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Retrotransposon

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https://www.readbyqxmd.com/read/29335544/transposon-derived-small-rnas-triggered-by-mir845-mediate-genome-dosage-response-in-arabidopsis
#1
Filipe Borges, Jean-Sébastien Parent, Frédéric van Ex, Philip Wolff, German Martínez, Claudia Köhler, Robert A Martienssen
Chromosome dosage has substantial effects on reproductive isolation and speciation in both plants and animals, but the underlying mechanisms are largely obscure 1 . Transposable elements in animals can regulate hybridity through maternal small RNA 2 , whereas small RNAs in plants have been postulated to regulate dosage response via neighboring imprinted genes3,4. Here we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of long terminal repeat (LTR) retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21-22-nucleotide (nt) small RNAs in a dose-dependent fashion via RNA polymerase IV...
January 15, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29328922/a-viral-arc-hive-for-metazoan-memory
#2
Nicholas F Parrish, Keizo Tomonaga
Arc, a master regulator of synaptic plasticity, contains sequence elements that are evolutionarily related to retrotransposon Gag genes. Two related papers in this issue of Cell show that Arc retains retroviral-like capsid-forming ability and can transmit mRNA between cells in the nervous system, a process that may be important for synaptic function.
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29328916/the-neuronal-gene-arc-encodes-a-repurposed-retrotransposon-gag-protein-that-mediates-intercellular-rna-transfer
#3
Elissa D Pastuzyn, Cameron E Day, Rachel B Kearns, Madeleine Kyrke-Smith, Andrew V Taibi, John McCormick, Nathan Yoder, David M Belnap, Simon Erlendsson, Dustin R Morado, John A G Briggs, Cédric Feschotte, Jason D Shepherd
The neuronal gene Arc is essential for long-lasting information storage in the mammalian brain, mediates various forms of synaptic plasticity, and has been implicated in neurodevelopmental disorders. However, little is known about Arc's molecular function and evolutionary origins. Here, we show that Arc self-assembles into virus-like capsids that encapsulate RNA. Endogenous Arc protein is released from neurons in extracellular vesicles that mediate the transfer of Arc mRNA into new target cells, where it can undergo activity-dependent translation...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29328915/retrovirus-like-gag-protein-arc1-binds-rna-and-traffics-across-synaptic-boutons
#4
James Ashley, Benjamin Cordy, Diandra Lucia, Lee G Fradkin, Vivian Budnik, Travis Thomson
Arc/Arg3.1 is required for synaptic plasticity and cognition, and mutations in this gene are linked to autism and schizophrenia. Arc bears a domain resembling retroviral/retrotransposon Gag-like proteins, which multimerize into a capsid that packages viral RNA. The significance of such a domain in a plasticity molecule is uncertain. Here, we report that the Drosophila Arc1 protein forms capsid-like structures that bind darc1 mRNA in neurons and is loaded into extracellular vesicles that are transferred from motorneurons to muscles...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29327725/whole-genome-sequencing-reveals-principles-of-brain-retrotransposition-in-neurodevelopmental-disorders
#5
Jasmine Jacob-Hirsch, Eran Eyal, Binyamin A Knisbacher, Jonathan Roth, Karen Cesarkas, Chen Dor, Sarit Farage-Barhom, Vered Kunik, Amos J Simon, Moran Gal, Michal Yalon, Sharon Moshitch-Moshkovitz, Rick Tearle, Shlomi Constantini, Erez Y Levanon, Ninette Amariglio, Gideon Rechavi
Neural progenitor cells undergo somatic retrotransposition events, mainly involving L1 elements, which can be potentially deleterious. Here, we analyze the whole genomes of 20 brain samples and 80 non-brain samples, and characterized the retrotransposition landscape of patients affected by a variety of neurodevelopmental disorders including Rett syndrome, tuberous sclerosis, ataxia-telangiectasia and autism. We report that the number of retrotranspositions in brain tissues is higher than that observed in non-brain samples and even higher in pathologic vs normal brains...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#6
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29321305/arabidopsis-rna-polymerase-v-mediates-enhanced-compaction-and-silencing-of-geminivirus-and-transposon-chromatin-during-host-recovery-from-infection
#7
Tami Coursey, Elizabeth Regedanz, David M Bisaro
Plants employ RNA-directed DNA methylation (RdDM) and dimethylation of histone 3 lysine 9 (H3K9me2) to silence geminiviruses and transposable elements (TEs). We previously showed that canonical RdDM (Pol IV-RdDM) involving RNA polymerases IV and V (Pol IV and Pol V) is required for Arabidopsis thaliana to recover from infection with Beet curly top virus lacking a suppressor protein that inhibits methylation (BCTV L2-). Recovery, which is characterized by reduced viral DNA levels and symptom remission, allows normal floral development...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29315404/interplay-between-rnaseh2-and-mov10-controls-line-1-retrotransposition
#8
Jongsu Choi, Sung-Yeon Hwang, Kwangseog Ahn
Long interspersed nuclear element 1 is an autonomous non-long terminal repeat retrotransposon that comprises ∼17% of the human genome. Its spontaneous retrotransposition and the accumulation of heritable L1 insertions can potentially result in genome instability and sporadic disorders. Moloney leukemia virus 10 homolog (MOV10), a putative RNA helicase, has been implicated in inhibiting L1 replication, although its underlying mechanism of action remains obscure. Moreover, the physiological relevance of MOV10-mediated L1 regulation in human disease has not yet been examined...
January 5, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29304730/genomic-abundance-and-transcriptional-activity-of-diverse-gypsy-and-copia-long-terminal-repeat-retrotransposons-in-three-wild-sunflower-species
#9
Fan Qiu, Mark C Ungerer
BACKGROUND: Long terminal repeat (LTR) retrotransposons are highly abundant in plant genomes and require transcriptional activity for their proliferative mode of replication. These sequences exist in plant genomes as diverse sublineages within the main element superfamilies (i.e., gypsy and copia). While transcriptional activity of these elements is increasingly recognized as a regular attribute of plant transcriptomes, it is currently unknown the extent to which different sublineages of these elements are transcriptionally active both within and across species...
January 5, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29301786/endogenous-line-1-long-interspersed-nuclear-element-1-reverse-transcriptase-activity-in-platelets-controls-translational-events-through-rna-dna-hybrids
#10
Hansjörg Schwertz, Jesse W Rowley, Gerald G Schumann, Ulrike Thorack, Robert A Campbell, Bhanu Kanth Manne, Guy A Zimmerman, Andrew S Weyrich, Matthew T Rondina
OBJECTIVE: One source of endogenous reverse transcriptase (eRT) activity in nucleated cells is the LINE-1/L1 (long interspersed nuclear element-1), a non-LTR retrotransposon that is implicated in the regulation of gene expression. Nevertheless, the presence and function of eRT activity and LINE-1 in human platelets, an anucleate cell, has not previously been determined. APPROACH AND RESULTS: We demonstrate that human and murine platelets possess robust eRT activity and identify the source as being LINE-1 ribonucleoprotein particles...
January 4, 2018: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/29297699/on-the-search-for-retrotransposons-alternative-protocols-to-obtain-sequences-to-learn-profile-hidden-markov-models
#11
Carlos N Fischer, Victor De A Campos, Victor H Barella
Profile hidden Markov models (pHMMs) have been used to search for transposable elements (TEs) in genomes. For the learning of pHMMs aimed to search for TEs of the retrotransposon class, the conventional protocol is to use the whole internal nucleotide portions of these elements as representative sequences. To further explore the potential of pHMMs in such a search, we propose five alternative ways to obtain the sets of representative sequences of TEs other than the conventional protocol. In this study, we are interested in Bel-PAO, Copia, Gypsy, and DIRS superfamilies from the retrotransposon class...
January 3, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29296019/extreme-haplotype-variation-in-the-desiccation-tolerant-clubmoss-selaginella-lepidophylla
#12
Robert VanBuren, Ching Man Wai, Shujun Ou, Jeremy Pardo, Doug Bryant, Ning Jiang, Todd C Mockler, Patrick Edger, Todd P Michael
Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content. Here we report the small 109 Mb genome of Selaginella lepidophylla, a clubmoss with extreme desiccation tolerance. Single-molecule sequencing enables accurate haplotype assembly of a single heterozygous S. lepidophylla plant, revealing extensive structural variation. We observe numerous haplotype-specific deletions consisting of largely repetitive and heavily methylated sequences, with enrichment in young Gypsy LTR retrotransposons...
January 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29288557/alu-element-insertion-in-pklr-gene-as-a-novel-cause-of-pyruvate-kinase-deficiency-in-middle-eastern-patients
#13
Harry Lesmana, Lisa Dyer, Xia Li, James Denton, Jenna Griffiths, Satheesh Chonat, Katie G Seu, Matthew M Heeney, Kejian Zhang, Robert J Hopkin, Theodosia A Kalfa
Pyruvate kinase deficiency (PKD) is the most frequent red blood cell enzyme abnormality of the glycolytic pathway and the most common cause of hereditary nonspherocytic hemolytic anemia. Over 250 PKLR-gene mutations have been described, including missense/nonsense, splicing and regulatory mutations, small insertions, small and gross deletions, causing PKD and hemolytic anemia of variable severity. Alu retrotransposons are the most abundant mobile DNA sequences in the human genome, contributing to almost 11% of its mass...
December 30, 2017: Human Mutation
https://www.readbyqxmd.com/read/29288153/l1-retrotransposon-antisense-rna-within-asar-lncrnas-controls-chromosome-wide-replication-timing
#14
Emily J Platt, Leslie Smith, Mathew J Thayer
Mammalian cells replicate their chromosomes via a temporal replication program. The ASAR6 and ASAR15 genes were identified as loci that when disrupted result in delayed replication and condensation of entire human chromosomes. ASAR6 and ASAR15 are monoallelically expressed long noncoding RNAs that remain associated with the chromosome from which they are transcribed. The chromosome-wide effects of ASAR6 map to the antisense strand of an L1 retrotransposon within ASAR6 RNA, deletion or inversion of which delayed replication of human chromosome 6...
December 29, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/29285312/rtl1-promotes-melanoma-proliferation-by-regulating-wnt-%C3%AE-catenin-signalling
#15
Guobiao Fan, Dan Ye, Songcheng Zhu, Jiajie Xi, Xudong Guo, Jing Qiao, Yukang Wu, Wenwen Jia, Guiying Wang, Guohuang Fan, Jiuhong Kang
Cutaneous melanoma is a highly malignant and metastatic skin cancer with high mortality. However, its underlying mechanisms remain largely unclear. Here, we found that retrotransposon-like 1 (RTL1) is highly enriched in melanoma tissue, especially in early and horizontal growth tissues. Knockdown of RTL1 in melanoma cells resulted in cell proliferation suppression; cell cycle arrest at G1 phase; and down-regulation of E2F1, CYCLIN D1, cyclin-dependent kinase 6 (CDK6) and c-MYC. Moreover, overexpression of RTL1 in melanoma cells accelerated cell proliferation, promoted passage of the cell cycle beyond G1 phase, and increased the expression of cell cycle related genes...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29278600/ovarian-cancer-prevention-screening-and-early-detection-report-from-the-11th-biennial-ovarian-cancer-research-symposium
#16
Jeremy Chien, Elizabeth M Poole
OBJECTIVE: The aim of this study is to provide a summary report on recent research advances in ovarian cancer prevention, screening, and early detection that were presented at the 11th Biennial Ovarian Cancer Research Symposium in Seattle, Wash. METHODS: At the symposium, researchers from around the world participated in the poster, invited oral presentation and keynote presentation, and discussed the latest advances in the areas of cancer prevention, screening, and early detection...
November 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/29259619/draft-sequencing-of-the-heterozygous-diploid-genome-of-satsuma-citrus-unshiu-marc-using-a-hybrid-assembly-approach
#17
Tokurou Shimizu, Yasuhiro Tanizawa, Takako Mochizuki, Hideki Nagasaki, Terutaka Yoshioka, Atsushi Toyoda, Asao Fujiyama, Eli Kaminuma, Yasukazu Nakamura
Satsuma (Citrus unshiu Marc.) is one of the most abundantly produced mandarin varieties of citrus, known for its seedless fruit production and as a breeding parent of citrus. De novo assembly of the heterozygous diploid genome of Satsuma ("Miyagawa Wase") was conducted by a hybrid assembly approach using short-read sequences, three mate-pair libraries, and a long-read sequence of PacBio by the PLATANUS assembler. The assembled sequence, with a total size of 359.7 Mb at the N50 length of 386,404 bp, consisted of 20,876 scaffolds...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29258254/recognizing-the-sines-of-infection-regulation-of-retrotransposon-expression-and-modulation-of-host-cell-processes
#18
REVIEW
William Dunker, Yang Zhao, Yu Song, John Karijolich
Short interspersed elements (SINEs) are a family of retrotransposons evolutionarily derived from cellular RNA polymerase III transcripts. Over evolutionary time, SINEs have expanded throughout the human genome and today comprise ~11% of total chromosomal DNA. While generally transcriptionally silent in healthy somatic cells, SINE expression increases during a variety of types of stresses, including DNA virus infection. The relevance of SINE expression to viral infection was largely unexplored, however, recent years have seen great progress towards defining the impact of SINE expression on viral replication and host gene expression...
December 18, 2017: Viruses
https://www.readbyqxmd.com/read/29239145/line-1-retrotransposons-in-healthy-and-diseased-human-brain
#19
REVIEW
Nicole A Suarez, Angela Macia, Alysson R Muotri
Long interspersed element-1 (LINE-1 or L1) is a transposable element with the ability to self-mobilize throughout the human genome. The L1 elements found in the human brain is hypothesized to date back 56 million years ago and has survived evolution, currently accounting for 17% of the human genome. L1 retrotransposition has been theorized to contribute to somatic mosaicism. This review focuses on the presence of L1 in the healthy and diseased human brain, such as in autism spectrum disorders (ASD). Throughout this exploration, we will discuss the impact L1 has on neurological disorders that can occur throughout the human lifetime...
December 14, 2017: Developmental Neurobiology
https://www.readbyqxmd.com/read/29234880/reorganization-of-wheat-and-rye-genomes-in-octoploid-triticale-%C3%A3-%C3%A2-triticosecale
#20
Anna Kalinka, Magdalena Achrem
The analysis of early generations of triticale showed numerous rearrangements of the genome. Complexed transformation included loss of chromosomes, t-heterochromatin content changes and the emergence of retrotransposons in new locations. This study investigated certain aspects of genomic transformations in the early generations (F5 and F8) of the primary octoploid triticale derived from the cross of hexaploid wheat with the diploid rye. Most of the plants tested were hypoploid; among eliminated chromosomes were rye chromosomes 4R and 5R and variable number of wheat chromosomes...
December 12, 2017: Planta
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