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Retrotransposon

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https://www.readbyqxmd.com/read/28535662/methylation-levels-of-line-1-as-a-useful-marker-for-venous-invasion-in-both-ffpe-and-frozen-tumor-tissues-of-gastric-cancer
#1
Jimin Min, Boram Choi, Tae-Su Han, Hyuk-Joon Lee, Seong-Ho Kong, Yun-Suhk Suh, Tae-Han Kim, Hwi-Nyeong Choe, Woo Ho Kim, Keun Hur, Han-Kwang Yang
Long interspersed nuclear element-1 (LINE-1) is a retrotransposon that contains a CpG island in its 5-untranslated region. The CpG island of LINE-1 is often heavily methylated in normal somatic cells, which is associated with poor prognosis in various cancers. DNA methylation can differ between formalin-fixed paraffin-embedded (FFPE) and frozen tissues. Therefore, this study aimed to compare the LINE-1 methylation status between the two tissue-storage conditions in gastric cancer (GC) clinical samples and to evaluate whether LINE-1 can be used as an independent prognostic marker for each tissue-storage type...
May 22, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28533438/high-resolution-mapping-of-crossover-events-in-the-hexaploid-wheat-genome-suggests-a-universal-recombination-mechanism
#2
Benoit Darrier, Hélène Rimbert, François Balfourier, Lise Pingault, Ambre-Aurore Josselin, Bertrand Servin, Julien Navarro, Frédéric Choulet, Etienne Paux, Pierre Sourdille
During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are almost limited to subtelomeric regions of chromosomes resulting in a substantial loss of breeding efficiency in the proximal regions though these latter carry ~60-70% of the genes. Identifying sequence and/or chromosome features impacting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed a fine-scale mapping of COs and we revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length...
May 22, 2017: Genetics
https://www.readbyqxmd.com/read/28524723/l1-retrotransposition-is-activated-by-ten-eleven-translocation-protein-1-and-repressed-by-methyl-cpg-binding-proteins
#3
Peng Zhang, Anne K Ludwig, Florian D Hastert, Cathia Rausch, Anne Lehmkuhl, Ines Hellmann, Martha Smets, Heinrich Leonhardt, M Cristina Cardoso
One of the major functions of DNA methylation is the repression of transposable elements, such as the long-interspersed nuclear element 1 (L1). The underlying mechanism(s), however, are unclear. Here, we addressed how retrotransposon activation and mobilization are regulated by methyl-cytosine modifying ten-eleven-translocation (Tet) proteins and how this is modulated by methyl-CpG binding domain (MBD) proteins. We show that Tet1 activates both, endogenous and engineered L1 retrotransposons. Furthermore, we found that Mecp2 and Mbd2 repress Tet1-mediated activation of L1 by preventing 5hmC formation at the L1 promoter...
May 19, 2017: Nucleus
https://www.readbyqxmd.com/read/28523221/reading-lines-within-the-cocaine-addicted-brain
#4
Glenn A Doyle, Tara T Doucet-O'Hare, Matthew J Hammond, Richard C Crist, Adam D Ewing, Thomas N Ferraro, Deborah C Mash, Haig H Kazazian, Wade H Berrettini
INTRODUCTION: Long interspersed element (LINE)-1 (L1) is a type of retrotransposon capable of mobilizing into new genomic locations. Often studied in Mendelian diseases or cancer, L1s may also cause somatic mutation in the developing central nervous system. Recent reports showed L1 transcription was activated in brains of cocaine-treated mice, and L1 retrotransposition was increased in cocaine-treated neuronal cell cultures. We hypothesized that the predisposition to cocaine addiction may result from inherited L1s or somatic L1 mobilization in the brain...
May 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28522611/long-terminal-repeats-power-evolution-of-genes-and-gene-expression-programs-in-mammalian-oocytes-and-zygotes
#5
Vedran Franke, Sravya Ganesh, Rosa Karlic, Radek Malik, Josef Pasulka, Filip Horvat, Maja Kuzman, Helena Fulka, Marketa Cernohorska, Jana Urbanova, Eliska Svobodova, Jun Ma, Yutaka Suzuki, Fugaku Aoki, Richard M Schultz, Kristian Vlahovicek, Petr Svoboda
Retrotransposons are 'copy-and-paste' insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of a group of LTRs from the mammalian endogenous retrovirus-related ERVL retrotransposon class on gene expression in the germline and beyond. In mouse, we identified >800 LTRs from ORR1, MT, MT2, and MLT families, which resemble mobile gene-remodeling platforms that supply promoters and first exons...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28515681/the-activity-induced-long-non-coding-rna-meg3-modulates-ampa-receptor-surface-expression-in-primary-cortical-neurons
#6
Men C Tan, Jocelyn Widagdo, Yu Q Chau, Tianyi Zhu, Justin J-L Wong, Allen Cheung, Victor Anggono
Transcription of new RNA is crucial for maintaining synaptic plasticity, learning and memory. Although the importance of synaptic plasticity-related messenger RNAs (mRNAs) is well established, the role of a large group of long non-coding RNAs (lncRNAs) in long-term potentiation (LTP) is not known. In this study, we demonstrated the expression of a lncRNA cluster, namely maternally expressed gene 3 (Meg3), retrotransposon-like gene 1-anti-sense (Rtl1-AS), Meg8 and Meg9, which is located in the maternally imprinted Dlk1-Dio3 region on mouse chromosome 12qF1, in primary cortical neurons following glycine stimulation in an N-Methyl-D-aspartate receptor (NMDAR)-dependent manner...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28510129/ltr-sequence-of-the-mdg4-retrotransposon-contains-the-mad-protein-binding-site-that-affects-the-east-dependent-repression
#7
A K Golovnin, V V Molodina, I S Shapovalov, P G Georgiev, L S Melnikova
Earlier, we showed in a model system of the yellow gene of D. melanogaster that an increase in the EAST protein concentration leads to repression in bristles, the mechanism of which remained obscure. In this study, an inverted repeat was localized by genetic methods in the long terminal repeat (LTR) sequence of the MDG4 retrotransposon. This repeat includes the binding site for the Mad protein-the key component of the of TGF-β/BMP signaling cascade. The results of this work suggest that the Mad protein recruits to chromatin a regulatory complex that functionally interacts with the EAST protein...
March 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28505260/evolution-of-two-short-interspersed-elements-in-callorhinchus-milii-chondrichthyes-holocephali-and-related-elements-in-sharks-and-the-coelacanth
#8
Andrea Luchetti, Federico Plazzi, Barbara Mantovani
Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s)...
May 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28497807/a-trim-insertion-in-the-promoter-of-ms2-causes-male-sterility-in-wheat
#9
Chuan Xia, Lichao Zhang, Cheng Zou, Yongqiang Gu, Jialei Duan, Guangyao Zhao, Jiajie Wu, Yue Liu, Xiaohua Fang, Lifeng Gao, Yuannian Jiao, Jiaqiang Sun, Yinghong Pan, Xu Liu, Jizeng Jia, Xiuying Kong
The male-sterile ms2 mutant has been known for 40 years and has become extremely important in the commercial production of wheat. However, the gene responsible for this phenotype has remained unknown. Here we report the map-based cloning of the Ms2 gene. The Ms2 locus is remarkable in several ways that have implications in basic biology. Beyond having no functional annotation, barely detectable transcription in fertile wild-type wheat plants, and accumulated destructive mutations in Ms2 orthologs, the Ms2 allele in the ms2 mutant has acquired a terminal-repeat retrotransposon in miniature (TRIM) element in its promoter...
May 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28496210/the-caterpillar-fungus-ophiocordyceps-sinensis-genome-provides-insights-into-highland-adaptation-of-fungal-pathogenicity
#10
En-Hua Xia, Da-Rong Yang, Jian-Jun Jiang, Qun-Jie Zhang, Yuan Liu, Yun-Long Liu, Yun Zhang, Hai-Bin Zhang, Cong Shi, Yan Tong, Changhoon Kim, Hua Chen, Yan-Qiong Peng, Yue Yu, Wei Zhang, Evan E Eichler, Li-Zhi Gao
To understand the potential genetic basis of highland adaptation of fungal pathogenicity, we present here the ~116 Mb de novo assembled high-quality genome of Ophiocordyceps sinensis endemic to the Qinghai-Tibetan Plateau. Compared with other plain-dwelling fungi, we find about 3.4-fold inflation of the O. sinensis genome due to a rapid amplification of long terminal repeat retrotransposons that occurred ~38 million years ago in concert with the uplift of the plateau. We also observe massive removal of thousands of genes related to the transport process and energy metabolism...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28491150/dynamic-silencing-of-somatic-l1-retrotransposon-insertions-reflects-the-developmental-and-cellular-contexts-of-their-genomic-integration
#11
Manoj Kannan, Jingfeng Li, Sarah E Fritz, Kathryn E Husarek, Jonathan C Sanford, Teresa L Sullivan, Pawan Kumar Tiwary, Wenfeng An, Jef D Boeke, David E Symer
BACKGROUND: The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. RESULTS: Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28487269/the-function-of-line-1-encoded-reverse-transcriptase-in-tumorigenesis
#12
Ye Zhongjie, Liu Qipeng, Cen Shan, Li Xiaoyu
The retrotransposon LINE-1 is the largest transposon family of humans with an estimated 500 000 copies representing 17% of the human genome. Meanwhile, it is also the sole autonomous transposon in humans. The reverse transcriptase encoded by LINE-1 is the key component required for its transposition process. Recent evidence suggests that the LINE-1-encoded reverse transcriptase is involved in many important physiological and pathological processes including tumorigenesis. The inhibition of LINE-1-encoded reverse transcriptase inhibits tumor progression, restores cancer cell differentiation and reprograms global transcription profiles...
May 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28486975/evidence-for-transcriptome-wide-rna-editing-among-sus-scrofa-pre-1-sine-elements
#13
Scott A Funkhouser, Juan P Steibel, Ronald O Bates, Nancy E Raney, Darius Schenk, Catherine W Ernst
BACKGROUND: RNA editing by ADAR (adenosine deaminase acting on RNA) proteins is a form of transcriptional regulation that is widespread among humans and other primates. Based on high-throughput scans used to identify putative RNA editing sites, ADAR appears to catalyze a substantial number of adenosine to inosine transitions within repetitive regions of the primate transcriptome, thereby dramatically enhancing genetic variation beyond what is encoded in the genome. RESULTS: Here, we demonstrate the editing potential of the pig transcriptome by utilizing DNA and RNA sequence data from the same pig...
May 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28483910/rna-binding-by-the-histone-methyltransferases-set1-and-set2
#14
Camille Sayou, Gonzalo Millán-Zambrano, Helena Santos-Rosa, Elisabeth Petfalski, Samuel Robson, Jonathan Houseley, Tony Kouzarides, David Tollervey
Histone methylation at H3K4 and H3K36 is commonly associated with genes actively transcribed by RNA polymerase II (RNAPII) and is catalyzed by yeast Set1 and Set2, respectively. Here we report that both methyltransferases can be UV-crosslinked to RNA in vivo. High-throughput sequencing of the bound RNAs revealed strong Set1 enrichment near the transcription start site, whereas Set2 was distributed along pre-mRNAs. A subset of transcripts showed notably high enrichment for Set1 or Set2 binding relative to RNAPII, suggesting functional post-transcriptional interactions...
May 8, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28483779/heritable-l1-retrotransposition-in-the-mouse-primordial-germline-and-early-embryo
#15
Sandra R Richardson, Patricia Gerdes, Daniel J Gerhardt, Francisco J Sanchez-Luque, Gabriela-Oana Bodea, Martin Munoz-Lopez, J Samuel Jesuadian, Marie-Jeanne H C Kempen, Patricia E Carreira, Jeffrey A Jeddeloh, Jose L Garcia-Perez, Haig H Kazazian, Adam D Ewing, Geoffrey J Faulkner
LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of ≥1 event per 8 births...
May 8, 2017: Genome Research
https://www.readbyqxmd.com/read/28476688/ltr-retrotransposons-in-plants-engines-of-evolution
#16
REVIEW
Leonardo Galindo-González, Corinne Mhiri, Michael K Deyholos, Marie-Angèle Grandbastien
LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. Among them, Ty1-copia elements can fall close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes...
May 2, 2017: Gene
https://www.readbyqxmd.com/read/28473262/the-tea-tree-genome-provides-insights-into-tea-flavor-and-independent-evolution-of-caffeine-biosynthesis
#17
En-Hua Xia, Hai-Bin Zhang, Jun Sheng, Kui Li, Qun-Jie Zhang, Changhoon Kim, Yun Zhang, Yuan Liu, Ting Zhu, Wei Li, Hui Huang, Yan Tong, Hong Nan, Cong Shi, Chao Shi, Jian-Jun Jiang, Shu-Yan Mao, Jun-Ying Jiao, Dan Zhang, Yuan Zhao, You-Jie Zhao, Li-Ping Zhang, Yun-Long Liu, Ben-Ying Liu, Yue Yu, Sheng-Fu Shao, De-Jiang Ni, Evan E Eichler, Li-Zhi Gao
Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation...
April 29, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28471262/mtv-sings-jubilation-for-telomere-biology-in-drosophila
#18
Lin Cheng, Ming Cui, Yikang S Rong
Telomere protects the ends of linear chromosomes. Telomere dysfunction fuels genome instability that can lead to diseases such as cancer. For over 30 years, Drosophila has fascinated the field as the only major model organism that does not rely on the conserved telomerase enzyme for end protection. Instead of short DNA repeats at chromosome ends, Drosophila has domesticated retrotransposons. In addition, telomere protection can be entirely sequence-independent under normal laboratory conditions, again dissimilar to what has been established for telomerase-maintained systems...
May 4, 2017: Fly
https://www.readbyqxmd.com/read/28466841/arabidopsis-proteins-with-a-transposon-related-domain-act-in-gene-silencing
#19
Yoko Ikeda, Thierry Pélissier, Pierre Bourguet, Claude Becker, Marie-Noëlle Pouch-Pélissier, Romain Pogorelcnik, Magdalena Weingartner, Detlef Weigel, Jean-Marc Deragon, Olivier Mathieu
Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein in TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation and short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 and MAIN define an alternative silencing pathway independent of DNA methylation and short interfering RNAs. Mutants for MAIL1 or MAIN exhibit release of silencing and appear to show impaired condensation of pericentromeric heterochromatin...
May 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28465726/evolutionary-history-of-ltr-retrotransposons-among-20-drosophila-species
#20
Nicolas Bargues, Emmanuelle Lerat
BACKGROUND: The presence of transposable elements (TEs) in genomes is known to explain in part the variations of genome sizes among eukaryotes. Even among closely related species, the variation of TE amount may be striking, as for example between the two sibling species, Drosophila melanogaster and D. simulans. However, not much is known concerning the TE content and dynamics among other Drosophila species. The sequencing of several Drosophila genomes, covering the two subgenus Sophophora and Drosophila, revealed a large variation of the repeat content among these species but no much information is known concerning their precise TE content...
2017: Mobile DNA
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