgA/Dim1 family are universally conserved with eukaryotic rADs separated into distinct cytosolic Dim1 and organellar KsgA/TFB homologs. Among the two putative KsgA proteins encoded by the Plasmodium falciparum genome, we found that PfKsgA1 was dually localised in the cytoplasm and the mitochondrion. The protein interacted specifically with small ribosomal subunit as detected by ribosome pull-down using anti-PfKsgA1 antibodies. Recombinant PfKsgA1 exhibited methyltransferase activity which was further confirmed by complementation in an Escherichia coli KsgA knockout strain...
June 14, 2018: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29908711/gene-editing-on-center-stage
#3
REVIEW
Rasmus O Bak, Natalia Gomez-Ospina, Matthew H Porteus
Smithies et al. (1985) and Jasin and colleagues (1994) provided proof of concept that homologous recombination (HR) could be applied to the treatment of human disease and that its efficiency could be improved by the induction of double-strand breaks (DSBs). A key advance was the discovery of engineered nucleases, such as zinc-finger nucleases (ZFNs) and transcription activator-like (TAL) effector nucleases (TALENs), that can generate site-specific DSBs. The democratization and widespread use of genome editing was enabled by the discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 nuclease system...
June 13, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29907308/advanced-editing-of-the-nuclear-and-plastid-genomes-in-plants
#4
Agnieszka A Piatek, Scott C Lenaghan, C Neal Stewart
Genome editing is a powerful suite of technologies utilized in basic and applied plant research. Both nuclear and plastid genomes have been genetically engineered to alter traits in plants. While the most frequent molecular outcome of gene editing has been knockouts resulting in a simple deletion of an endogenous protein of interest from the host's proteome, new genes have been added to plant genomes and, in several instances, the sequence of endogenous genes have been targeted for a few coding changes. Targeted plant characteristics for genome editing range from single gene targets for agronomic input traits to metabolic pathways to endow novel plant function...
August 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29906450/inactivation-of-cdk12-delineates-a-distinct-immunogenic-class-of-advanced-prostate-cancer
#5
Yi-Mi Wu, Marcin Cieślik, Robert J Lonigro, Pankaj Vats, Melissa A Reimers, Xuhong Cao, Yu Ning, Lisha Wang, Lakshmi P Kunju, Navonil de Sarkar, Elisabeth I Heath, Jonathan Chou, Felix Y Feng, Peter S Nelson, Johann S de Bono, Weiping Zou, Bruce Montgomery, Ajjai Alva, Dan R Robinson, Arul M Chinnaiyan
Using integrative genomic analysis of 360 metastatic castration-resistant prostate cancer (mCRPC) samples, we identified a novel subtype of prostate cancer typified by biallelic loss of CDK12 that is mutually exclusive with tumors driven by DNA repair deficiency, ETS fusions, and SPOP mutations. CDK12 loss is enriched in mCRPC relative to clinically localized disease and characterized by focal tandem duplications (FTDs) that lead to increased gene fusions and marked differential gene expression. FTDs associated with CDK12 loss result in highly recurrent gains at loci of genes involved in the cell cycle and DNA replication...
June 14, 2018: Cell
https://www.readbyqxmd.com/read/29905759/biomarker-assessment-of-the-cbcsg006-trial-a-randomized-phase-iii-trial-of-cisplatin-plus-gemcitabine-compared-with-paclitaxel-plus-gemcitabine-as-first-line-therapy-for-patients-with-metastatic-triple-negative-breast-cancer
#6
J Zhang, Y Lin, X J Sun, B Y Wang, Z H Wang, J F Luo, L P Wang, S Zhang, J Cao, Z H Tao, J Wu, Z M Shao, W T Yang, X C Hu
Background: CBCSG006 trial reported the superior efficacy of cisplatin plus gemcitabine (GP) regimen than paclitaxel plus gemcitabine (GT) regimen as first-line treatment of metastatic triple-negative breast cancer (mTNBC). This study focused on the updated survival data and the explorations of potential biomarkers for efficacy. Patients and methods: Germ-line mutations of homologous recombination (HR) panel, BRCA1/2 included, were evaluated in 55.9% (132/236) patients...
June 14, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29905492/lrhmgb1-shares-structural-similarities-with-human-hmgb1-and-its-expression-is-induced-in-bacterial-infection-antiviral-vaccination-and-pathogen-associated-molecular-patterns-stimulation
#7
Saswati S Lenka, Mahismita Paichha, Madhubanti Basu, Mrinal Samanta
The high-mobility group box 1 (HMGB1) protein is a highly conserved nonhistone chromosomal protein ubiquitously present in almost all cell types. In the nucleus, it facilitates DNA repair and replication, V(D)J recombination, stabilization of nucleosome, and in the cytoplasm, it regulates autophagy and apoptosis. In addition to these intracellular functions, HMGB1 also facilitates activation of innate immune responses and plays key roles in host defense. To investigate its role in fish, we cloned and characterized HMGB1 in Labeo rohita (LrHMGB1), the most important freshwater fish species in the Indian subcontinent...
June 15, 2018: DNA and Cell Biology
https://www.readbyqxmd.com/read/29903880/real-time-genomic-characterization-of-advanced-pancreatic-cancer-to-enable-precision-medicine
#8
Andrew J Aguirre, Jonathan A Nowak, Nicholas D Camarda, Richard A Moffitt, Arezou A Ghazani, Mehlika Hazar-Rethinam, Srivatsan Raghavan, Jaegil Kim, Lauren K Brais, Dorisanne Ragon, Marisa W Welch, Emma Reilly, Devin McCabe, Lori Marini, Kristin Anderka, Karla Helvie, Nelly Oliver, Ana Babic, Annacarolina Da Silva, Brandon Nadres, Emily E Van Seventer, Heather A Shahzade, Joseph P St Pierre, Kelly P Burke, Thomas E Clancy, James M Cleary, Leona A Doyle, Kunal Jajoo, Nadine J McCleary, Jeffrey A Meyerhardt, Janet E Murphy, Kimmie Ng, Anuj K Patel, Kimberly Perez, Michael H Rosenthal, Douglas A Rubinson, Marvin Ryou, Geoffrey I Shapiro, Ewa Sicinska, Stuart G Silverman, Rebecca J Nagy, Richard B Lanman, Deborah Knoerzer, Dean J Welsch, Matthew B Yurgelun, Charles S Fuchs, Levi A Garraway, Gad Getz, Jason L Hornick, Bruce E Johnson, Matthew H Kulke, Robert J Mayer, Jeffrey W Miller, Paul B Shyn, David A Tuveson, Nikhil Wagle, Jen Jen Yeh, William C Hahn, Ryan B Corcoran, Scott L Carter, Brian M Wolpin
Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole exome sequencing and RNA-sequencing for patients with advanced PDAC. Therapeutically relevant genomic alterations were identified in 48% (34/71) and pathogenic/likely pathogenic germline alterations in 18% (13/71) of patients. Overall, 30% (21/71) of enrolled patients experienced a change in clinical management as a result of genomic data...
June 14, 2018: Cancer Discovery
https://www.readbyqxmd.com/read/29902865/co-targeting-poly-adp-ribose-polymerase-parp-and-histone-deacetylase-hdac-in-triple-negative-breast-cancer-higher-synergism-in-brca-mutated-cells
#9
Hélène Marijon, Dhong Hyun Lee, LingWen Ding, Haibo Sun, Sigal Gery, Aimery de Gramont, H Phillip Koeffler
PURPOSE: Despite similarities with BRCA-mutated breast cancers, triple-negative breast cancers (TNBC) remain resistant to poly(ADP-ribose) polymerase (PARP) inhibitors as single agents. Histone deacetylase inhibitors (HDACi) can decrease expression of proteins involved in DNA repair. We thus hypothesized that a HDACi (suberoylanilide hydroxamic acid (SAHA) or belinostat) could sensitize TNBC to the PARP inhibitor olaparib. METHODS: Human TNBC cells were co-treated with olaparib and either SAHA or belinostat, and their effects on survival, proliferation, cell cycle, apoptosis and DNA repair pathways were evaluated...
March 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29901759/recbcd-coordinates-repair-of-two-ends-at-a-dna-double-strand-break-preventing-aberrant-chromosome-amplification
#10
Martin A White, Benura Azeroglu, Manuel A Lopez-Vernaza, A M Mahedi Hasan, David R F Leach
DNA double-strand break (DSB) repair is critical for cell survival. A diverse range of organisms from bacteria to humans rely on homologous recombination for accurate DSB repair. This requires both coordinate action of the two ends of a DSB and stringent control of the resultant DNA replication to prevent unwarranted DNA amplification and aneuploidy. In Escherichia coli, RecBCD enzyme is responsible for the initial steps of homologous recombination. Previous work has revealed recD mutants to be nuclease defective but recombination proficient...
June 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29901196/telomerase-reverse-transcriptase-induced-thyroid-carcinoma-cell-proliferation-through-pten-akt-signaling-pathway
#11
Hao Zhang, Ning Hu
Thyroid carcinoma is the most common endocrine malignant tumor in the world, and so, there is a requirement to develop novel molecular targets for thyroid cancer diagnosis and treatment. Telomerase reverse transcriptase (TERT) was revealed to promote cell proliferation in a number of types of cell. To evaluate whether and how TERT functioned on papillary thyroid cancer (PTC) cell proliferation, the present study constructed TERT over‑expression [recombined (r)TERT plasmid group] and interference [small interfering RNA (si)‑TERT group] models by liposome transfection respectively to study the molecular mechanisms...
June 1, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29901146/genistein-and-ag1024-synergistically-increase-the-radiosensitivity-of-prostate-cancer-cells
#12
Qisheng Tang, Jianjun Ma, Jinbo Sun, Longfei Yang, Fan Yang, Wei Zhang, Ruixiao Li, Lei Wang, Yong Wang, He Wang
Radiosensitivity of prostate cancer (PCa) cells promotes the curative treatment for PCa. The present study was designed to investigate the synergistic effect of genistein and AG1024 on the radiosensitivity of PCa cells. The optimal X‑irradiation dose (4 Gy) and genistein concentration (30 µM) were selected by using the CCK‑8 assay. Before X‑irradiation (4 Gy), PC3 and DU145 cells were treated with genistein (30 µM), AG1024 (10 µM) and their combination. All treatments significantly reduced cell proliferation and enhanced cell apoptosis...
May 30, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29899825/vx-984-is-a-selective-inhibitor-of-non-homologous-end-joining-with-possible-preferential-activity-in-transformed-cells
#13
Atif J Khan, Sarah M Misenko, Aditya Thandoni, Devora Schiff, Sachin R Jhawar, Samuel F Bunting, Bruce G Haffty
Purpose: DNA double-strand breaks (DSBs) can be repaired by non-homologous end joining (NHEJ) or homologous recombination (HR). We demonstrate the selectivity of VX-984, a DNA-PK inhibitor, using assays not previously reported. Experimental Design: The class switch recombination assay (CSR) in primary B cells was used to measure efficiency of NHEJ. A cellular reporter assay (U2OS EJ-DR) was used to assess the efficiency of HR and NHEJ in cells treated with VX-984...
May 25, 2018: Oncotarget
https://www.readbyqxmd.com/read/29899143/separable-roles-for-mec1-atr-in-genome-maintenance-dna-replication-and-checkpoint-signaling
#14
Michael Charles Lanz, Susannah Oberly, Ethan James Sanford, Sushma Sharma, Andrei Chabes, Marcus Bustamante Smolka
The Mec1/ATR kinase coordinates multiple cellular responses to replication stress. In addition to its canonical role in activating the checkpoint kinase Rad53, Mec1 also plays checkpoint-independent roles in genome maintenance that are not well understood. Here we used a combined genetic-phosphoproteomic approach to manipulate Mec1 activation and globally monitor Mec1 signaling, allowing us to delineate distinct checkpoint-independent modes of Mec1 action. Using cells in which endogenous Mec1 activators were genetically ablated, we found that expression of "free" Mec1 activation domains (MADs) can robustly activate Mec1 and rescue the severe DNA replication and growth defects of these cells back to wild-type levels...
June 13, 2018: Genes & Development
https://www.readbyqxmd.com/read/29899105/efficient-genome-engineering-of-a-virulent-klebsiella-bacteriophage-using-crispr-cas9
#15
Juntao Shen, Jinjie Zhou, Guo-Qiang Chen, Zhi-Long Xiu
Klebsiella pneumoniae is one of the most common nosocomial opportunistic pathogens usually with multiple drug-resistance. Phage therapy, a potential new therapeutics to replace or supplement antibiotics, has attracted much attention. However, very few Klebsiella phages have been well-characterized as the lack of efficient genome editing tools. Here, Cas9 from Streptococcus pyogenes and a single guide RNA (sgRNA) were used to modify a virulent Klebsiella bacteriophage phiKpS2. We firstly evaluated the distribution of sgRNA activity in phages and proved that it's largely inconsistent with the predicted activity from current models trained on eukaryotic cell datasets...
June 13, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29898980/two-distinct-approaches-for-crispr-cas9-mediated-gene-editing-in-cryptococcus-neoformans-and-related-species
#16
Ping Wang
Cryptococcus neoformans and related species are encapsulated basidiomycetous fungi that cause meningoencephalitis in individuals with immune deficiency. This pathogen has a tractable genetic system; however, gene disruption via electroporation remains difficult, while biolistic transformation is often limited by lack of multiple genetic markers and the high initial cost of equipment. The approach using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has become the technology of choice for gene editing in many organisms due to its simplicity, efficiency, and versatility...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29898918/mutations-that-prevent-methylation-of-cohesin-render-sensitivity-to-dna-damage
#17
Swastika Sanyal, Lucia Molnarova, Judita Richterova, Barbora Huraiova, Zsigmond Benko, Silvia Polakova, Ingrid Cipakova, Andrea Sevcovicova, Katarina Gaplovska-Kysela, Karl Mechtler, Lubos Cipak, Juraj Gregan
The canonical role of cohesin is to mediate sister chromatid cohesion. In addition, cohesin plays important roles in processes such as DNA repair and regulation of gene expression. Mounting evidence suggests that various post-translational modifications including phosphorylation, acetylation and SUMOylation regulate cohesin functions. Our mass-spectrometry analysis of cohesin purified from Schizosaccharomyces pombe cells revealed that the cohesin subunit Psm1 is methylated on two evolutionarily conserved lysine residues K536 and K1200...
June 13, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29898385/simultaneous-targeting-of-parp1-and-rad52-triggers-dual-synthetic-lethality-in-brca-deficient-tumor-cells
#18
Katherine Sullivan-Reed, Elisabeth Bolton-Gillespie, Yashodhara Dasgupta, Samantha Langer, Micheal Siciliano, Margaret Nieborowska-Skorska, Kritika Hanamshet, Elizaveta A Belyaeva, Andrea J Bernhardy, Jaewong Lee, Morgan Moore, Huaqing Zhao, Peter Valent, Ksenia Matlawska-Wasowska, Markus Müschen, Smita Bhatia, Ravi Bhatia, Neil Johnson, Mariusz A Wasik, Alexander V Mazin, Tomasz Skorski
PARP inhibitors (PARPis) have been used to induce synthetic lethality in BRCA-deficient tumors in clinical trials with limited success. We hypothesized that RAD52-mediated DNA repair remains active in PARPi-treated BRCA-deficient tumor cells and that targeting RAD52 should enhance the synthetic lethal effect of PARPi. We show that RAD52 inhibitors (RAD52is) attenuated single-strand annealing (SSA) and residual homologous recombination (HR) in BRCA-deficient cells. Simultaneous targeting of PARP1 and RAD52 with inhibitors or dominant-negative mutants caused synergistic accumulation of DSBs and eradication of BRCA-deficient but not BRCA-proficient tumor cells...
June 12, 2018: Cell Reports
https://www.readbyqxmd.com/read/29897968/evolution-via-recombination-cell-to-cell-contact-facilitates-larger-recombination-events-in-streptococcus-pneumoniae
#19
Lauren A Cowley, Fernanda C Petersen, Roger Junges, Med Jimson D Jimenez, Donald A Morrison, William P Hanage
Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae is thought to be important in the adaptation and evolution of this pathogen. While competent pneumococci are able to scavenge DNA added to laboratory cultures, large-scale transfers of multiple kb are rare under these conditions. We used whole genome sequencing (WGS) to map transfers in recombinants arising from contact of competent cells with non-competent 'target' cells, using strains with known genomes, distinguished by a total of ~16,000 SNPs...
June 13, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29897905/identifying-functional-groups-among-the-diverse-recombining-antigenic-var-genes-of-the-malaria-parasite-plasmodium-falciparum-from-a-local-community-in-ghana
#20
Mary M Rorick, Edward B Baskerville, Thomas S Rask, Karen P Day, Mercedes Pascual
A challenge in studying diverse multi-copy gene families is deciphering distinct functional types within immense sequence variation. Functional changes can in some cases be tracked through the evolutionary history of a gene family; however phylogenetic approaches are not possible in cases where gene families diversify primarily by recombination. We take a network theoretical approach to functionally classify the highly recombining var antigenic gene family of the malaria parasite Plasmodium falciparum. We sample var DBLα sequence types from a local population in Ghana, and classify 9,276 of these variants into just 48 functional types...
June 13, 2018: PLoS Computational Biology
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