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https://www.readbyqxmd.com/read/28930601/a-role-of-line-1-in-telomere-regulation
#1
Catharina Mueller, Thomas Aschacher, Brigitte Wolf, Michael Bergmann
Long interspersed nuclear elements (LINE-1) are well known as retrotransposons. A number of reports indicate that down-regulation of LINE-1 substantially affects growth of malignant cells and epithelial mesenchymal transition, which is difficult to be explained by its function as retrotransposon. More recent data indicate that LINE-1 is broadly involved in the regulation of telomere maintenance. This explains the essential role of LINE-1 for survival of malignant cells and further supports a global function of active LINE-1 elements in cell proliferation...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930600/line-1-as-a-therapeutic-target-for-castration-resistant-prostate-cancer
#2
Nadine Houede, Pier Vincenzo Piazza, Philippe Pourquier
Prostate cancer is the third leading cause of death by cancer in men. Surgery or hormone deprivation usually contains the progression of the local forms of the disease. In metastatic situations, chemotherapy or second generation hormone therapies are used with an overall survival that never exceeds 36 months when tumors become resistant to castration. In the search for new alternatives, clinical trials with various classes of anticancer drugs have been performed, including chemotherapies, targeted therapies with kinase inhibitors, radium-223, or immunotherapies with somehow limited efficacy...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28924058/localization-of-cdc7-protein-kinase-during-dna-replication-in-saccharomyces-cerevisiae
#3
Daniel Rossbach, D Suzi Bryan, Jay R Hesselberth, Robert Sclafani
DDK, a conserved serine-threonine protein kinase composed of a regulatory subunit, Dbf4, and a catalytic subunit, Cdc7, is essential for DNA replication initiation during S phase of the cell cycle through MCM2-7 helicase phosphorylation. The biological significance of DDK is well characterized, but the full mechanism of how DDK associates with substrates remains unclear. Cdc7 is bound to chromatin in the Saccharomyces cerevisiae genome throughout the cell cycle, but there is little empirical evidence as to specific Cdc7 binding locations...
September 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28923009/apophysomyces-variabilis-draft-genome-sequence-and-comparison-of-predictive-virulence-determinants-with-other-medically-important-mucorales
#4
Hariprasath Prakash, Shivaprakash Mandya Rudramurthy, Prasad S Gandham, Anup Kumar Ghosh, Milner M Kumar, Chandan Badapanda, Arunaloke Chakrabarti
BACKGROUND: Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28920925/expression-of-piwi-protein-miwi2-defines-a-distinct-population-of-multiciliated-cells
#5
Gregory A Wasserman, Aleksander D Szymaniak, Anne C Hinds, Kazuko Yamamoto, Hirofumi Kamata, Nicole Ms Smith, Kristie L Hilliard, Claudia Carrieri, Adam T Labadorf, Lee J Quinton, Xingbin Ai, Xaralabos Varelas, Felicia Chen, Joseph P Mizgerd, Alan Fine, Dónal O'Carroll, Matthew R Jones
P-element-induced wimpy testes (Piwi) proteins are known for suppressing retrotransposon activation in the mammalian germline. However, whether Piwi protein or Piwi-dependent functions occur in the mammalian soma is unclear. Contrary to germline-restricted expression, we observed that Piwi-like Miwi2 mRNA is indeed expressed in epithelial cells of the lung in adult mice and that it is induced during pneumonia. Further investigation revealed that MIWI2 protein localized to the cytoplasm of a discrete population of multiciliated airway epithelial cells...
September 18, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28919299/the-retrotransposon-gag-domain-containing-protein-rgag4-is-an-ikaros-target-in-the-pituitary
#6
Zhongyi Shen, Sylvia L Asa, Shereen Ezzat
Previous studies have established the common and critical involvement of the zinc finger protein Ikaros in lymphoid and pituitary cell development and expansion. Key to the assembly of several transcriptional networks, we have demonstrated up-regulation of Ikaros and its interacting partner the C-terminal Binding Protein (CtBP) in response to hypoxia. This prompted us to explore common transcriptional targets using a chromatin immunoprecipitate (ChIP) screen of DNA from pituitary corticotroph cells. This strategy yielded a finite list of targets common to both transcription factors that included the metalloprotease ADAMTS10...
September 14, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28916913/centromeric-enrichment-of-line-1-retrotransposons-and-its-significance-for-the-chromosome-evolution-of-phyllostomid-bats
#7
Cibele Gomes de Sotero-Caio, Diogo Cavalcanti Cabral-de-Mello, Merilane da Silva Calixto, Guilherme Targino Valente, Cesar Martins, Vilma Loreto, Maria José de Souza, Neide Santos
Despite their ubiquitous incidence, little is known about the chromosomal distribution of long interspersed elements (LINEs) in mammalian genomes. Phyllostomid bats, characterized by lineages with distinct trends of chromosomal evolution coupled with remarkable ecological and taxonomic diversity, represent good models to understand how these repetitive sequences contribute to the evolution of genome architecture and its link to lineage diversification. To test the hypothesis that LINE-1 sequences were important modifiers of bat genome architecture, we characterized the distribution of LINE-1-derived sequences on genomes of 13 phyllostomid species within a phylogenetic framework...
September 15, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28903034/piwi-is-required-to-limit-exhaustion-of-aging-somatic-stem-cells
#8
Pedro Sousa-Victor, Arshad Ayyaz, Rippei Hayashi, Yanyan Qi, David T Madden, Victoria V Lunyak, Heinrich Jasper
Sophisticated mechanisms that preserve genome integrity are critical to ensure the maintenance of regenerative capacity while preventing transformation of somatic stem cells (SCs), yet little is known about mechanisms regulating genome maintenance in these cells. Here, we show that intestinal stem cells (ISCs) induce the Argonaute family protein Piwi in response to JAK/STAT signaling during acute proliferative episodes. Piwi function is critical to ensure heterochromatin maintenance, suppress retrotransposon activation, and prevent DNA damage in homeostasis and under regenerative pressure...
September 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/28900080/-dynamics-of-line-1-retrotransposon-methylation-levels-in-circulating-dna-from-lung-cancer-patients-undergoing-antitumor-therapy
#9
A A Ponomaryova, N V Cherdyntseva, A A Bondar, A Y Dobrodeev, A A Zavyalov, S A Tuzikov, V V Vlassov, E L Choinzonov, P P Laktionov, E Y Rykova
Malignant cell transformation is accompanied with abnormal DNA methylation, such as the hypermethylation of certain gene promoters and hypomethylation of retrotransposons. In particular, the hypomethylation of the human-specific family of LINE-1 retrotransposons was observed in lung cancer tissues. It is also known that the circulating DNA (cirDNA) of blood plasma and cell-surface-bound circulating DNA (csb-cirDNA) of cancer patients accumulate tumor-specific aberrantly methylated DNA fragments, which are currently considered to be valuable cancer markers...
July 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28887438/-silencing-of-retrotransposons-by-setdb1-inhibits-the-interferon-response-in-acute-myeloid-leukemia
#10
Trinna L Cuellar, Anna-Maria Herzner, Xiaotian Zhang, Yogesh Goyal, Colin Watanabe, Brad A Friedman, Vasantharajan Janakiraman, Steffen Durinck, Jeremy Stinson, David Arnott, Tommy K Cheung, Subhra Chaudhuri, Zora Modrusan, Jonas Martin Doerr, Marie Classon, Benjamin Haley
A propensity for rewiring genetic and epigenetic regulatory networks, thus enabling sustained cell proliferation, suppression of apoptosis, and the ability to evade the immune system, is vital to cancer cell propagation. An increased understanding of how this is achieved is critical for identifying or improving therapeutic interventions. In this study, using acute myeloid leukemia (AML) human cell lines and a custom CRISPR/Cas9 screening platform, we identify the H3K9 methyltransferase SETDB1 as a novel, negative regulator of innate immunity...
September 8, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28878503/assessment-of-genetic-diversity-and-population-structure-of-an-endemic-moroccan-tree-argania-spinosa-l-based-in-irap-and-issr-markers-and-implications-for-conservation
#11
Ouafae Pakhrou, Leila Medraoui, Chaimaa Yatrib, Mohammed Alami, Abdelkarim Filali-Maltouf, Bouchra Belkadi
Argan Tree is well known for its precious oil extracted from its seeds particularly used for the nutritional and cosmetic benefits. Because of the high international demand, the argan tree suffers from overexploitation and its cultivation is rare. Thus, the assessment of the genetic variation of this endemic tree is critically important for designing conservation strategies. In the present study and for the first time, genetic diversity of the global natural distribution of argan tree (Argania spinosa L.) in Morocco was assessed...
July 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/28877662/genome-wide-characterization-of-non-reference-transposable-element-insertion-polymorphisms-reveals-genetic-diversity-in-tropical-and-temperate-maize
#12
Xianjun Lai, James C Schnable, Zhengqiao Liao, Jie Xu, Gengyun Zhang, Chuan Li, Erliang Hu, Tingzhao Rong, Yunbi Xu, Yanli Lu
BACKGROUND: Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation...
September 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28869113/cold-induced-retrotransposition-of-fish-lines
#13
Shue Chen, Mengchao Yu, Xu Chu, Wenhao Li, Xiujuan Yin, Liangbiao Chen
Classes of retrotransposons constitute a large portion of metazoan genome. There have been cases reported that genomic abundance of retrotransposons is correlated with the severity of low environmental temperatures. However, the molecular mechanisms underlying such correlation are unknown. We show here by cell transfection assays that retrotransposition (RTP) of a long interspersed nuclear element (LINE) from an Antarctic notothenioid fish Dissostichus mawsoni (dmL1) could be activated by low temperature exposure, causing increased dmL1 copies in the host cell genome...
July 24, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28867564/different-histories-of-two-highly-variable-ltr-retrotransposons-in-sunflower-species
#14
Flavia Mascagni, Andrea Cavallini, Tommaso Giordani, Lucia Natali
In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus...
August 31, 2017: Gene
https://www.readbyqxmd.com/read/28860009/evolution-of-ribosomal-internal-transcribed-spacers-in-deuterostomia
#15
Alexander Dyomin, Valeria Volodkina, Elena Koshel, Svetlana Galkina, Alsu Saifitdinova, Elena Gaginskaya
Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown...
August 30, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28854222/rahu-is-a-mutant-allele-of-dnmt3c-encoding-a-dna-methyltransferase-homolog-required-for-meiosis-and-transposon-repression-in-the-mouse-male-germline
#16
Devanshi Jain, Cem Meydan, Julian Lange, Corentin Claeys Bouuaert, Nathalie Lailler, Christopher E Mason, Kathryn V Anderson, Scott Keeney
Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs-Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l-that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called 'rahu', which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28846101/line-1-activation-after-fertilization-regulates-global-chromatin-accessibility-in-the-early-mouse-embryo
#17
Joanna W Jachowicz, Xinyang Bing, Julien Pontabry, Ana Bošković, Oliver J Rando, Maria-Elena Torres-Padilla
After fertilization, to initiate development, gametes are reprogramed to become totipotent. Approximately half of the mammalian genome consists of repetitive elements, including retrotransposons, some of which are transcribed after fertilization. Retrotransposon activation is generally assumed to be a side effect of the extensive chromatin remodeling underlying the epigenetic reprogramming of gametes. Here, we used a targeted epigenomic approach to address whether specific retrotransposon families play a direct role in chromatin organization and developmental progression...
August 28, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28840860/tsrnas-new-players-in-mammalian-retrotransposon-control
#18
Yunfang Zhang, Junchao Shi, Qi Chen
A recent study led by Professor Rob Martienssen in Cell showed that 3'-tRNA-derived small RNAs can suppress long terminal repeat retrotransposon activity in mammalian cells by mechanisms independent of DNA-associated epigenetic marks, suggesting how the genome may defend itself from retrotransposon invasion during epigenetic reprogramming.
August 25, 2017: Cell Research
https://www.readbyqxmd.com/read/28833526/perinatal-lead-pb-exposure-results-in-sex-and-tissue-dependent-adult-dna-methylation-alterations-in-murine-iap-transposons
#19
L Montrose, C Faulk, J Francis, D C Dolinoy
Epidemiological and animal data suggest that adult chronic disease is influenced by early-life exposure-induced changes to the epigenome. Previously, we observed that perinatal lead (Pb) exposure results in persistent murine metabolic- and activity-related effects. Using phylogenetic and DNA methylation analysis, we have also identified novel intracisternal A particle (IAP) retrotransposons exhibiting regions of variable methylation as candidate loci for environmental effects on the epigenome. Here, we now evaluate brain and kidney DNA methylation profiles of four representative IAPs in adult mice exposed to human physiologically relevant levels of Pb two weeks prior to mating through lactation...
August 19, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28831052/rapid-amplification-of-four-retrotransposon-families-promoted-speciation-and-genome-size-expansion-in-the-genus-panax
#20
Junki Lee, Nomar Espinosa Waminal, Hong-Il Choi, Sampath Perumal, Sang-Choon Lee, Van Binh Nguyen, Woojong Jang, Nam-Hoon Kim, Li-Zhi Gao, Tae-Jin Yang
Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata...
August 22, 2017: Scientific Reports
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