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https://www.readbyqxmd.com/read/28916913/centromeric-enrichment-of-line-1-retrotransposons-and-its-significance-for-the-chromosome-evolution-of-phyllostomid-bats
#1
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/28916648/genome-dynamics-of-hybrid-saccharomyces-cerevisiae-during-vegetative-and-meiotic-divisions
#2
Abhishek Dutta, Gen Lin, Ajith V Pankajam, Parijat Chakraborty, Nahush Bhat, Lars M Steinmetz, Koodali T Nishant
Mutation and recombination are the major sources of genetic diversity in all organisms. In the baker's yeast, all mutation rate estimates are in homozygous background. We determined the extent of genetic change through mutation and loss of heterozygosity (LOH) in a heterozygous Saccharomyces cerevisiae genome during successive vegetative and meiotic divisions. We measured genome wide LOH and base mutation rates during vegetative and meiotic divisions in a hybrid (S288c/YJM789) S. cerevisiae strain. The S288c/YJM789 hybrid showed nearly complete reduction in heterozygosity within 31 generations of meioses and improved spore viability...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28900618/comparative-genomic-in-situ-hybridization-and-the-possible-role-of-retroelements-in-the-karyotypic-evolution-of-three-akodontini-species
#3
Naiara Pereira Araújo, Gustavo Campos Silva Kuhn, Flávia Nunes Vieira, Thaís Queiroz Morcatty, Adriano Pereira Paglia, Marta Svartman
South American Akodontini rodents are characterized by a large number of chromosome rearrangements. Among them, the genus Akodon has been extensively analyzed with classical and molecular cytogenetics, which allowed the identification of a large number of intra- and interspecific chromosomal variation due to Robertsonian rearrangements, pericentric inversions, and heterochromatin additions/deletions. In order to shed some light on the cause of these rearrangements, we comparatively analyzed the karyotypes of three Akodontini species, Akodon cursor (2n = 14, FN = 19), A...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28900080/-dynamics-of-line-1-retrotransposon-methylation-levels-in-circulating-dna-from-lung-cancer-patients-undergoing-antitumor-therapy
#4
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/28886359/the-trex1-dinosaur-bites-the-brain-through-the-line
#5
José Luis García Pérez, Marta E Alarcón-Riquelme
In this issue of Cell Stem Cell, Thomas et al. (2017) define the nature of accumulated ssDNA present in the neuron and astrocyte cytoplasm of TREX1 mutated stem cell-derived organoids. Accumulated ssDNAs are derived from LINE-1 endogenous retroelements, providing new clues as to the development of Aicardi-Goutières syndrome in the neural system.
September 7, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28883657/deamination-independent-restriction-of-line-1-retrotransposition-by-apobec3h
#6
Yuqing Feng, Mariam H Goubran, Tyson B Follack, Linda Chelico
The APOBEC3 family of cytosine deaminase enzymes are able to restrict replication of retroelements, such as LINE-1. However, each of the seven APOBEC3 enzymes have been reported to act differentially to prevent LINE-1 retrotransposition and the mechanisms of APOBEC3-mediated LINE-1 inhibition has not been well understood. The prevailing view for many years was that APOBEC3-mediated LINE-1 inhibition was deamination-independent and relied on APOBEC3s blocking the LINE-1 reverse transcriptase DNA polymerization or transport of the LINE-1 RNA into the nucleus...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28878216/environmental-stress-is-the-major-cause-of-transcriptomic-and-proteomic-changes-in-gm-and-non-gm-plants
#7
Rita Batista, Cátia Fonseca, Sébastien Planchon, Sónia Negrão, Jenny Renaut, M Margarida Oliveira
The approval of genetically modified (GM) crops is preceded by years of intensive research to demonstrate safety to humans and environment. We recently showed that in vitro culture stress is the major factor influencing proteomic differences of GM vs. non-GM plants. This made us question the number of generations needed to erase such "memory". We also wondered about the relevance of alterations promoted by transgenesis as compared to environment-induced ones. Here we followed three rice lines (1-control, 1-transgenic and 1-negative segregant) throughout eight generations after transgenesis combining proteomics and transcriptomics, and further analyzed their response to salinity stress on the F6 generation...
September 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28865728/gender-specific-association-of-exposure-to-non-dioxin-like-polychlorinated-biphenyls-during-pregnancy-with-methylation-levels-of-h19-and-long-interspersed-nuclear-element-1-in-cord-blood-in-the-hokkaido-study
#8
Sumitaka Kobayashi, Fumihiro Sata, Chihiro Miyashita, Ryu Miura, Kaoru Azumi, Sachiko Kobayashi, Houman Goudarzi, Atsuko Araki, Mayumi Ishizuka, Takashi Todaka, Jumboku Kajiwara, Tsuguhide Hori, Reiko Kishi
BACKGROUND: Associations between prenatal exposure to polychlorinated biphenyls (PCBs) and reduced birth-size, and between DNA methylation of insulin-like growth factor-2 (IGF-2), H19 locus, and long interspersed nuclear element-1 (LINE-1) and reduced birth-size are well established. To date, however, studies on the associations between prenatal exposure to PCBs and alterations in methylation of IGF-2, H19, and LINE-1 are lacking. Thus, in this study, we examined these associations with infant-gender stratification...
August 30, 2017: Toxicology
https://www.readbyqxmd.com/read/28856682/tumor-expression-of-calcium-sensing-receptor-casr-and-colorectal-cancer-survival-results-from-the-nurses-health-study-and-health-professionals-follow-up-study
#9
Fatemeh Momen-Heravi, Yohei Masugi, Zhi Rong Qian, Reiko Nishihara, Li Liu, Stephanie Smith-Warner, NaNa Keum, Lanjing Zhang, Nairi Tchrakian, Jonathan A Nowak, Wanshui Yang, Yanan Ma, Michaela Bowden, Annacarolina da Silva, Molin Wang, Charles S Fuchs, Jeffrey A Meyerhardt, Kimmie Ng, Kana Wu, Edward Giovannucci, Shuji Ogino, Xuehong Zhang
Although experimental evidence suggests calcium-sensing receptor (CASR) as a tumor-suppressor, the prognostic role of tumor CASR expression in colorectal carcinoma remains unclear. We hypothesized that higher tumor CASR expression might be associated with improved survival among colorectal cancer patients. We evaluated tumor expression levels of CASR by immunohistochemistry in 809 incident colorectal cancer patients within the Nurses' Health Study and the Health Professionals Follow-up Study. We used Cox proportional hazards regression models to estimate multivariable hazard ratio (HR) for the association of tumor CASR expression with colorectal cancer-specific and all-cause mortality...
August 30, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28854904/line-1-hypermethylation-in-white-blood-cell-dna-is-associated-with-high-grade-cervical-intraepithelial-neoplasia
#10
Martina Barchitta, Annalisa Quattrocchi, Andrea Maugeri, Carolina Canto, Nadia La Rosa, Maria Antonietta Cantarella, Giuseppa Spampinato, Aurora Scalisi, Antonella Agodi
BACKGROUND: Long Interspersed Nuclear Elements-1 (LINEs-1) methylation from white blood cells (WBCs) DNA has been proposed as biomarker associated with different types of cancer. The aim of the present study was to investigate the degree of WBCs LINE-1 methylation, according to high-risk Human Papilloma Virus (hrHPV) status in a healthy population, and the association with high-grade Cervical Intraepithelial Neoplasia (CIN2+) in hrHPV positive women. METHODS: Women with abnormal cervical cells were enrolled and classified by histological diagnosis and hrHPV infection...
August 30, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28851942/a-combination-of-species-identification-and-str-profiling-identifies-cross-contaminated-cells-from-482-human-tumor-cell-lines
#11
Xiaocui Bian, Zhenli Yang, Hailiang Feng, Hao Sun, Yuqin Liu
Human tumor cell lines are extremely important tools for cancer research, but a significant percentage is cross-contaminated with other cells. Short tandem repeat (STR) profiling is the prevailing standard for authenticating cell lines that originate from human tissues. Based on the analysis of 482 different human tumor cell lines used in China by STR, up to 96 cell lines were misidentified. More importantly, the study has found that STR profiling alone is insufficient to exclude inter-species cross-contamination of human cell lines...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28851390/tumoral-line-1-hypomethylation-is-associated-with-poor-survival-of-patients-with-intrahepatic-cholangiocarcinoma
#12
Seorin Jeong, Kyoungbun Lee, Xianyu Wen, Younghoon Kim, Nam-Yun Cho, Ja-June Jang, Gyeong Hoon Kang
BACKGROUND: DNA methylation changes occurring in cancer cells are featured with both promoter CpG island hypermethylation and diffuse genomic hypomethylation. Long interspersed element-1 (LINE-1) is repeated in an interspersed manner with an estimated 500,000 copies per genome. LINE-1 has its CpG sites of the 5' untranslated region methylated heavily in normal cells and undergoes demethylation in association with cancerization. However, little information is available regarding LINE-1 hypomethylation and its prognostic implication in intrahepatic cholangiocarcinomas...
August 29, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28846570/macrophage-migration-inhibitory-factor-induced-autophagy-contributes-to-thrombin-triggered-endothelial-hyperpermeability-in-sepsis
#13
Chiao-Hsuan Chao, Hong-Ru Chen, Yung-Chun Chuang, Trai-Ming Yeh
Vascular leakage contributes to the high morbidity and mortality associated with sepsis. Exposure of the endothelium to inflammatory mediators, such as thrombin and cytokines, during sepsis leads to hyperpermeability. We recently observed that autophagy, a cellular process for protein turnover, is involved in macrophage migration inhibitory factor (MIF)-induced endothelial hyperpermeability. Even though it is known that thrombin induces endothelial cells to secrete MIF and to increase vascular permeability, the possible role of autophagy in this process is unknown...
August 25, 2017: Shock
https://www.readbyqxmd.com/read/28846101/line-1-activation-after-fertilization-regulates-global-chromatin-accessibility-in-the-early-mouse-embryo
#14
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/28821874/global-methylation-correlates-with-clinical-status-in-multiple-sclerosis-patients-in-the-first-year-of-ifnbeta-treatment
#15
María Jesús Pinto-Medel, Begoña Oliver-Martos, Patricia Urbaneja-Romero, Isaac Hurtado-Guerrero, Jesús Ortega-Pinazo, Pedro Serrano-Castro, Óscar Fernández, Laura Leyva
The alteration of DNA methylation patterns are a key component of disease onset and/or progression. Our objective was to evaluate the differences in Long Interspersed Nuclear Element-1 (LINE-1) methylation levels, as a surrogate marker of global DNA methylation, between multiple sclerosis (MS) patients and healthy controls. In addition, we assessed the association of LINE-1 methylation with clinical disease activity in patients treated with IFNbeta (IFNβ). We found that individuals with high levels of LINE-1 methylation showed 6-fold increased risk of suffering MS...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28813472/an-intronic-line-1-insertion-in-mertk-is-strongly-associated-with-retinopathy-in-swedish-vallhund-dogs
#16
Richard Everson, Louise Pettitt, Oliver P Forman, Olivia Dower-Tylee, Bryan McLaughlin, Saija Ahonen, Maria Kaukonen, András M Komáromy, Hannes Lohi, Cathryn S Mellersh, Jane Sansom, Sally L Ricketts
The domestic dog segregates a significant number of inherited progressive retinal diseases, several of which mirror human retinal diseases and which are collectively termed progressive retinal atrophy (PRA). In 2014, a novel form of PRA was reported in the Swedish Vallhund breed, and the disease was mapped to canine chromosome 17. The causal mutation was not identified, but expression analyses of the retinas of affected Vallhunds demonstrated a 6-fold increased expression of the MERTK gene compared to unaffected dogs...
2017: PloS One
https://www.readbyqxmd.com/read/28810637/binding-of-line-1-rna-to-psf-transcriptionally-promotes-gage6-and-regulates-cell-proliferation-and-tumor-formation-in-vitro
#17
Jiao Lv, Ziyi Zhao
Hepatocellular carcinoma (HCC) has one of the highest mortality rates among numerous types of cancer. It has been demonstrated that in hepatitis B (HBV)-associated HCC, the expression of chimeric fusion transcript HBx-long interspersed nuclear element-1 (LINE-1) initiated by HBV integration is correlated with hepatocarcinogenesis and poor patient survival rates. Furthermore, increased rates of LINE-1 hypomethylation have been detected in HCC tissues compared with adjacent tissues. This suggests that individual LINE-1 RNA (L1 RNA) serves an important role in the processes of hepatocarcinogenesis...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28809129/effect-of-methotrexate-vitamin-b12-on-dna-methylation-as-a-potential-factor-in-leukemia-treatment-related-neurotoxicity
#18
Victoria J Forster, Alex McDonnell, Rachel Theobald, Jill A McKay
Methotrexate (MTX) is administered to treat childhood acute lymphoblastic leukemia (ALL). It acts by inhibiting dihydrofolate reductase which reduces methyltetrahydrofolate, a key component in one carbon metabolism, thus reducing cell proliferation. Further perturbations to one carbon metabolism, such as reduced vitamin B12 levels via the use of nitrous oxide for sedation during childhood ALL treatment, may increase neurotoxicity risk. With B12 as an enzymatic cofactor, methyltetrahydrofolate is essential to produce methionine, which is critical for DNA methylation...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28808048/epigenetic-repression-of-line-1-elements-protects-drug-resistant-cells
#19
(no author information available yet)
H3K9me3-dependent heterochromatin formation maintains drug-tolerant persister (DTP) cell viability.
August 14, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28806172/mobilization-of-line-1-retrotransposons-is-restricted-by-tex19-1-in-mouse-embryonic-stem-cells
#20
Marie MacLennan, Marta García-Cañadas, Judith Reichmann, Elena Khazina, Gabriele Wagner, Christopher J Playfoot, Carmen Salvador-Palomeque, Abigail R Mann, Paula Peressini, Laura Sanchez, Karen Dobie, David Read, Chao-Chun Hung, Ragnhild Eskeland, Richard R Meehan, Oliver Weichenrieder, Jose Luis García-Pérez, Ian R Adams
Mobilization of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution, but these mutagenic events can also cause genetic disorders. In humans, retrotransposon mobilization is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilize in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilization...
August 14, 2017: ELife
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