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Homologous recombination

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https://www.readbyqxmd.com/read/29220651/replication-fork-reversal-players-and-guardians
#1
REVIEW
Annabel Quinet, Delphine Lemaçon, Alessandro Vindigni
Replication fork reversal is a rapidly emerging and remarkably frequent mechanism of fork stabilization in response to genotoxic insults. Here, we summarize recent findings that uncover key molecular determinants for reversed fork formation and describe how the homologous recombination factors BRCA1, BRCA2, and RAD51 protect these structures from extended nucleolytic degradation.
December 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29220506/a-molecular-portrait-of-de-novo-genes-in-yeasts
#2
Nikolaos N Vakirlis, Alex S Hebert, Dana A Opulente, Guillaume Achaz, Chris Todd Hittinger, Gilles Fischer, Joshua J Coon, Ingrid Lafontaine
New genes, with novel protein functions, can evolve "from scratch" out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29218515/screening-and-scale-up-of-glut-transporter-constructs-suitable-for-biochemical-and-structural-studies
#3
Grégory Verdon, Hae Joo Kang, David Drew
Identifying membrane proteins that can be produced and isolated in homogenous form in detergent is a lengthy trial-and-error process that can be facilitated by fluorescence-based screening approaches. We describe (1) the strategy and protocol of cloning by homologous recombination, (2) whole-cell and in-gel fluorescence measurements to estimate GLUT-GFP fusion protein yields, (3) use of size-exclusion chromatography monitored by fluorescence (FSEC) for assessing the homogeneity of the GLUT-GFP fusion proteins, and (4) the protocol for large-scale production and purification of the Bos taurus GLUT5 construct that enabled its crystal structure determination...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29217771/rad52-is-required-for-rna-templated-recombination-repair-in-post-mitotic-neurons
#4
Starr Welty, Yaqun Teng, Zhuobin Liang, Weixing Zhao, Laurie Sanders, J Timothy Greenamyre, Maria Eulalia Rubio, Amantha Thathiah, Ravindra Kodali, Ronald Wetzel, Arthur S Levine, Li Lan
It has been long assumed that post-mitotic neurons only utilize the error-prone non-homologous end joining (NHEJ) pathway to repair double strand breaks (DSBs) associated with oxidative damage to DNA, given the inability of non-replicating neuronal DNA to utilize a sister chromatid template in the less error-prone homologous recombination (HR) repair pathway. However, we and others recently have found that active transcription triggers a replication-independent recombinational repair mechanism in the G0/G1 phase of the cell cycle...
December 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29216366/lncrna-lnc-ri-regulates-homologous-recombination-repair-of-dna-double-strand-breaks-by-stabilizing-rad51-mrna-as-a-competitive-endogenous-rna
#5
Liping Shen, Qi Wang, Ruixue Liu, Zhongmin Chen, Xueqing Zhang, Pingkun Zhou, Zhidong Wang
DNA double-strand break (DSB) repair is critical for the maintenance of genome stability. The current models of the mechanism of DSB repair are based on studies of DNA repair proteins. Long non-coding RNAs (lncRNAs) have recently emerged as new regulatory molecules, with diverse functions in biological processes. In the present study, we found that expression of the ionizing radiation-inducible lncRNA, lnc-RI, was correlate negatively with micronucleus frequencies in human peripheral blood lymphocytes. Knockdown of lnc-RI significantly increased spontaneous DSBs levels, which was confirmed to be associated with the decreased efficiency of homologous recombination (HR) repair of DSBs...
December 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29215009/the-end-joining-factor-ku-acts-in-the-end-resection-of-double-strand-break-free-arrested-replication-forks
#6
Ana Teixeira-Silva, Anissia Ait Saada, Julien Hardy, Ismail Iraqui, Marina Charlotte Nocente, Karine Fréon, Sarah A E Lambert
Replication requires homologous recombination (HR) to stabilize and restart terminally arrested forks. HR-mediated fork processing requires single stranded DNA (ssDNA) gaps and not necessarily double strand breaks. We used genetic and molecular assays to investigate fork-resection and restart at dysfunctional, unbroken forks in Schizosaccharomyces pombe. Here, we report that fork-resection is a two-step process regulated by the non-homologous end joining factor Ku. An initial resection mediated by MRN-Ctp1 removes Ku from terminally arrested forks, generating ~110 bp sized gaps obligatory for subsequent Exo1-mediated long-range resection and replication restart...
December 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/29214498/cloning-and-aggregation-characterization-of-rubber-elongation-factor-and-small-rubber-particle-protein-from-ficus-carica
#7
Saki Yokota, Yurina Suzuki, Keisuke Saitoh, Sakihito Kitajima, Norimasa Ohya, Takeshi Gotoh
Rubber elongation factor (REF) and small rubber particle protein (SRPP) are major latex proteins harvested from Hevea brasiliensis (the rubber tree; HbREF and HbSRPP, respectively). Their amino acid sequences exhibit high homology with each other. In the present study, we cloned two cDNAs encoding REF/SRPP-family proteins (FcREF/SRPP-1 and -2) from the laticifers of Ficus carica (fig tree). The amino acid sequences of these proteins showed high homology not only with each other but also with HbREF and HbSRPP...
December 6, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/29214031/parp-inhibitors-as-potential-therapeutic-agents-for-various-cancers-focus-on-niraparib-and-its-first-global-approval-for-maintenance-therapy-of-gynecologic-cancers
#8
REVIEW
Mekonnen Sisay, Dumessa Edessa
Poly (ADP-ribose) polymerases (PARPs) are an important family of nucleoproteins highly implicated in DNA damage repair. Among the PARP families, the most studied are PARP1, PARP2 and PARP 3. PARP1 is found to be the most abundant nuclear enzyme under the PARP series. These enzymes are primarily involved in base excision repair as one of the major single strand break (SSB) repair mechanisms. Being double stranded, DNA engages itself in reparation of a sub-lethal SSB with the aid of PARP. Moreover, by having a sister chromatid, DNA can also repair double strand breaks with either error-free homologous recombination or error-prone non-homologous end-joining...
2017: Gynecologic Oncology Research and Practice
https://www.readbyqxmd.com/read/29212152/prpf8-is-important-for-brca1-mediated-homologous-recombination
#9
David O Onyango, Gabriella Lee, Jeremy M Stark
Disruption of RNA splicing causes genome instability, which could contribute to cancer etiology. Furthermore, RNA splicing is an emerging anti-cancer target. Thus, we have evaluated the influence of the spliceosome factor PRPF8 and the splicing inhibitor Pladienolide B (PlaB) on homologous recombination (HR). We find that PRPF8 depletion and PlaB treatment cause a specific defect in homology-directed repair (HDR), and single strand annealing (SSA), which share end resection as a common intermediate, and BRCA1 as a required factor...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29212043/inhibition-of-mitochondrial-ucp1-and-ucp3-by-purine-nucleotides-and-phosphate
#10
Gabriel Macher, Melanie Koehler, Anne Rupprecht, Jürgen Kreiter, Peter Hinterdorfer, Elena E Pohl
Mitochondrial membrane uncoupling protein 3 (UCP3) is not only expressed in skeletal muscle and heart, but also in brown adipose tissue (BAT) alongside UCP1, which facilitates a proton leak to support non-shivering thermogenesis. In contrast to UCP1, the transport function and molecular mechanism of UCP3 regulation are poorly investigated, although it is generally agreed upon that UCP3, analogous to UCP1, transports protons, is activated by free fatty acids (FFAs) and is inhibited by purine nucleotides (PN)...
December 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29211859/transformation-asymmetry-and-the-evolution-of-the-bacterial-accessory-genome
#11
Katinka J Apagyi, Christophe Fraser, Nicholas J Croucher
Bacterial transformation can insert or delete genomic islands (GIs), depending on the donor and recipient genotypes, if an homologous recombination spans the GI's integration site and includes sufficiently long flanking homologous arms. Combining mathematical models of recombination with experiments using pneumococci found GI insertion rates declined geometrically with the GI's size. The decrease in acquisition frequency with length (1.08x10-3 bp-1) was higher than a previous estimate of the analogous rate at which core genome recombinations terminated...
December 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29210569/modulating-dna-repair-pathways-to-improve-precision-genome-engineering
#12
Katherine S Pawelczak, Navnath S Gavande, Pamela S VanderVere-Carozza, John J Turchi
Programmable nucleases like the popular CRISPR/Cas9 system allow for precision genome engineering by inducing a site-specific DNA double strand break (DSB) within a genome. The DSB is repaired by endogenous DNA repair pathways, either non-homologous end joining (NHEJ) or homology directed repair (HDR). The predominant and error-prone NHEJ pathway often results in small nucleotide insertions or deletions that can be used to construct knockout alleles. Alternatively, HDR activity can result in precise modification incorporating exogenous DNA fragments into the cut site...
December 6, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29209909/biochemical-and-biophysical-characterisation-of-higher-oligomeric-structure-of-rat-nucleosome-assembly-protein-1
#13
Divya Reddy, Saikat Bhattacharya, Vinod Jani, Uddhavesh Sonavane, Rajendra Joshi, Sanjay Gupta
Nucleosome assembly protein 1 (NAP1) is a histone chaperone that exchanges histone H2A-H2B dimer from chromatin templates. Studies with yeast NAP1 (yNAP1) have revealed its existence as multiple oligomeric species in solution. Here, rat NAP1 (rNAP1), which is 98% identical to the human NAP1 (hNAP1) was used as a model to characterize the oligomeric structures of this protein in higher eukaryotes. Gel filtration chromatography and Dynamic light scattering of recombinant rNAP1 indicated that the protein exists as a complex mixture of multimeric species even at 500 mM ionic strength...
December 5, 2017: Protein Journal
https://www.readbyqxmd.com/read/29209046/cdc7-dbf4-mediated-phosphorylation-of-hsp90-s164-stabilizes-hsp90-hclk2-mrn-complex-to-enhance-atr-atm-signaling-that-overcomes-replication-stress-in-cancer
#14
An Ning Cheng, Chi-Chen Fan, Yu-Kang Lo, Cheng-Liang Kuo, Hui-Chun Wang, I-Hsin Lien, Shu-Yu Lin, Chung-Hsing Chen, Shih Sheng Jiang, I-Shou Chang, Hsueh-Fen Juan, Ping-Chiang Lyu, Alan Yueh-Luen Lee
Cdc7-Dbf4 kinase plays a key role in the initiation of DNA replication and contributes to the replication stress in cancer. The activity of human Cdc7-Dbf4 kinase remains active and acts as an effector of checkpoint under replication stress. However, the downstream targets of Cdc7-Dbf4 contributed to checkpoint regulation and replication stress-support function in cancer are not fully identified. In this work, we showed that aberrant Cdc7-Dbf4 induces DNA lesions that activate ATM/ATR-mediated checkpoint and homologous recombination (HR) DNA repair...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29207996/crispr-cas9-mediated-gene-deletions-in-lager-yeast-saccharomyces-pastorianus
#15
Arthur R Gorter de Vries, Philip A de Groot, Marcel van den Broek, Jean-Marc G Daran
BACKGROUND: The ease of use of CRISPR-Cas9 reprogramming, its high efficacy, and its multiplexing capabilities have brought this technology at the forefront of genome editing techniques. Saccharomyces pastorianus is an aneuploid interspecific hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus that has been domesticated for centuries and is used for the industrial fermentation of lager beer. For yet uncharacterised reasons, this hybrid yeast is far more resilient to genetic alteration than its ancestor S...
December 5, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29207658/overexpression-of-rad51b-predicts-a-preferable-prognosis-for-non-small-cell-lung-cancer-patients
#16
Mengyin Wu, Zufeng Sheng, Lingyan Jiang, Zhengyuan Liu, Yuhua Bi, Yueping Shen
Lung cancer is the leading cause of cancer-related death. The majority of patients are diagnosed at an incurable advanced stage with poor prognosis. A recent study associated the methylation of homologous recombination genes with expression of immune checkpoints in lung squamous cell carcinoma. However, the correlation between them remains unclear. In our study, we propose that RAD51B, a repair gene in the homologous recombination process, which is noticed to be a key player in the maintenance of chromosome integrity and in sensing DNA damage, can act as an independent factor affecting the prognosis of non-small-cell lung cancer (NSCLC)...
October 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/29207607/cyclin-a2-regulates-homologous-recombination-dna-repair-and-sensitivity-to-dna-damaging-agents-and-poly-adp-ribose-polymerase-parp-inhibitors-in-human-breast-cancer-cells
#17
Wei Wei Gu, Jie Lin, Xing Yu Hong
Defects in homologous recombination (HR) repair are found in breast cancers. Intriguingly, breast cancers with defective HR show increased sensitivity to DNA crosslinking agents and poly(ADP-ribose) polymerase (PARP) inhibitors. As such, genes that can affect HR functions have been of high interest in studies aiming to develop biomarkers for predicting response to treatment with these agents. Cyclin A2 is a key component of the core cell cycle machinery. However, whether cyclin A2 dysfunctions could cause HR defect and mediate sensitivity to DNA damaging agents remain unclear...
October 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/29207604/canis-familiaris-allergen-can-f-6-expression-purification-and-analysis-of-b-cell-epitopes-in-chinese-dog-allergic-children
#18
Yu-Jie Wang, Lin Li, Wei-Juan Song, Yan-Jun Zhou, Meng-Da Cao, Xiang-Rong Zuo, Ji-Fu Wei
Dog allergy is common worldwide. However, the allergenicity of dog allergy is still unclear in China as well as in special group, such as children. In this study, we chose Can f 6, a major dog allergen which belongs to the lipocalin to study its allergenicity in Chinese dog allergic children. Can f 6 gene was subcloned into pET-28a vector and transformed into E. coli BL21 (DE3) cells for expression. The recombinant Can f 6 was purified by nickel affinity chromatography, identified by SDS-PAGE, and tested for its allergenicity by Western blot with sera and basophil activation test...
October 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/29204698/fumarase-is-involved-in-dna-double-strand-break-resection-through-a-functional-interaction-with-sae2
#19
Michael Leshets, Dharanidharan Ramamurthy, Michael Lisby, Norbert Lehming, Ophry Pines
One of the most severe forms of DNA damage is the double-strand break (DSB). Failure to properly repair the damage can cause mutation, gross chromosomal rearrangements and lead to the development of cancer. In eukaryotes, homologous recombination (HR) and non-homologous end joining (NHEJ) are the main DSB repair pathways. Fumarase is a mitochondrial enzyme which functions in the tricarboxylic acid cycle. Intriguingly, the enzyme can be readily detected in the cytosolic compartment of all organisms examined, and we have shown that cytosolic fumarase participates in the DNA damage response towards DSBs...
December 4, 2017: Current Genetics
https://www.readbyqxmd.com/read/29203787/crispr-cas9-derived-models-of-ovarian-high-grade-serous-carcinoma-targeting-brca1-pten-and-nf1-and-correlation-with-platinum-sensitivity
#20
Josephine B Walton, Malcolm Farquharson, Susan Mason, Jennifer Port, Bjorn Kruspig, Suzanne Dowson, David Stevenson, Daniel Murphy, Martin Matzuk, Jaeyeon Kim, Seth Coffelt, Karen Blyth, Iain A McNeish
Transplantable murine models of ovarian high grade serous carcinoma (HGSC) remain an important research tool. We previously showed that ID8, a widely-used syngeneic model of ovarian cancer, lacked any of the frequent mutations in HGSC, and used CRISPR/Cas9 gene editing to generate derivatives with deletions in Trp53 and Brca2. Here we have used one ID8 Trp53 -/- clone to generate further mutants, with additional mutations in Brca1, Pten and Nf1, all of which are frequently mutated or deleted in HGSC. We have also generated clones with triple deletions in Trp53, Brca2 and Pten...
December 4, 2017: Scientific Reports
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