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homologous dependent recombination

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https://www.readbyqxmd.com/read/29042561/aunip-c1orf135-directs-dna-double-strand-breaks-towards-the-homologous-recombination-repair-pathway
#1
Jiangman Lou, Hongxia Chen, Jinhua Han, Hanqing He, Michael S Y Huen, Xin-Hua Feng, Ting Liu, Jun Huang
DNA double-strand breaks (DSBs) are mainly repaired by either homologous recombination (HR) or non-homologous end-joining (NHEJ). Here, we identify AUNIP/C1orf135, a largely uncharacterized protein, as a key determinant of DSB repair pathway choice. AUNIP physically interacts with CtIP and is required for efficient CtIP accumulation at DSBs. AUNIP possesses intrinsic DNA-binding ability with a strong preference for DNA substrates that mimic structures generated at stalled replication forks. This ability to bind DNA is necessary for the recruitment of AUNIP and its binding partner CtIP to DSBs, which in turn drives CtIP-dependent DNA-end resection and HR repair...
October 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29036698/chromosomal-context-affects-the-molecular-evolution-of-sex-linked-genes-and-their-autosomal-counterparts-in-turtles-and-other-vertebrates
#2
Srihari Radhakrishnan, Nicole Valenzuela
Sex chromosomes evolve differently from autosomes because natural selection acts distinctly on them given their reduced recombination and smaller population size. Various studies of sex-linked genes compared to different autosomal genes within species support these predictions. Instead, here we take a novel alternative approach comparing the rate of evolution between subsets of genes that are sex-linked in selected reptiles/vertebrates and the same genes located in autosomes in other amniotes. We report for the first time the faster evolution of Z-linked genes in a turtle (the Chinese soft-shell turtle Pelodiscus sinensis) relative to autosomal orthologs in other taxa, including turtles with temperature-dependent sex determination (TSD)...
September 27, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036662/parp2-controls-double-strand-break-repair-pathway-choice-by-limiting-53bp1-accumulation-at-dna-damage-sites-and-promoting-end-resection
#3
Alexis Fouquin, Josée Guirouilh-Barbat, Bernard Lopez, Janet Hall, Mounira Amor-Guéret, Vincent Pennaneach
Double strand breaks (DSBs) are one of the most toxic lesions to cells. DSB repair by the canonical non-homologous end-joining (C-EJ) pathway involves minor, if any, processing of the broken DNA-ends, whereas the initiation of DNA resection channels the broken-ends toward DNA repair pathways using various lengths of homology. Mechanisms that control the resection initiation are thus central to the regulation to the choice of DSB repair pathway. Therefore, understanding the mechanisms which regulate the initiation of DNA end-resection is of prime importance...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29022135/pcal_1311-an-alcohol-dehydrogenase-homologue-from-pyrobaculum-calidifontis-displays-nadh-dependent-high-aldehyde-reductase-activity
#4
Raza Ashraf, Naeem Rashid, Tamotsu Kanai, Tadayuki Imanaka, Muhammad Akhtar
Genome sequence of Pyrobaculum calidifontis, a hyperthermophilic archaeon, harbors three open-reading frames annotated as alcohol dehydrogenases. One of them, Pcal_1311, does not display a significantly high homology with any of the characterized alcohol dehydrogenases. Highest homology of 38% was found with the characterized counterpart from Geobacillus stearothermophilus. To examine the biochemical properties of Pcal_1311, we have cloned and functionally expressed the gene in Escherichia coli. Purified recombinant Pcal_1311 catalyzed the NAD(H)-dependent oxidation of various alcohols and reduction of aldehydes, with a marked preference for substrates with functional group at the terminal carbon...
October 11, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29021238/asy2-mer2-an-evolutionarily-conserved-mediator-of-meiotic-recombination-pairing-and-global-chromosome-compaction
#5
Sophie Tessé, Henri-Marc Bourbon, Robert Debuchy, Karine Budin, Emeline Dubois, Zhang Liangran, Romain Antoine, Tristan Piolot, Nancy Kleckner, Denise Zickler, Eric Espagne
Meiosis is the cellular program by which a diploid cell gives rise to haploid gametes for sexual reproduction. Meiotic progression depends on tight physical and functional coupling of recombination steps at the DNA level with specific organizational features of meiotic-prophase chromosomes. The present study reveals that every step of this coupling is mediated by a single molecule: Asy2/Mer2. We show that Mer2, identified so far only in budding and fission yeasts, is in fact evolutionarily conserved from fungi (Mer2/Rec15/Asy2/Bad42) to plants (PRD3/PAIR1) and mammals (IHO1)...
October 11, 2017: Genes & Development
https://www.readbyqxmd.com/read/29018417/molecular-mechanisms-that-contribute-to-horizontal-transfer-of-plasmids-by-the-bacteriophage-spp1
#6
Ana Valero-Rello, María López-Sanz, Alvaro Quevedo-Olmos, Alexei Sorokin, Silvia Ayora
Natural transformation and viral-mediated transduction are the main avenues of horizontal gene transfer in Firmicutes. Bacillus subtilis SPP1 is a generalized transducing bacteriophage. Using this lytic phage as a model, we have analyzed how viral replication and recombination systems contribute to the transfer of plasmid-borne antibiotic resistances. Phage SPP1 DNA replication relies on essential phage-encoded replisome organizer (G38P), helicase loader (G39P), hexameric replicative helicase (G40P), recombinase (G35P) and in less extent on the partially dispensable 5'→3' exonuclease (G34...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29018197/the-chromosomal-organization-of-horizontal-gene-transfer-in-bacteria
#7
Pedro H Oliveira, Marie Touchon, Jean Cury, Eduardo P C Rocha
Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome organization. We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species. This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements...
October 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28986875/gene-targeted-mice-with-conditional-knock-in-out-of-nmdar-mutations
#8
Rolf Sprengel, Ahmed Eltokhi, Frank N Single
For the genetic alterations of NMDA receptor (NMDAR) properties like Ca(2+)-permeability or voltage-dependent gating in mice and for the experimental analysis of nonsense or missense mutations that were identified in human patients, single nucleotide mutations have to be introduced into the germ line of mice (Burnashev and Szepetowski, Curr Opin Pharmacol 20:73-82, 2015; Endele et al., Nat Genet 42:1021-1026, 2010). This can be done with very high precision by the well-established method of gene replacement, which makes use of homologous recombination in pluripotent embryonic stem (ES) cells of mice...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28979292/drosophila-model-for-the-analysis-of-genesis-of-lim-kinase-1-dependent-williams-beuren-syndrome-cognitive-phenotypes-indels-transposable-elements-of-the-tc1-mariner-superfamily-and-micrornas
#9
Elena V Savvateeva-Popova, Aleksandr V Zhuravlev, Václav Brázda, Gennady A Zakharov, Alena N Kaminskaya, Anna V Medvedeva, Ekaterina A Nikitina, Elena V Tokmatcheva, Julia F Dolgaya, Dina A Kulikova, Olga G Zatsepina, Sergei Y Funikov, Sergei S Ryazansky, Michail B Evgen'ev
Genomic disorders, the syndromes with multiple manifestations, may occur sporadically due to unequal recombination in chromosomal regions with specific architecture. Therefore, each patient may carry an individual structural variant of DNA sequence (SV) with small insertions and deletions (INDELs) sometimes less than 10 bp. The transposable elements of the Tc1/mariner superfamily are often associated with hotspots for homologous recombination involved in human genetic disorders, such as Williams Beuren Syndromes (WBS) with LIM-kinase 1-dependent cognitive defects...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28977643/regulation-of-mitotic-recombination-between-dna-repeats-in-centromeres
#10
Faria Zafar, Akiko K Okita, Atsushi T Onaka, Jie Su, Yasuhiro Katahira, Jun-Ichi Nakayama, Tatsuro S Takahashi, Hisao Masukata, Takuro Nakagawa
Centromeres that are essential for faithful segregation of chromosomes consist of unique DNA repeats in many eukaryotes. Although recombination is under-represented around centromeres during meiosis, little is known about recombination between centromere repeats in mitotic cells. Here, we compared spontaneous recombination that occurs between ade6B/ade6X inverted repeats integrated at centromere 1 (cen1) or at a non-centromeric ura4 locus in fission yeast. Remarkably, distinct mechanisms of homologous recombination (HR) were observed in centromere and non-centromere regions...
August 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28973861/ctcf-prevents-genomic-instability-by-promoting-homologous-recombination-directed-dna-double-strand-break-repair
#11
Fengchao Lang, Xin Li, Wenhai Zheng, Zhuoran Li, Danfeng Lu, Guijun Chen, Daohua Gong, Liping Yang, Jinlin Fu, Peng Shi, Jumin Zhou
CTCF is an essential epigenetic regulator mediating chromatin insulation, long-range regulatory interactions, and the organization of large topological domains in the nucleus. Phenotypes of CTCF haploinsufficient mutations in humans, knockout in mice, and depletion in cells are often consistent with impaired genome stability, but a role of CTCF in genome maintenance has not been fully investigated. Here, we report that CTCF maintains genome stability, is recruited to sites of DNA damage, and promotes homologous recombination repair of DNA double-strand breaks (DSBs)...
September 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28972172/a-lower-isoelectric-point-increases-signal-sequence-mediated-secretion-of-recombinant-proteins-through-a-bacterial-abc-transporter
#12
Hyunjong Byun, Jiyeon Park, Sun Chang Kim, Jung Hoon Ahn
Efficient protein production for industrial and academic purposes often involves engineering microorganisms to produce and secrete target proteins into the culture. Pseudomonas fluorescens has a TliDEF ATP-binding cassette transporter, a type I secretion system, which recognizes C-terminal LARD3 signal sequence of thermostable lipase TliA. Many proteins are secreted by TliDEF in vivo when recombined with LARD3, but there are still others that cannot be secreted by TliDEF even when LARD3 is attached. However, the factors that determine whether or not a recombinant protein can be secreted through TliDEF are still unknown...
September 29, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28969871/alternative-lengthening-of-telomeres-dna-repair-pathways-converge
#13
REVIEW
Alexander P Sobinoff, Hilda A Pickett
Telomeres shorten during each cellular division, with cumulative attrition resulting in telomeric damage and replicative senescence. Bypass of replicative senescence precipitates catastrophic telomere shortening or crisis, and is characterized by widespread genomic instability. Activation of a telomere maintenance mechanism (TMM) is necessary to stabilise the genome and establish cellular immortality through the reconstitution of telomere capping function. The alternative lengthening of telomeres (ALT) pathway is a TMM frequently activated in tumors of mesenchymal or neuroepithelial origin...
September 29, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28967905/akt-overactivation-can-suppress-dna-repair-via-p70s6-kinase-dependent-downregulation-of-mre11
#14
D Piscitello, D Varshney, S Lilla, M G Vizioli, C Reid, V Gorbunova, A Seluanov, D A Gillespie, P D Adams
Deregulated AKT kinase activity due to PTEN deficiency in cancer cells contributes to oncogenesis by incompletely understood mechanisms. Here, we show that PTEN deletion in HCT116 and DLD1 colon carcinoma cells leads to suppression of CHK1 and CHK2 activation in response to irradiation, impaired G2 checkpoint proficiency and radiosensitization. These defects are associated with reduced expression of MRE11, RAD50 and NBS1, components of the apical MRE11/RAD50/NBS1 (MRN) DNA damage response complex. Consistent with reduced MRN complex function, PTEN-deficient cells fail to resect DNA double-strand breaks efficiently after irradiation and show greatly diminished proficiency for DNA repair via the error-free homologous recombination (HR) repair pathway...
October 2, 2017: Oncogene
https://www.readbyqxmd.com/read/28964767/the-angiotensin-converting-enzyme-ace-inhibitor-captopril-disrupts-the-motility-activation-of-sperm-from-the-silkworm-bombyx-mori
#15
Sumiharu Nagaoka, Saori Kawasaki, Hideki Kawasaki, Kaeko Kamei
Angiotensin I-converting enzyme (also known as peptidyl dicarboxypeptidase A, ACE, and EC 3.4.15.1), which is found in a wide range of organisms, cleaves C-terminal dipeptides from relatively short oligopeptides. Mammalian ACE plays an important role in the regulation of blood pressure. However, the precise physiological functions of insect ACE homologs have not been understood. As part of our effort to elucidate new physiological roles of insect ACE, we herein report a soluble ACE protein in male reproductive secretions from the silkmoth, Bombyx mori...
September 28, 2017: Journal of Insect Physiology
https://www.readbyqxmd.com/read/28961460/bacillus-subtilis-disa-helps-to-circumvent-replicative-stress-during-spore-revival
#16
Marina Raguse, Rubén Torres, Elena M Seco, Carolina Gándara, Silvia Ayora, Ralf Moeller, Juan C Alonso
The mechanisms that allow to circumvent replicative stress, and to resume DNA synthesis are poorly understood in Bacillus subtilis. To study the role of the diadenylate cyclase DisA and branch migration translocase (BMT) RadA/Sms in restarting a stalled replication fork, we nicked and broke the circular chromosome of an inert mature haploid spore, damaged the bases, and measured survival of reviving spores. During undisturbed ripening, nicks and breaks should be repaired by pathways that do not invoke long-range end resection or genetic exchange by homologous recombination, after which DNA replication might be initiated...
September 22, 2017: DNA Repair
https://www.readbyqxmd.com/read/28959974/regulation-of-dna-repair-pathway-choice-in-s-and-g2-phases-by-the-nhej-inhibitor-cyren
#17
Nausica Arnoult, Adriana Correia, Jiao Ma, Anna Merlo, Sara Garcia-Gomez, Marija Maric, Marco Tognetti, Christopher W Benner, Simon J Boulton, Alan Saghatelian, Jan Karlseder
Classical non-homologous end joining (cNHEJ) and homologous recombination compete for the repair of double-stranded DNA breaks during the cell cycle. Homologous recombination is inhibited during the G1 phase of the cell cycle, but both pathways are active in the S and G2 phases. However, it is unclear why cNHEJ does not always outcompete homologous recombination during the S and G2 phases. Here we show that CYREN (cell cycle regulator of NHEJ) is a cell-cycle-specific inhibitor of cNHEJ. Suppression of CYREN allows cNHEJ to occur at telomeres and intrachromosomal breaks during the S and G2 phases, and cells lacking CYREN accumulate chromosomal aberrations upon damage induction, specifically outside the G1 phase...
September 20, 2017: Nature
https://www.readbyqxmd.com/read/28956018/evaluation-of-the-efficiency-and-utility-of-recombinant-enzyme-free-seamless-dna-cloning-methods
#18
Ken Motohashi
Simple and low-cost recombinant enzyme-free seamless DNA cloning methods have recently become available. In vivo Escherichia coli cloning (iVEC) can directly transform a mixture of insert and vector DNA fragments into E. coli, which are ligated by endogenous homologous recombination activity in the cells. Seamless ligation cloning extract (SLiCE) cloning uses the endogenous recombination activity of E. coli cellular extracts in vitro to ligate insert and vector DNA fragments. An evaluation of the efficiency and utility of these methods is important in deciding the adoption of a seamless cloning method as a useful tool...
March 2017: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/28954869/the-long-3-utr-mrna-of-camkii-is-essential-for-translation-dependent-plasticity-of-spontaneous-release-in-drosophila-melanogaster
#19
Elena A Kuklin, Stephen Alkins, Baskar Bakthavachalu, Maria C Genco, Indulekha Sudhakaran, K Vijay Raghavan, Mani Ramaswami, Leslie C Griffith
A null mutation of the Drosophila calcium/calmodulin-dependent protein kinase II gene (CaMKII) was generated using homologous recombination. Null animals survive to larval and pupal stages due to a large maternal contribution of CaMKII mRNA, which consists of a short 3'- u n t ranslated r egion (UTR) form lacking regulatory elements that guide local translation. The selective loss of the long 3'UTR mRNA in CaMKII null larvae allows us to test its role in plasticity. Development and evoked function of the larval neuromuscular junction are surprisingly normal, but the resting rate of miniature excitatory junctional potentials (mEJPs) is significantly lower in CaMKII mutants...
September 27, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28942922/age-dependent-alterations-in-meiotic-recombination-cause-chromosome-segregation-errors-in-spermatocytes
#20
Maciej J Zelazowski, Maria Sandoval, Lakshmi Paniker, Holly M Hamilton, Jiaying Han, Mikalah A Gribbell, Rhea Kang, Francesca Cole
Faithful chromosome segregation in meiosis requires crossover (CO) recombination, which is regulated to ensure at least one CO per homolog pair. We investigate the failure to ensure COs in juvenile male mice. By monitoring recombination genome-wide using cytological assays and at hotspots using molecular assays, we show that juvenile mouse spermatocytes have fewer COs relative to adults. Analysis of recombination in the absence of MLH3 provides evidence for greater utilization in juveniles of pathways involving structure-selective nucleases and alternative complexes, which can act upon precursors to generate noncrossovers (NCOs) at the expense of COs...
September 20, 2017: Cell
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