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Chromosome homology search

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https://www.readbyqxmd.com/read/28554658/prolonged-exposure-to-particulate-chromate-inhibits-rad51-nuclear-import-mediator-proteins
#1
Cynthia L Browning, John Pierce Wise
Particulate hexavalent chromium (Cr(VI)) is a human lung carcinogen and a human health concern. The induction of structural chromosome instability is considered to be a driving mechanism of Cr(VI)-induced carcinogenesis. Homologous recombination repair protects against Cr(VI)-induced chromosome damage, due to its highly accurate repair of Cr(VI)-induced DNA double strand breaks. However, recent studies demonstrate Cr(VI) inhibits homologous recombination repair through the misregulation of RAD51. RAD51 is an essential protein in HR repair that facilitates the search for a homologous sequence...
May 26, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28489851/global-analysis-of-double-strand-break-processing-reveals-in-vivo-properties-of-the-helicase-nuclease-complex-addab
#2
Anjana Badrinarayanan, Tung B K Le, Jan-Hendrik Spille, Ibrahim I Cisse, Michael T Laub
In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear...
May 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28410191/loss-of-pten-expression-in-breast-cancer-association-with-clinicopathological-characteristics-and-prognosis
#3
Shuting Li, Yanwei Shen, Mengying Wang, Jiao Yang, Meng Lv, Pan Li, Zheling Chen, Jin Yang
Various studies have evaluated the significance of PTEN (phosphatase and tensin homolog deleted from chromosome 10) expression in breast cancer, but their results remain controversial. We conducted a meta-analysis to evaluate the associations of PTEN expression with clinicopathological characteristics and prognosis in breast cancer. PubMed, Embase, Web of Science, and China National Knowledge Infrastructure were searched to identify relevant publications. The associations between PTEN expression and clinicopathological parameters, disease-free survival (DFS), and overall survival (OS) were then assessed via meta-analyses of odds ratio (ORs) and hazard ratio (HRs) with 95% confidence intervals (CIs)...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28387353/characterization-and-genomic-analyses-of-two-newly-isolated-morganella-phages-define-distant-members-among-tevenvirinae-and-autographivirinae-subfamilies
#4
Hugo Oliveira, Graça Pinto, Ana Oliveira, Jean-Paul Noben, Hanne Hendrix, Rob Lavigne, Małgorzata Łobocka, Andrew M Kropinski, Joana Azeredo
Morganella morganii is a common but frequent neglected environmental opportunistic pathogen which can cause deadly nosocomial infections. The increased number of multidrug-resistant M. morganii isolates motivates the search for alternative and effective antibacterials. We have isolated two novel obligatorily lytic M. morganii bacteriophages (vB_MmoM_MP1, vB_MmoP_MP2) and characterized them with respect to specificity, morphology, genome organization and phylogenetic relationships. MP1's dsDNA genome consists of 163,095 bp and encodes 271 proteins, exhibiting low DNA (<40%) and protein (<70%) homology to other members of the Tevenvirinae...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28282376/the-transjugation-machinery-of-thermus-thermophilus-identification-of-tdta-an-atpase-involved-in-dna-donation
#5
Alba Blesa, Ignacio Baquedano, Nieves G Quintáns, Carlos P Mata, José R Castón, José Berenguer
In addition to natural competence, some Thermus thermophilus strains show a high rate of DNA transfer via direct cell-to-cell contact. The process is bidirectional and follows a two-step model where the donor cell actively pushes out DNA and the recipient cell employs the natural competence system to take up the DNA, in a hybrid transformation-dependent conjugation process (transjugation). While the DNA uptake machinery is well known as in other bacterial species that undergo transformation, the pushing step of transjugation remains to be characterized...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28257444/mechanisms-of-fast-and-stringent-search-in-homologous-pairing-of-double-stranded-dna
#6
Amir Bitran, Wei-Yin Chiang, Erel Levine, Mara Prentiss
Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets. Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment. In systems with many nearly matched targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28223359/peptide-recognition-by-heterochromatin-protein-1-hp1-chromoshadow-domains-revisited-plasticity-in-the-pseudosymmetric-histone-binding-site-of-human-hp1
#7
Yanli Liu, Su Qin, Ming Lei, Wolfram Tempel, Yuzhe Zhang, Peter Loppnau, Yanjun Li, Jinrong Min
Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PXVXL motif but also with a region of histone H3 that bears the similar PXXVXL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PXXVXL motif of histone H3...
April 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28223252/the-origin-and-evolution-of-basigin-bsg-gene-a-comparative-genomic-and-phylogenetic-analysis
#8
Xinyan Zhu, Shenglan Wang, Mingjie Shao, Jie Yan, Fei Liu
Basigin (BSG), also known as extracellular matrix metalloproteinase inducer (EMMPRIN) or cluster of differentiation 147 (CD147), plays various fundamental roles in the intercellular recognition involved in immunologic phenomena, differentiation, and development. In this study, we aimed to compare the similarities and differences of BSG among organisms and explore possible evolutionary relationships based on the comparison result. We used the extensive BLAST tool to search the metazoan genomes, N-glycosylation sites, the transmembrane region and other functional sites...
July 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28218778/identification-and-cloning-of-golden2-like1-glk1-a-transcription-factor-associated-with-chloroplast-development-in-brassica-napus-l
#9
Y L Pan, Y Pan, C M Qu, C G Su, J H Li, X G Zhang
Photosynthesis is the process by which dry matter accumulates, which affects rapeseed yield. In this study, we identified GOLDEN2-LIKE1 (GLK1), located on chromosome A07 and 59.2 kb away from the single nucleotide polymorphism marker SNP16353A07, which encodes a transcription factor associated with the rate of photosynthesis in leaves. We then identified 96 GLK1 family members from 53 species using a hidden Markov model (HMM) search and found 24 of these genes, which were derived from 17 Brassicaceae species...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28077560/mechanistic-insights-into-type-i-toxin-antitoxin-systems-in-helicobacter-pylori-the-importance-of-mrna-folding-in-controlling-toxin-expression
#10
Hélène Arnion, Dursun Nizam Korkut, Sara Masachis Gelo, Sandrine Chabas, Jérémy Reignier, Isabelle Iost, Fabien Darfeuille
Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori. We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial expression in H. pylori induces cell death. The synthesis of this toxin is prevented by the transcription of an antitoxin RNA, named IsoA1, expressed on the opposite strand of the toxin gene. We further reveal additional layers of post-transcriptional regulation that control toxin expression: (i) transcription of the aapA1 gene generates a full-length transcript whose folding impedes translation (ii) a 3΄ end processing of this message generates a shorter transcript that, after a structural rearrangement, becomes translatable (iii) but this rearrangement also leads to the formation of two stem-loop structures allowing formation of an extended duplex with IsoA1 via kissing-loop interactions...
May 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28024295/characterization-of-two-novel-fancg-mutations-in-indian-fanconi-anemia-patients
#11
Avani Solanki, C Kumar Selvaa, Frenny Sheth, Nita Radhakrishnan, Manas Kalra, Babu Rao Vundinti
FA is a rare recessive genetic disorder with autosomal or X-linked mode of inheritance and is associated with 19 different FA complementation groups. We have studied three patients clinically diagnosed as FA. All three patients showed a high frequency chromosomal breakage in MMC induced blood cultures and FANCD2 non-monoubiquitination by western blotting. The molecular analysis using direct sequencing revealed two novel mutations in FANCG; 2 novel mutations c.1143+5G>C and c.883dupG, and a reported mutation c...
November 29, 2016: Leukemia Research
https://www.readbyqxmd.com/read/27902773/genomic-landscape-of-experimental-bladder-cancer-in-rodents-and-its-application-to-human-bladder-cancer-gene-amplification-and-potential-overexpression-of-cyp2a5-cyp2a6-are-associated-with-the-invasive-phenotype
#12
Kazuhiro Kanemoto, Katsuhiro Fukuta, Noriyasu Kawai, Keiichi Tozawa, Masako Ochiai, Koji Okamoto, Sumiko Ohnami, Hiromi Sakamoto, Teruhiko Yoshida, Yae Kanai, Masaru Katoh, Takahiro Yasui, Kenjiro Kohri, Tadao Kakizoe, Hitoshi Nakagama
Non-muscle invasive (superficial) bladder cancer is a low-grade malignancy with good prognosis, while muscle invasive (invasive) bladder cancer is a high-grade malignancy with poor prognosis. N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) induces superficial bladder cancers with papillary morphology in rats and invasive bladder cancers with infiltrating phenotype in mice. In this study, we analyzed genomic landscapes of rodent BBN-induced bladder cancers using array-based comparative genomic hybridization (array CGH)...
2016: PloS One
https://www.readbyqxmd.com/read/27900493/mining-the-cicer-arietinum-genome-for-the-mildew-locus-o-mlo-gene-family-and-comparative-evolutionary-analysis-of-the-mlo-genes-from-medicago-truncatula-and-some-other-plant-species
#13
Reena Deshmukh, V K Singh, Brahma Deo Singh
The mildew locus O (Mlo) gene family is ubiquitous in land plants. Some members of this gene family are involved in negative regulation of powdery mildew resistance, while others are involved in several other biological functions. Mlo proteins have characteristic seven transmembrane domains and a calmodulin-binding domain at their C-termini, and are associated with plasma membrane. The Mlo gene family has been studied in several economically important cereals, but little information is available on this gene family in the important legumes, Medicago truncatula Gaertn...
November 30, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27892792/e2fl1-is-a-meiosis-specific-transcription-factor-in-the-protist-tetrahymena-thermophila
#14
Jing Zhang, Miao Tian, Guan-Xiong Yan, Anura Shodhan, Wei Miao
Members of the E2F family of transcription factors have been reported to regulate the expression of genes involved in cell cycle control, DNA replication, and DNA repair in multicellular eukaryotes. Here, E2FL1, a meiosis-specific E2F transcription factor gene, was identified in the model ciliate Tetrahymena thermophila. Loss of this gene resulted in meiotic arrest prior to anaphase I. The cytological experiments revealed that the meiotic homologous pairing was not affected in the absence of E2FL1, but the paired homologous chromosomes did not separate and assumed a peculiar tandem arrangement...
January 2, 2017: Cell Cycle
https://www.readbyqxmd.com/read/27833625/dart-markers-effectively-target-gene-space-in-the-rye-genome
#15
Piotr Gawroński, Magdalena Pawełkowicz, Katarzyna Tofil, Grzegorz Uszyński, Saida Sharifova, Shivaksh Ahluwalia, Mirosław Tyrka, Maria Wędzony, Andrzej Kilian, Hanna Bolibok-Brągoszewska
Large genome size and complexity hamper considerably the genomics research in relevant species. Rye (Secale cereale L.) has one of the largest genomes among cereal crops and repetitive sequences account for over 90% of its length. Diversity Arrays Technology is a high-throughput genotyping method, in which a preferential sampling of gene-rich regions is achieved through the use of methylation sensitive restriction enzymes. We obtained sequences of 6,177 rye DArT markers and following a redundancy analysis assembled them into 3,737 non-redundant sequences, which were then used in homology searches against five Pooideae sequence sets...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27831816/genome-wide-analysis-of-the-dna-binding-with-one-zinc-finger-dof-transcription-factor-family-in-bananas
#16
Chen Dong, Huigang Hu, Jianghui Xie
DNA-binding with one finger (Dof) domain proteins are a multigene family of plant-specific transcription factors involved in numerous aspects of plant growth and development. In this study, we report a genome-wide search for Musa acuminata Dof (MaDof) genes and their expression profiles at different developmental stages and in response to various abiotic stresses. In addition, a complete overview of the Dof gene family in bananas is presented, including the gene structures, chromosomal locations, cis-regulatory elements, conserved protein domains, and phylogenetic inferences...
December 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27818673/identification-of-nitrogen-use-efficiency-genes-in-barley-searching-for-qtls-controlling-complex-physiological-traits
#17
Mei Han, Julia Wong, Tao Su, Perrin H Beatty, Allen G Good
Over the past half century, the use of nitrogen (N) fertilizers has markedly increased crop yields, but with considerable negative effects on the environment and human health. Consequently, there has been a strong push to reduce the amount of N fertilizer used by maximizing the nitrogen use efficiency (NUE) of crops. One approach would be to use classical genetics to improve the NUE of a crop plant. This involves both conventional breeding and quantitative trait loci (QTL) mapping in combination with marker-assisted selection (MAS) to track key regions of the chromosome that segregate for NUE...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27811955/cytological-basis-of-sterility-in-male-and-female-hybrids-between-sibling-species-of-grey-voles-microtus-arvalis-and-m-levis
#18
Anna A Torgasheva, Pavel M Borodin
To make insight into the cytological basis of reproductive isolation, we examined chromosome synapsis and recombination in sterile male and female hybrids between Microtus arvalis and M. levis. These sibling species differ by a series of chromosomal rearrangements (fusions, inversions, centromere shifts and heterochromatin insertions). We found that meiosis in male hybrids was arrested at leptotene with complete failure of chromosome pairing and DNA double-strand breaks repair. In the female hybrids meiosis proceeded to pachytene; however, the oocytes varied in the degree of pairing errors...
November 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27791086/chromosome-refolding-model-of-mating-type-switching-in-yeast
#19
Barış Avşaroğlu, Gabriel Bronk, Kevin Li, James E Haber, Jane Kondev
Chromosomes are folded into cells in a nonrandom fashion, with particular genetic loci occupying distinct spatial regions. This observation raises the question of whether the spatial organization of a chromosome governs its functions, such as recombination or transcription. We consider this general question in the specific context of mating-type switching in budding yeast, which is a model system for homologous recombination. Mating-type switching is induced by a DNA double-strand break (DSB) at the MAT locus on chromosome III, followed by homologous recombination between the cut MAT locus and one of two donor loci (HMLα and HMRa), located on the same chromosome...
October 24, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27790846/identifying-homomorphic-sex-chromosomes-from-wild-caught-adults-with-limited-genomic-resources
#20
Alan Brelsford, Guillaume Lavanchy, Roberto Sermier, Anna Rausch, Nicolas Perrin
We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on noninvasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered data set (411 446 RAD tags) was more successful than searches from a filtered data set (33 073 RAD tags) for markers showing sex differences in heterozygosity or in allele frequencies...
October 28, 2016: Molecular Ecology Resources
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