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Retrotransposon

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https://www.readbyqxmd.com/read/28212378/sequencing-the-extrachromosomal-circular-mobilome-reveals-retrotransposon-activity-in-plants
#1
Sophie Lanciano, Marie-Christine Carpentier, Christel Llauro, Edouard Jobet, Dagmara Robakowska-Hyzorek, Eric Lasserre, Alain Ghesquière, Olivier Panaud, Marie Mirouze
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28209295/aluternative-regulation-for-gene-expression
#2
REVIEW
Ling-Ling Chen, Li Yang
Alu elements belong to the primate-specific SINE family of retrotransposons and constitute almost 11% of the human genome. Alus are transcribed by RNA polymerase (Pol) III and are inserted back into the genome with the help of autonomous LINE retroelements. Since Alu elements are preferentially located near to or within gene-rich regions, they can affect gene expression by distinct mechanisms of action at both DNA and RNA levels. In this review we focus on recent advances of how Alu elements are pervasively involved in gene regulation...
February 10, 2017: Trends in Cell Biology
https://www.readbyqxmd.com/read/28188449/xylitol-production-by-genetically-modified-industrial-strain-of-saccharomyces-cerevisiae-using-glycerol-as-co-substrate
#3
Anushree B Kogje, Anand Ghosalkar
Xylitol is commercially used in chewing gum and dental care products as a low calorie sweetener having medicinal properties. Industrial yeast strain of S. cerevisiae was genetically modified to overexpress an endogenous aldose reductase gene GRE3 and a xylose transporter gene SUT1 for the production of xylitol. The recombinant strain (XP-RTK) carried the expression cassettes of both the genes and the G418 resistance marker cassette KanMX integrated into the genome of S. cerevisiae. Short segments from the 5' and 3' delta regions of the Ty1 retrotransposons were used as homology regions for integration of the cassettes...
February 10, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28188229/the-human-long-interspersed-element-1-retrotransposon-an-emerging-biomarker-of-neoplasia
#4
REVIEW
Daniel Ardeljan, Martin S Taylor, David T Ting, Kathleen H Burns
BACKGROUND: A large portion of intronic and intergenic space in our genome consists of repeated sequences. One of the most prevalent is the long interspersed element-1 (LINE-1, L1) mobile DNA. LINE-1 is rightly receiving increasing interest as a cancer biomarker. CONTENT: Intact LINE-1 elements are self-propagating. They code for RNA and proteins that function to make more copies of the genomic element. Our current understanding is that this process is repressed in most normal cells, but that LINE-1 expression is a hallmark of many types of malignancy...
February 10, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28187749/identification-of-a-large-intronic-transposal-insertion-in-slc17a5-causing-sialic-acid-storage-disease
#5
Maja Tarailo-Graovac, Britt I Drögemöller, Wyeth W Wasserman, Colin J D Ross, Ans M W van den Ouweland, Niklas Darin, Gittan Kollberg, Clara D M van Karnebeek, Maria Blomqvist
BACKGROUND: Sialic acid storage diseases are neurodegenerative disorders characterized by accumulation of sialic acid in the lysosome. These disorders are caused by mutations in SLC17A5, the gene encoding sialin, a sialic acid transporter located in the lysosomal membrane. The most common form of sialic acid storage disease is the slowly progressive Salla disease, presenting with hypotonia, ataxia, epilepsy, nystagmus and findings of cerebral and cerebellar atrophy. Hypomyelination and corpus callosum hypoplasia are typical as well...
February 10, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28186206/unbiased-k-mer-analysis-reveals-changes-in-copy-number-of-highly-repetitive-sequences-during-maize-domestication-and-improvement
#6
Sanzhen Liu, Jun Zheng, Pierre Migeon, Jie Ren, Ying Hu, Cheng He, Hongjun Liu, Junjie Fu, Frank F White, Christopher Toomajian, Guoying Wang
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28174588/eare-1-a-transcriptionally-active-ty1-copia-like-retrotransposon-has-colonized-the-genome-of-excoecaria-agallocha-through-horizontal-transfer
#7
Jianhua Huang, Yushuai Wang, Wenwen Liu, Xu Shen, Qiang Fan, Shuguang Jian, Tian Tang
Long terminal repeat (LTR) retrotransposons constitute the majority of the content of angiosperm genomes, but their evolutionary dynamics remain poorly understood. Here, we report the isolation and characterization of a putative full-length (~9550 bp) Ty1/copia-like retrotransposon in Excoecaria agallocha and its evolution in Euphorbiaceae. The so-called EARE-1 is phylogenetically closely related to RIRE-1 from Oryza australiensis, and has proliferated recently (~7.19 Mya) in the E. agallocha genome. An RT-PCR analysis revealed substantial transcription of EARE-1 in all examined organs (leaves, staminate flowers, pistillate flowers, seeds, and roots) in unstressed E...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28168328/patterns-of-evolutionary-trajectories-and-domestication-history-within-the-genus-hordeum-assessed-by-remap-markers
#8
Georgi Bonchev, Roman Dusinský, Pavol Hauptvogel, Miroslav Švec
The patterns of genetic diversity related to the taxonomy and domestication history of 85 accessions representing the main four species of the genus Hordeum were examined by retrotransposon-microsatellite amplified polymorphism (REMAP) markers based on the retrotransposon BARE-1. A substantial level of genetic polymorphisms at among- and within-species level was observed showing that this retrotransposon family and its adjacent genomic regions has been a target for genome dynamics during the evolution and domestication of barley...
February 6, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28166262/l1-retrotransposon-expression-in-circulating-tumor-cells
#9
Ioannis Papasotiriou, Katerina Pantopikou, Panagiotis Apostolou
Long interspersed nuclear element 1 (LINE-1 or L1) belongs to the non-long terminal repeat (non-LTR) retrotransposon family, which has been implicated in carcinogenesis and disease progression. Circulating tumor cells (CTCs) are also known to be involved in cancer progression. The present study aimed to compare the L1 expression between circulating tumor cells and non-cancerous samples. Blood samples were collected from 10 healthy individuals and 22 patients with different types of cancer. The whole blood cells were isolated using enrichment protocols and the DNA and RNA were extracted...
2017: PloS One
https://www.readbyqxmd.com/read/28165867/hypermethylated-ltr-retrotransposon-exhibits-enhancer-activity
#10
Tianxiang Hu, Xingguo Zhu, Wenhu Pi, Miao Yu, Huidong Shi, Dorothy Tuan
LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. They are silenced by hypermethylation of cytosines in CpG dinucleotides and are considered parasitic DNA serving no useful function for the host genome. However, hypermethylated LTRs contain enhancer and promoter sequences and can promote tissue-specific transcription of cis-linked genes. To resolve the apparent paradox of hypermethylated LTRs possessing transcriptional activities, we studied the ERV-9 LTR retrotransposon located at the 5' border of the transcriptionally active β-globin gene locus in human erythroid progenitor and erythroleukemia K562 cells...
February 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28165062/hybridogenesis-and-a-potential-case-of-r2-non-ltr-retrotransposon-horizontal-transmission-in-bacillus-stick-insects-insecta-phasmida
#11
Claudia Scavariello, Andrea Luchetti, Francesco Martoni, Livia Bonandin, Barbara Mantovani
Horizontal transfer (HT) is an event in which the genetic material is transferred from one species to another, even if distantly related, and it has been demonstrated as a possible essential part of the lifecycle of transposable elements (TEs). However, previous studies on the non-LTR R2 retrotransposon, a metazoan-wide distributed element, indicated its vertical transmission since the Radiata-Bilateria split. Here we present the first possible instances of R2 HT in stick insects of the genus Bacillus (Phasmida)...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28164239/massive-expansion-of-gypsy-like-retrotransposons-in-microbotryum-fungi
#12
Felix Horns, Elsa Petit, Michael E Hood
No abstract text is available yet for this article.
February 2, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28139237/retrotransposon-expression-and-incorporation-of-cloned-human-and-mouse-retroelements-in-human-spermatozoa
#13
Leandros Lazaros, Chrysoula Kitsou, Charilaos Kostoulas, Sofia Bellou, Elissavet Hatzi, Paris Ladias, Theodoros Stefos, Sofia Markoula, Vasiliki Galani, Georgios Vartholomatos, Theodore Tzavaras, Ioannis Georgiou
OBJECTIVE: To investigate the expression of long interspersed element (LINE) 1, human endogenous retrovirus (HERV) K10, and short interspersed element-VNTR-Alu element (SVA) retrotransposons in ejaculated human spermatozoa by means of reverse-transcription (RT) polymerase chain reaction (PCR) analysis as well as the potential incorporation of cloned human and mouse active retroelements in human sperm cell genome. DESIGN: Laboratory study. SETTING: University research laboratories and academic hospital...
January 27, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28134931/g-quadruplex-structures-within-the-3-utr-of-line-1-elements-stimulate-retrotransposition
#14
Aleksandr B Sahakyan, Pierre Murat, Clemens Mayer, Shankar Balasubramanian
Long interspersed nuclear elements (LINEs) are ubiquitous transposable elements in higher eukaryotes that have a significant role in shaping genomes, owing to their abundance. Here we report that guanine-rich sequences in the 3' untranslated regions (UTRs) of hominoid-specific LINE-1 elements are coupled with retrotransposon speciation and contribute to retrotransposition through the formation of G-quadruplex (G4) structures. We demonstrate that stabilization of the G4 motif of a human-specific LINE-1 element by small-molecule ligands stimulates retrotransposition...
January 30, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28134354/isolation-and-characterization-of-centromeric-repetitive-dna-sequences-in-saccharum-spontaneum
#15
Wenpan Zhang, Sheng Zuo, Zhanjie Li, Zhuang Meng, Jinlei Han, Junqi Song, Yong-Bao Pan, Kai Wang
Sugarcane (Saccharum hybrids spp.) is the most important sugar crop that accounts for ~75% of the world's sugar production. Recently, a whole-genome sequencing project was launched on the wild species S. spontaneum. To obtain information on the DNA composition of the repeat-enriched region of the centromere, we conducted a genome-wide analysis of the DNA sequences associated with CenH3 (a mutant of histone H3 located in eukaryote centromeres) using chromatin immunoprecipitation followed by sequencing (ChIP-seq) method...
January 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28132025/long-non-coding-rnas-transcribed-by-erv-9-ltr-retrotransposon-act-in-cis-to-modulate-long-range-ltr-enhancer-function
#16
Tianxiang Hu, Wenhu Pi, Xingguo Zhu, Miao Yu, Hongseok Ha, Huidong Shi, Jeong-Hyeon Choi, Dorothy Tuan
LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. However, LTR sequences are disproportionately present in human long, non-coding RNAs (lncRNAs). Whether and how the LTR lncRNAs serve biological functions are largely unknown. Here we show that in primary human erythroblasts, lncRNAs transcribed from the LTR retrotransposons of ERV-9 human endogenous retrovirus activated transcription of key erythroid genes and modulated ex vivo erythropoiesis. To dissect the functional mechanism of ERV-9 lncRNAs, we performed genome-wide RNA and ChIRP analyses before and after global knockdown or locus-specific deletion of ERV-9 lncRNAs in human erythroblasts carrying ∼4000 copies of the ERV-9 LTRs and in transgenic mouse erythroblasts carrying a single copy of the primate-specific ERV-9 LTR in the 100 kb human β-globin gene locus...
January 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28127581/dataset-for-distribution-of-sider2-elements-in-the-leishmania-major-genome-and-transcriptome
#17
Jose M Requena, Alberto Rastrojo, Esther Garde, Manuel C López, M Carmen Thomas, Begoña Aguado
This paper contains data related to the research article entitled "Genomic cartography and proposal of nomenclature for the repeated, interspersed elements of the Leishmania major SIDER2 family and identification of SIDER2-containing transcripts" [1]. SIDER2 elements are repeated sequences, derived from, nowadays, extinct retrotransposons, that populate the genomes of protist of the genera Leishmania. This dataset (Supplementary file 1), an inventory of 1100 SIDER2 elements, was generated by surveying the L...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28115634/roles-of-miwi-mili-and-pld6-in-small-rna-regulation-in-mouse-growing-oocytes
#18
Yuka Kabayama, Hidehiro Toh, Ami Katanaya, Takayuki Sakurai, Shinichiro Chuma, Satomi Kuramochi-Miyagawa, Yumiko Saga, Toru Nakano, Hiroyuki Sasaki
The mouse PIWI-interacting RNA (piRNA) pathway produces a class of 26-30-nucleotide (nt) small RNAs and is essential for spermatogenesis and retrotransposon repression. In oocytes, however, its regulation and function are poorly understood. In the present study, we investigated the consequences of loss of piRNA-pathway components in growing oocytes. When MILI (or PIWIL2), a PIWI family member, was depleted by gene knockout, almost all piRNAs disappeared. This severe loss of piRNA was accompanied by an increase in transcripts derived from specific retrotransposons, especially IAPs...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28111885/severe-damage-to-the-placental-fetal-capillary-network-causes-mid-to-late-fetal-lethality-and-reduction-in-placental-size-in-peg11-rtl1-ko-mice
#19
Moe Kitazawa, Masaru Tamura, Tomoko Kaneko-Ishino, Fumitoshi Ishino
Paternally expressed 11/Retrotransposon-like 1 (Peg11/Rtl1) knockout (KO) mice show mid- to late fetal lethality or late fetal growth retardation associated with frequent neonatal lethality. The lethal phenotype is largely dependent on genetic background and becomes more severe with each succeeding generation in the course of backcross experiments to C57BL/6 (B6). We previously suggested that these lethal and growth phenotypes in the fetal stages were due to severe defects in placental fetal capillaries in the labyrinth layer...
January 23, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28110755/the-phylogeny-of-placental-evolution-through-dynamic-integrations-of-retrotransposons
#20
K Imakawa, S Nakagawa
Trophoblasts, a major constituent of the placenta, are known to express genes derived from various endogenous retroviruses (ERVs) as well as LTR retrotransposons. However, the evolutionary significance of ERV-derived genes involved in placental development has not been well characterized. In this review, we catalog the diverse morphology of placental structure among mammalian species with note of counterintuitive developments. We then detail the history of ancient placenta development with paternally expressed gene 10 (Peg10/Sirh1), Peg11/Sirh2, and Sirh7/Ldoc1 as LTR retrotransposons, followed by independent captures of ERV-env-related genes such as Syncytin-1, -2, -A, -B, -Rum1, and Fematrin-1 responsible for trophoblast cell fusion, resulting in multinucleate syncytiotrophoblast formation, and possibly morphological diversification of placentas...
2017: Progress in Molecular Biology and Translational Science
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