Relevant bibliographies by topics / Retroelement

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Academic literature on the topic 'Retroelement'

Author: Grafiati
Published: 4 June 2021
Last updated: 9 June 2025

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Journal articles on the topic "Retroelement"

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Mustafin, R. N. "Participation of retroelements in chromoanagenesis in cancer development." Siberian journal of oncology 23, no. 5 (November 15, 2024): 146–56. http://dx.doi.org/10.21294/1814-4861-2024-23-5-146-156.

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Purpose of the study: to determine the role of retroelements in chromoanagenesis mechanisms in cancer etiopathogenesis.Material and Methods. The search for relevant sources was carried out in the Scopus, Web of Science, PubMed, Elibrary systems, including publications from February 2002 to December 2023. Of the 864 scientifc articles found, 60 were used to write a systematic review.Results. According to original works and meta-analyses results, the cause of complex chromosomal rearrangements during cancer development may be retroelement pathological activation. Chromoanagenesis involves LINE1, SVA, Alu, HERV, which cause double-stranded DNA breaks, insertions in tumor suppressor genes region, the formation of chimeric oncogenes due to retroelement use as new promoters, and function as molecular “band-aids” in non-homologous end junctions and form bridges of distal DNA fragments. Global structural rearrangements of chromosomes observed during chromoanagenesis may be consequences of retroelements activation, which participate in non-allelic homologous recombination and in microhomology-mediated joining of ends characteristic. Certain types of neoplasms, such as colon cancer, are characterized by both high levels of chromothripsis and retroelement activity. In head and neck squamous cell carcinoma, chromoplexy is specifc, the sources of sequences at the breakpoints of which are retroelements. During chromoanagenesis, activation of proto-oncogenes and inactivation of tumor suppressor genes are observed, which is also a consequence of retroelement activation. This is due to the presence of retroelement sequences in proto-oncogenes promoter regions and introns (which become the basis for chimeric oncogene formation) and hot spots of insertional mutagenesis in tumor suppressor genes (transpositions into these regions inactivate these genes).Conclusion. The results obtained on the driver effect of retroelements in chromothripsis, chromoplexy and chromoanasynthesis mechanisms, which are the basis for the formation of clonal evolution of tumors, indicate promise of targeted therapy aimed at silencing the activity of retroelements in cancer patients treatment. For this purpose, it is possible to use microRNAs complementary to retroelements, which are also involved in tumor development, as tools.
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Honda, Tomoyuki, Keiko Takemoto, and Keiji Ueda. "Identification of a Retroelement-Containing Human Transcript Induced in the Nucleus by Vaccination." International Journal of Molecular Sciences 20, no. 12 (June 13, 2019): 2875. http://dx.doi.org/10.3390/ijms20122875.

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Endogenous retroelements constitute almost half of the mammalian genome. Given that more than 60% of human genomic bases are transcribed, transcripts containing these retroelements may impact various biological processes. However, the physiological roles of most retroelement-containing transcripts are yet to be revealed. Here, we profiled the expression of retroelement-containing human transcripts during vaccination and found that vaccination upregulated transcripts containing only particular retroelements, such as the MLT-int element of endogenous retroviruses. MLT-int-containing transcripts were distributed mainly in the nucleus, suggesting their unique roles in the nucleus. Furthermore, we demonstrated that MLT-int RNA suppressed interferon promoter activity in the absence of immune stimuli. Based on these lines of evidence, we speculate a model of a role of the previously unnoticed MLT-int element in preventing excess innate immune activation after elimination of immune stimuli. Our results may emphasize the importance of retroelement-containing transcripts in maintaining host immune homeostasis.
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Springer, Mark S., Erin K. Molloy, Daniel B. Sloan, Mark P. Simmons, and John Gatesy. "ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets." Journal of Heredity 111, no. 2 (December 14, 2019): 147–68. http://dx.doi.org/10.1093/jhered/esz076.

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Abstract DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroelement insertions satisfy the “no intralocus-recombination” assumption of summary coalescent methods because they are singular events and better approximate neutrality relative to DNA loci commonly sampled in phylogenomic studies. Retroelements have traditionally been analyzed with parsimony, distance, and network methods. Here, we analyze retroelement data sets for vertebrate clades (Placentalia, Laurasiatheria, Balaenopteroidea, Palaeognathae) with 2 ILS-aware methods that operate by extracting, weighting, and then assembling unrooted quartets into a species tree. The first approach constructs a species tree from retroelement bipartitions with ASTRAL, and the second method is based on split-decomposition with parsimony. We also develop a Quartet-Asymmetry test to detect hybridization using retroelements. Both ILS-aware methods recovered the same species-tree topology for each data set. The ASTRAL species trees for Laurasiatheria have consecutive short branch lengths in the anomaly zone whereas Palaeognathae is outside of this zone. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both ILS-aware methods resolved balaeonopterids as paraphyletic. Application of the Quartet-Asymmetry test to this data set detected 19 different quartets of species for which historical introgression may be inferred. Evidence for introgression was not detected in the other data sets.
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Carotti, Elisa, Edith Tittarelli, Adriana Canapa, Maria Assunta Biscotti, Federica Carducci, and Marco Barucca. "LTR Retroelements and Bird Adaptation to Arid Environments." International Journal of Molecular Sciences 24, no. 7 (March 28, 2023): 6332. http://dx.doi.org/10.3390/ijms24076332.

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TEs are known to be among the main drivers in genome evolution, leading to the generation of evolutionary advantages that favor the success of organisms. The aim of this work was to investigate the TE landscape in bird genomes to look for a possible relationship between the amount of specific TE types and environmental changes that characterized the Oligocene era in Australia. Therefore, the mobilome of 29 bird species, belonging to a total of 11 orders, was analyzed. Our results confirmed that LINE retroelements are not predominant in all species of this evolutionary lineage and highlighted an LTR retroelement dominance in species with an Australian-related evolutionary history. The bird LTR retroelement expansion might have happened in response to the Earth’s dramatic climate changes that occurred about 30 Mya, followed by a progressive aridification across most of Australian landmasses. Therefore, in birds, LTR retroelement burst might have represented an evolutionary advantage in the adaptation to arid/drought environments.
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Murata, Hitoshi, and Akiyoshi Yamada. "marY1, a Member of the gypsyGroup of Long Terminal Repeat Retroelements from the Ectomycorrhizal Basidiomycete Tricholoma matsutake." Applied and Environmental Microbiology 66, no. 8 (August 1, 2000): 3642–45. http://dx.doi.org/10.1128/aem.66.8.3642-3645.2000.

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ABSTRACT We cloned an intact copy of a long terminal repeat retroelement designated marY1 from the ectomycorrhizal basidiomyceteTricholoma matsutake. The reverse transcriptase domain is found in T. matsutake and Tricholoma magnivelare worldwide. This finding suggests that retroelements associate with ectomycorrhizal basidiomycetes and may be useful as genetic markers for identification, phylogenetic analysis, and mutagenesis of this fungal group.
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Chung, Kevin, Ling Xu, Pengxin Chai, Junhui Peng, Swapnil C. Devarkar, and Anna Marie Pyle. "Structures of a mobile intron retroelement poised to attack its structured DNA target." Science 378, no. 6620 (November 11, 2022): 627–34. http://dx.doi.org/10.1126/science.abq2844.

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Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam the genome, integrating by reversal of forward splicing. Here we show that retrotransposition is achieved by a tertiary complex between a structurally elaborate ribozyme, its protein mobility factor, and a structured DNA substrate. We solved cryo–electron microscopy structures of an intact group IIC intron-maturase retroelement that was poised for integration into a DNA stem-loop motif. By visualizing the RNP before and after DNA targeting, we show that it is primed for attack and fits perfectly with its DNA target. This study reveals design principles of a prototypical retroelement and reinforces the hypothesis that group II introns are ancient elements of genetic diversification.
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Ishak, Charles A., and Daniel D. De Carvalho. "Reactivation of Endogenous Retroelements in Cancer Development and Therapy." Annual Review of Cancer Biology 4, no. 1 (March 9, 2020): 159–76. http://dx.doi.org/10.1146/annurev-cancerbio-030419-033525.

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Domesticated retroelements contribute extensively as regulatory elements within host gene networks. Upon germline integration, retroelement mobilization is restricted through epigenetic silencing, mutational degradation, and innate immune defenses described as the viral mimicry response. Recent discoveries reveal how early events in tumorigenesis reactivate retroelements to facilitate onco-exaptation, replication stress, retrotransposition, mitotic errors, and sterile inflammation, which collectively disrupt genome integrity. The characterization of altered epigenetic homeostasis at retroelements in cancer cells also reveals new epigenetic targets whose inactivation can bolster responses to cancer therapies. Recent discoveries reviewed here frame reactivated retroelements as both drivers of tumorigenesis and therapy responses, where their reactivation by emerging epigenetic therapies can potentiate immune checkpoint blockade, cancer vaccines, and other standard therapies.
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Mota, Ines Frutuoso, Jaspreet Osean, Eric Song, Cristina C. Clement, Jack Lenz, Danny E. Miller, Giorgio Inghirami, et al. "Characterization of the HLA-F ligandome in T-cell lymphoma." Journal of Immunology 210, no. 1_Supplement (May 1, 2023): 222.06. http://dx.doi.org/10.4049/jimmunol.210.supp.222.06.

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Abstract Identifying tumor-specific antigens across different types of malignancies and HLA haplotypes remains challenging. Recently, the expression of tumor-specific Human Endogenous Retroelements emerged as a potential new class of cytotoxic T-cell response mediators (1). HLA-F, a non-classic HLA-I molecule, has been hypothesized to present peptides to T-cells and to regulate immunity through interactions with distinct NK-cell receptors (2). HLA-F low genetic diversity and limited peptide repertoire represent an unexplored avenue in cancer immunotherapy. HLA-F-bound peptides were eluted from five patient-derived T-cell lymphoma cell lines and total T-cells purified from ten healthy donor PBMCs; Retroelement peptides were identified in the HLA-F ligandome. To quantify and validate their expression, RNA-sequencing data from the same samples were screened using ERVmap database (3). Lastly, to characterize their expression, we incorporate genome-wide characterization of DNA methylation patterns. We identified a set of retroelement peptides bound to HLA-F shared by patient-derived T-cell lymphoma cell lines but not total T-cells isolated from healthy donor PBMCs, suggesting a potential role of HLA-F in cancer-immune responses. Among those we characterized four tumor-specific retroelement peptides, validated by the presence of their RNA transcripts as well as by DNA integration and chromosomal location. Tumor-specific HLA-F-bound retroelement peptides hold great promise for the discovery of previously unknown tumor-specific markers and therapeutic targets. More importantly, the characterization of their immunogenicity may yield insights broadly applicable to a greater number of patients due to HLA-F monomorphism.
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Lee, Gloria, Nicholas A. Sherer, Neil H. Kim, Ema Rajic, Davneet Kaur, Niko Urriola, K. Michael Martini, Chi Xue, Nigel Goldenfeld, and Thomas E. Kuhlman. "Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell." Proceedings of the National Academy of Sciences 115, no. 49 (November 19, 2018): 12465–70. http://dx.doi.org/10.1073/pnas.1807709115.

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Phylogenetic evidence suggests that the invasion and proliferation of retroelements, selfish mobile genetic elements that copy and paste themselves within a host genome, was one of the early evolutionary events in the emergence of eukaryotes. Here we test the effects of this event by determining the pressures retroelements exert on simple genomes. We transferred two retroelements, human LINE-1 and the bacterial group II intron Ll.LtrB, into bacteria, and find that both are functional and detrimental to growth. We find, surprisingly, that retroelement lethality and proliferation are enhanced by the ability to perform eukaryotic-like nonhomologous end-joining (NHEJ) DNA repair. We show that the only stable evolutionary consequence in simple cells is maintenance of retroelements in low numbers, suggesting how retrotransposition rates and costs in early eukaryotes could have been constrained to allow proliferation. Our results suggest that the interplay between NHEJ and retroelements may have played a fundamental and previously unappreciated role in facilitating the proliferation of retroelements, elements of which became the ancestors of the spliceosome components in eukaryotes.
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Furini, Antonella. "CDT retroelement." Plant Signaling & Behavior 3, no. 12 (December 2008): 1129–31. http://dx.doi.org/10.4161/psb.3.12.7076.

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Dissertations / Theses on the topic "Retroelement"

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Thomson, Gabrielle Anne Biotechnology &amp Biomolecular Sciences Faculty of Science UNSW. "Retroelements as controlling elements in mammals." Awarded by:University of New South Wales. Biotechnology and Biomolecular Sciences, 2006. http://handle.unsw.edu.au/1959.4/26203.

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Retroelements are genomic parasites which make up ~42% of the human genome and 38% of the mouse genome. Most are degenerate, but a large number have relatively intact promoter elements, suggesting that they are capable of transcription. Transcriptionally active retroelements can perturb normal transcription units in their vicinity through a variety of mechanisms, leading to phenotypic effects and in some cases disease. This phenomenon of transcriptional interference has been observed in organisms as diverse as maize, Drosophila, and the mouse. We analysed the extent of retroelement transcription in normal and diseased tissues, by searching the mouse and human EST databases for transcripts originating in retroelement promoters, and found a large number of transcripts from LINEs, SINEs and ERVs. Retroelement transcripts were found to be initiated in both sense and antisense orientations, and to be equally as common in normal and diseased tissue. Several of these transcripts were chimeric, appearing to initiate in retroelements and reading through to cellular genes, suggestive of transcriptional interference. We have used transposon display to identify and recover retroelement transcripts in the mouse. Transcripts initiated in LINE, SINE and ERV promoters are numerous, and many are chimeric with cellular genes. Although the numbers of recovered chimeric transcripts are too large to permit rigorous analysis of more than a small proportion, some of those we have studied further appear to be authentic transcripts that may represent interference with the canonical promoters of the genes in question. Our results suggest that transcriptional interference by retroelements may be a relatively common occurrence in mammals.
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ORICCHIO, ELISA. "I retroelementi nella tumorigenesi: ruoli distinti di LINE-1 ed HERV-K nella progressione tumorale." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2008. http://hdl.handle.net/2108/399.

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I retroelementi sono sequenze altamente ripetute disperse nel genoma, che codificano per una Trascrittasi Inversa (RT). Cellule e tessuti caratterizzati da una elevata capacità di proliferazione e un basso grado di differenziamento (come cellule tumorali o embrionali) esprimono alti livelli di RT che al contrario è scarsamente espressa in tessuti terminalmente differenziati. E’ noto da precedenti studi condotti nel nostro laboratorio che il trattamento di diverse linee cellulari tumorali con due inibitori non nucleosidici della RT, la nevirapina ed l’efavirenz, induce una riduzione della proliferazione e della tumorigenicità in in vitro e d in vivo e ne promuove il differenziamento (Mangiacasale et al., 2003; Sciamanna et al., 2005; per una review Sinibaldi- Vallebona et al., 2006). In questo lavoro ho dimostrato che gli inibitori della RT, inibiscono la proliferazione solo delle cellule tumorali mentre non hanno alcun effetto significativo sulle cellule normali. Inoltre, utilizzando la tecnica dellRNA interference (RNAi) ho identificato due famiglie di retroelementi, LINE-1 e HERV-K, che hanno ruoli diversi nella tumorigenesi. Infettando cellule di melanoma A375 con vettori retrovirali adeguatamente ingegnerizzati allo scopo, ho prodotto due linee cellulari in cui l’espressione di questi due retroelementi sia stabilmente interferita. Le cellule interferite per il LINE-1 hanno una ridotta proliferazione, una morfologia alterata ed un’espressione alterata di alcuni geni che regolano la proliferazione e il differenziamento. Al contrario, le cellule A375 interferite per HERV-K non mostrano nessun cambiamento in vitro. A differenza di quanto osservato in vitro, entrambe le linee cellulari inoculate in topi nudi atimici hanno una ridotta tumorigenicità rispetto alle cellule della linea parentale. Infine, allo scopo di sviluppare una possibile terapia genica differenziativa dei tumori, ho sviluppato un sistema di vettori adenovirali in sostituzione di quelli retro virali; i primi infatti offrono una serie di vantaggi rispetto ai vettori retrovirali, primo fra tutti il fatto che queste le sequenze rimangono in forma episomale consentendo quindi di ripetere l’infezione diverse volte allo scopo di migliorarne l’efficienza.<br>Retroelements are sequences highly repeated present in all eucaryotic genomes and they encode for a RT that is expressed at high levels in cells and tissue types characterized by a high proliferative potential and a low degree of differentiation (e.g. embryonic tissues and tumor cells), whereas low RT levels are generally found in terminally differentiated, non pathological tissue. Previous studies have showed that inhibition of endogenous RT, using pharmacological inhibitors, (nevirapine and efavirenz) reduces proliferation and promotes differentiation of human tumorigenic cell lines and strongly antagonizes tumor progression in murine models (Mangiacasaele et al., 2003 Sciamanna et al., 2005; reviewed by Sinibaldi-Vallebona et al., 2006). In this work I have showed that the RT inhibitors, in contrast to what observed in tumorigenic cells, does not exert any effect on normal cells. In addition, I using a RNA interference approach (RNAi), I assessed the different roles of two retroelements LINE-1 and HERV-K in tumorigenesis and tumor progression. Using retroviral vectors, I produced two cell lines, derived from A375 melanoma cells, stably interfered for the expression of these elements. The cells in which LINE-1 expression was interfered exhibit a reduced proliferation and significant changes in morphology, suggestive of that a differentiation was activated. Moreover, these cells showed a reduced tumorigenecity when injected in nude mice. Instead, cells in which HERV-K expression was interfered the rate of proliferation and differentiation remain unchanged compared to the parental A375 cells. However, in vivo essays their tumorigenic potential was found to be reduced. Finally, aiming at the development of a novel gene therapy approach for cancer differentiation I developed an adenoviral delivery system which offers several advantages compared to retroviruses, most important the fact that adenodelivered sequences remain as non-integrated episomes and the infection can be repeated several times to improve the efficiency of infection.
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Lightbourn, Gordon James. "Development of intermonoploid somatic hybrids of potato and their molecular analysis based on polymorphism for retroelement Tst1." Diss., Virginia Tech, 2004. http://hdl.handle.net/10919/28810.

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Inbred lines for hybrid crop production have been a mainstay of plant breeding. Biotechnological approaches to hasten the process are available including anther culture to halve the genome and protoplast fusion to create hybrids between incompatible partners. We applied these techniques to potato to evaluate their potential for breeding highly heterozygous, cross-pollinating species. Four families of monoploids (2n=1x=12), developed from diploid hybrids with diverse genomic constitutions but heavily favoring Solanum phureja, a primitive cultivated potato, were used in electrofusion experiments to create intermonoploid somatic hybrids (SH). The "monoploid sieve" results in the survival of only those gametes free of lethal and deleterious genes but generates sterile sporophytes, necessitating protoplast fusion for SH development. From six intermonoploid electrofusion combinations, 276 plants were regenerated over 6-9 months. Fusion conditions were optimized. Ploidy was determined by flow-cytometry and SH confirmed by microsatellite analysis. Field evaluations over three years revealed that intermonoploid SH were inferior to cultivars. Dihaploids derived by anther culture of a tetraploid intermonoploid SH were reduced in vigor with an increase in homozygosity, while 2x X 2x sexually derived populations had better yield than the SH, suggesting that producing SH introduced or eliminated factors required for productivity. Molecular analysis of the SH was conducted to examine genomic stability through protoplast isolation and plant regeneration. Sequence specific amplified polymorphism (S-SAP) represents a hybrid system incorporating amplified fragment length polymorphism (AFLP) technology in conjunction with the use of a defined genomic sequence, e.g., retrotransposon display (RD) when the defined sequence is anchored into a consensus sequence of a retrotransposon such as the long terminal repeat (LTR) sequence of Tst1. Parental monoploids, SH and various Solanaceae were evaluated by RD. Fluorescently-labeled retrotransposon-based primers were used in the ALFexpress automated fragment analyzer system. Eleven probes from RD were created for Southern blot analysis and used to verify taxonomic relationships between selected Solanaceae. Blots of intermonoploid somatic hybrids confirmed hybridity and occasional loss of genomic fragments. No activation or replication of retrotransposons was detected. Sequencing of inter-retrotransposon amplified polymorphism (IRAP) and S-SAP fragments revealed that all fragments had the expected Tst1 retroelement and/or the AFLP adaptor sequence. BLAST analysis identified 4 of the 17 fragments sequenced as part of the chloroplast genome, a tobacco anther-specific gene, repetitive DNA, and the phytochrome F gene.<br>Ph. D.
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Meyn, Malcolm Anthony 1967. "A genetic, biochemical, and population analysis of MGL, a non-LTR retroelement from the plant pathogenic fungus Magnaporthe grisea." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/288755.

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This dissertation describes the characterization of a novel transposable element isolated from the plant pathogenic fungus Magnaporthe grisea. The sequence of MGR583, a previously reported repeated DNA fragment, was completed and shown to have features characteristic of non-LTR retroelements (LINEs). These include an element length of 5.9 kb, the lack of flanking long terminal repeats, the presence of short (6-13 bp) direct repeats flanking many element copies, and two principal open reading frames (ORFs). The first ORF is 570 amino acids in length and contains homology to the gag ORFs found in many retroelements. The second ORF is 1,295 amino acids in length and has strong homology to reverse transcriptases (RT) ORFs found in non-LTR retroelements (LINEs). In accordance with these results, the name of the repeat was changed to MGL for Magnaporthe grisea LINE. Analysis of the 3' terminus of MGL showed 90% homology to the 3' terminus of Mg-SINE, suggesting an evolutionary relationship between these two elements. A survey of the distribution of MGL in populations of M. grisea showed the element to be present in all isolates tested. Copy number was not uniform between isolates, with approximately fifty copies present in rice isolates and between less than 10 and up to 50 copies in the 17 non-rice isolates tested. A PCR-based assay was designed and used to screen M. grisea isolates for polymorphic MGL insertion loci. Thirteen polymorphic MGL insertions were scored and used to construct a phylogenetic tree that included 11 non-rice isolates and 20 rice isolates. The results strongly suggested that development of virulence on rice was a single event correlated with the acquisition of virulence on several other grass species. In addition, the observation that rearrangements occurred at one of the insertion loci in some rice isolate strains support the proposal that there is considerable plasticity in the genomes of these isolates. Finally, a yeast transposon ( Tyl) system was used to express and test the second ORF for RT activity. No activity was detected for any of the MGL RT constructs tested.
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Volkmann, Bianca [Verfasser], Thomas [Akademischer Betreuer] Gramberg, Andreas [Gutachter] Burkovski, and Andreas [Gutachter] Burkovski. "The role of TRIM proteins in retrovirus and retroelement restriction / Bianca Volkmann ; Gutachter: Andreas Burkovski, Andreas Burkovski ; Betreuer: Thomas Gramberg." Erlangen : Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2020. http://d-nb.info/1216332967/34.

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Adhya, Indranil. "Exhaustive Identification of the retroelement Ty1 Integrase partners in yeast Saccharomyces cerevisiae : characterization of the role of Casein kinase II in Ty1 retrotransposition in vivo." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS589.

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Les rétrotransposons LTR sont des éléments transposables très répandus chez les eucaryotes. Comme les rétrovirus, ils se répliquent par transcription inverse de leur ARN en ADNc, qui est intégré dans le génome hôte par leur propre intégrase (IN). Des études de séquençage à haut débit ont clairement établi que l'intégration ne se fait pas de façon aléatoire dans l'ensemble du génome de la cellule hôte. Des connaissances approfondies sur la biologie rétrovirale ont été acquises grâce à leur étude sur la levure utilisant le Ty1 LTR-retrotransposon comme modèle de travail. Le rétrotransposon Ty1 de la levure Saccharomyces cerevisiae intègre en amont des gènes de classe III, les gènes transcrits par l'ARN polymérase III (Pol III). Des données récentes ont révélé l'importance de l'AC40, une sous-unité de Pol III dans ce ciblage. Une interaction entre le Ty1 IN et l'AC40 est nécessaire pour le choix du site d'intégration des gènes Pol III. Néanmoins, le mécanisme moléculaire reste largement inconnu. Afin d'obtenir une vision globale de l'ensemble du phénomène qui se produit sur le site d'intégration, nous aimerions déterminer de manière exhaustive les protéines qui interagissent avec Ty1 IN et analyser leur rôle dans l'intégration de Ty1 et la transcription de l'ARN Pol III. Pour atteindre cet objectif, nous avons développé des approches protéomiques pour identifier de nouveaux partenaires cellulaires Ty1 intégraux. Nous avons identifié plusieurs nouveaux partenaires Ty1 IN qui semblent intéressants et leur rôle moléculaire dans la rétrotransposition de Ty1 sera étudié. Cependant, dans le cadre de mon doctorat, j'ai particulièrement travaillé à déchiffrer le rôle moléculaire de la protéine caséine kinase II dans la rétrotransposition de Ty1<br>LTR-retrotransposons are widespread transposable elements in eukaryotes. Like retroviruses, they replicate by reverse transcription of their RNA into cDNA, which is integrated into the host genome by their own integrase (IN). High-throughput sequencing studies clearly established that integration does not occur randomly throughout the host-cell genome. Deep insights on retroviral biology have been gained by their study in yeast using the Ty1 LTR-retrotransposon as a working model. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream of class III genes, the genes transcribed by RNA polymerase III (Pol III). Recent data revealed the importance of AC40, a Pol III subunit in this targeting. An interaction between the Ty1 IN and AC40 is necessary for integration site choice at the Pol III genes. Nevertheless, the molecular mechanism remains largely unknown. To obtain a global view of the entire phenomenon that occurs on the integration site we would like to exhaustively determine the proteins that interact with Ty1 IN and analyze their role in both Ty1 integration and RNA Pol III transcription. To achieve this goal, we have developed proteomic approaches to identify new Ty1 integrase cellular partners. We have identified several novel Ty1 IN partners that seem interesting and their molecular role in Ty1 retrotransposition will be studied. However, in the tenure of my PhD, I have particularly worked to decipher the molecular role of the casein kinase II protein in Ty1 retrotransposition
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Hodes, Asher Benjamin. "Diversity-generating retroelements." Diss., Restricted to subscribing institutions, 2009. http://proquest.umi.com/pqdweb?did=1835260431&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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Nottensteiner, Mathias [Verfasser], Ralph [Akademischer Betreuer] [Gutachter] Hückelhoven, Erich J. [Gutachter] Glawischnig, and Aurélien [Gutachter] Tellier. "Molecular Characterization of Retroelement Encoded ROPIP1 as Virulence Effector of Blumeria graminis f.sp. hordei / Mathias Nottensteiner ; Gutachter: Erich J. Glawischnig, Aurélien Tellier, Ralph Hückelhoven ; Betreuer: Ralph Hückelhoven." München : Universitätsbibliothek der TU München, 2015. http://d-nb.info/112273834X/34.

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Wilson, Williamina. "Ribosomal frameshifting in retroelements." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670301.

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Mu, Sen. "Detection of Bacterial Retroelements Using Genomics." Digital Commons @ East Tennessee State University, 2013. https://dc.etsu.edu/etd/1110.

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The reverse flow of genetic information can occur when a special DNA polymerase called Reverse Transcriptase (RT) copies the genetic information in an RNA molecule back into a complementary DNA. One type of RT encoding gene found in bacteria is called a retron element. Recent bacterial genome sequencing projects have revealed many examples of retron RT genes. This gene assignment is based on comparison with a few known retron RT proteins. However, RT proteins are highly diverse in their amino acid sequences, and thus the assigned identity of these RT proteins as retrons in genome databases is questionable. One way to prove that these postulated RTs are indeed from retron elements is to see if they can produce msDNA. Retron RTs are known to synthesize a structurally unique satellite DNA called msDNA in the bacterial cells that contain them. Based on GenBank database matches to a known protein, 7 proteins designated as retron RTs were tested for their ability to synthesize msDNA. Five of these retron RTs did show evidence of producing msDNA and are from very different bacterial hosts. The other 2 RT proteins did not show any evidence that they produce msDNA.
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Books on the topic "Retroelement"

1

Yves, Christen, and SpringerLink (Online service), eds. Retrotransposition, Diversity and the Brain. Berlin, Heidelberg: Springer-Verlag, 2008.

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Brindley, Paul J. Mobile genetic elements in metazoan parasites. Austin, Tex: Landes Bioscience, 2009.

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Koito, Atsushi, and Yukihito Ishizaka, eds. Retroviruses, retroelements and their restrictions. Frontiers SA Media, 2015. http://dx.doi.org/10.3389/978-2-88919-401-8.

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Lochmüller, Hanns. Beiträge zur Charakterisierung eines neuen Retroelements (Ty4) aus der Hefe Saccharomyces cerevisiae. 1991.

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Mobile genetic elements in metazoan parasites. Austin, Tex: Landes Bioscience, 2009.

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Book chapters on the topic "Retroelement"

1

Refsland, Eric W., and Reuben S. Harris. "The APOBEC3 Family of Retroelement Restriction Factors." In Current Topics in Microbiology and Immunology, 1–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-37765-5_1.

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Chalopin, Domitille, Marta Tomaszkiewicz, Delphine Galiana, and Jean-Nicolas Volff. "LTR Retroelement-Derived Protein-Coding Genes and Vertebrate Evolution." In Viruses: Essential Agents of Life, 269–82. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4899-6_13.

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Fujii, Yoichi Robertus. "The RNA Gene Information: Retroelement-MicroRNA Entangling as the RNA Quantum Code." In MicroRNA Protocols, 47–67. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-083-0_4.

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Garfinkel, David J. "Retroelements in Microorganisms." In The Retroviridae, 107–58. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4615-3372-6_4.

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Hull, Roger, and Simon N. Covey. "Retroelements: Propagation and Adaptation." In Molecular Evolution of Viruses — Past and Present, 33–46. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4613-1407-3_4.

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Leib-Mösch, Christine, and Wolfgang Seifarth. "Evolution and Biological Significance of Human Retroelements." In Molecular Evolution of Viruses — Past and Present, 61–73. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4613-1407-3_6.

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Richert-Pöggeler, Katja R., and Trude Schwarzacher. "Impact of Retroelements in Shaping the Petunia Genome." In Petunia, 343–63. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-84796-2_16.

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Guo, Huatao, Li Arambula, Partho Ghosh, and Jeff F. Miller. "Diversity-generating Retroelements in Phage and Bacterial Genomes." In Mobile DNA III, 1237–52. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555819217.ch53.

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Brosius, Jürgen. "Genomes were forged by massive bombardments with retroelements and retrosequences." In Transposable Elements and Genome Evolution, 209–38. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4156-7_23.

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Román, Ángel Carlos, Antonio Morales-Hernández, and Pedro M. Fernández-Salguero. "RNA-Seq Analysis to Measure the Expression of SINE Retroelements." In Methods in Molecular Biology, 107–16. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3372-3_7.

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Conference papers on the topic "Retroelement"

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Panina, E. A., I. V. Babkin, V. A. Fedorets, and N. V. Tikunova. "ANALYSIS OF PHAGE DGR CASSETTES ON THE BASIS OF THE EXAMPLE OF PHAGE LMMB." In XI МЕЖДУНАРОДНАЯ КОНФЕРЕНЦИЯ МОЛОДЫХ УЧЕНЫХ: БИОИНФОРМАТИКОВ, БИОТЕХНОЛОГОВ, БИОФИЗИКОВ, ВИРУСОЛОГОВ, МОЛЕКУЛЯРНЫХ БИОЛОГОВ И СПЕЦИАЛИСТОВ ФУНДАМЕНТАЛЬНОЙ МЕДИЦИНЫ. IPC NSU, 2024. https://doi.org/10.25205/978-5-4437-1691-6-265.

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DGR cassettes are Diversity Generating Retroelements (DGRs), a recently discovered class of retroelements that utilize reverse transcription to generate a huge number of sequence variants in specific target genes. In the Laboratory of Molecular Microbiology of ICBFM SB RAS, a new crAss-like genome containing a diversity-generating retroelement was discovered during the study of a sample of human virome.
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Cooles, Faye, Gemma Vidal Pedrola, Amy Anderson, Najib Naamane, Andrew Skelton, Arthur Pratt, Catharien Hilkens, Ruchi Shukla, and John Isaacs. "AB0024 WHOLE BLOOD ENDOGENOUS RETROELEMENT ACTIVITY ASSOCIATES WITH ANTI-CCP TITRES IN EARLY DRUG NAïVE RA AND IS PREFERENTIALLY INCREASED IN CD5+ AND NAïVE B CELLS." In Annual European Congress of Rheumatology, EULAR 2019, Madrid, 12–15 June 2019. BMJ Publishing Group Ltd and European League Against Rheumatism, 2019. http://dx.doi.org/10.1136/annrheumdis-2019-eular.2980.

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Solovyova, A. I., A. A. Ponomaryova, E. Yu Rykova, A. S. Tarasova, D. N. Kostromitsky, A. Yu Dobrodeev, S. A. Afanasiev та N. V. Cherdyntseva. "СIRCULATING DNA-MARKERS FOR PROGNOSIS AND PREDICTION OF ANTITUMOR THERAPY IN COLORECTAL CANCER". У X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-374.

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Colorectal cancer (CRC) is one of the frequent malignant diseases worldwide. The analysis of epigenetic factors contributed to the CRC development is needed for improvement of diagnostic and therapeutic strategies. “Liquid biopsy” seems to be an adequate approach to detect changes associated with cancer. This study devoted to investigation of methylation of LINE-1 retroelements and SEPTIN9, IKZF1 genes in blood cirDNA from CRC patients before and after treatment.
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Leonova, Katerina, Brittany Lipchick, Leonid Brodsky, Elena Komarova, and Andrei V. Gudkov. "Abstract 2959: p53 as a guardian of genomic junk: A novel role for p53 in epigenetic silencing of retroelements." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-2959.

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Mavragani, Clio, Kyriakos Kirou, Adrianos Nezos, Surya V. Seshan, Teresa Wild, Sharon M. Wahl, Haralampos M. Moutsopoulos, and Mary K. Crow. "THU0228 EXPRESSION OF APOBEC FAMILY MEMBERS AS REGULATORS OF ENDOGENOUS RETROELEMENTS AND MALIGNANCY IN SYSTEMIC LUPUS ERYTHEMATOSUS AND SJÖGREN’S SYNDROME." In Annual European Congress of Rheumatology, EULAR 2019, Madrid, 12–15 June 2019. BMJ Publishing Group Ltd and European League Against Rheumatism, 2019. http://dx.doi.org/10.1136/annrheumdis-2019-eular.6152.

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Mavragani, Clio P., Irina Sagalovskiy, Qiu Guo, Adrianos Nezos, Efstathia K. Kapsogeorgou, Pin Lu, Jun Liang Zhou, et al. "I-06 Long interspersed nuclear element-1 retroelements are expressed in patients with systemic lupus erythematosus and primary SJOGREN’S syndrome and induce type I interferon." In Abstracts of the Third Biannual Scientific Meeting of the North and South American Lupus Community, Armonk, New York, USA, September 29 – October 1, 2016. Lupus Foundation of America, 2016. http://dx.doi.org/10.1136/lupus-2016-000179.71.

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Reports on the topic "Retroelement"

1

Belancio, Victoria P., and Prescott L. Deininger. Retroelements and Genetic Instability in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, April 2005. http://dx.doi.org/10.21236/ada436906.

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Perepelitsa, Victoria P. Retroelements and Genetic Instability in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, April 2003. http://dx.doi.org/10.21236/ada424037.

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Belancio, Victoria P., and Prescott L. Deininger. Retroelements and Genetic Instability in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, April 2004. http://dx.doi.org/10.21236/ada425722.

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Avihingsanon, Yingyos, Jongkonnee Wongpiyabovorn, and Nattiya Hirankarn. Biomarker discovery in systemic lupus erythematosus: genome-methylation approaches : Research report. Chulalongkorn University, 2010. https://doi.org/10.58837/chula.res.2010.15.

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Discovery of novel biomarkers in lupus nephritis Biomarkers are needed for making diagnosis and prognosis. In lupus nephritis, conventional tests like urinalysis or serum creatinine remain inadequate for patient care. In this proposal, we focused on non-invasive tools like blood and urine mRNAs or proteins. We chose candidate genes involving regulatory T-cell, B-lymphocyte signatures or vascular protective factors. Expression of regulatory cell signature (FOXP3) in peripheral blood mononuclear cells is associated with activity of lupus nephritis. We found FOXP3 mRNA levels in PBMCs from patients with active lupus nephritis were significantly lower than inactive lupus nephritis. Expression levels of FOXP3 mRNA were associated with pathological activity index, cellular crescent and fibrinoid necrosis. BLyS and APRIL are B-lymphocyte related cytokines that play an important role in generating and maintaining the mature B-cell pool. In this study, we found blood APRIL correlated with activity of lupus nephritis. Blood APRIL levels could precisely predict failure of standard treatment treatment. APRIL is a potential biomarker for predicting treatment failure. Lastly, we found an expression of VEGF in renal tissue may serve as a molecular marker of renal damage from LN and may be a predictive factor for short-term loss of kidney function in lupus nephritis patients. We proposed that reduction of intra-renal VEGF level caused by losses of podocyte cells. Genetic polymorphism of drug toxicity or pharmacokinetics in SLE patients We began to explore the pharmacokinetics and pharmacogenomics of two important immunosuppressants, azathioprine and mycophenolate. In this study, we report TPMT polymorphisms and TPMT enzyme activity were important predictors of AZA-induced myelosuppression. The tests are available for routine care. Mycophenolic acid (MPA) is active metabolite of mycophenalate. We found MPA levels is important predictor of therapeutic response. The therapeutic drug monitoring is now an important issue of patient care. We found UGT1A9 polymorphism may play a pivotal role in drug metabolisms. Methylation study We examined and compared the methylation levels of long terminal repeats (LTRs) and non-LTR retroelements in normal and SLE CD4+ T lymphocytes, CD8+ T lymphocytes and B lymphocytes. Hypomethylation of LINE-1 but not Alu was found in CD4+ T lymphocytes, CD8+ T lymphocytes, and B lymphocytes of SLE patient. Moreover, when the SLE patients were divided into active and inactive groups, LINE-1 hypomethylation was more significantly distinguished in both CD4+ and CD8+ T lymphocytes of patients from the active SLE group when compared to the controls. Genome-wide scanning using SNP microarrays In this study, we applied case-control association study including pooling genome wide association (GWA) and candidate gene association studies to search for SNPs associated with SLE susceptibility and/or severity. We could not identify any SNPs with distinct p-value or odds ratio from our pooling GWA result due to limited power. We selected IFIX for further study in candidate gene’s part. Besides IFIX, we also focus on MNDA, IFI16 and AIM2 genes which located in the same region and are all IFN-inducible genes. They are important SLE susceptibility genes due to several reasons including 1) genetic mapping from lupus murine model and 2) an upregulated IFN-inducible genes in patients with SLE from microarray studies and 3) IFI16 was identified as new autoantigen for patients with SLE. We genotyped 10 SNPs from these 4 genes and found that SNP within IFIX and IFI16 are independently important.
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