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Journal articles on the topic 'Retroelement'

Author: Grafiati

Published: 4 June 2021

Last updated: 21 February 2023

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1

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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2

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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3

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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4

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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5

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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6

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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7

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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8

Leblanc, Pascal, Bernard Dastugue, and Chantal Vaury. "The Integration Machinery of ZAM, a Retroelement from Drosophila melanogaster, Acts as a Sequence-Specific Endonuclease." Journal of Virology 73, no. 8 (August 1, 1999): 7061–64. http://dx.doi.org/10.1128/jvi.73.8.7061-7064.1999.

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ABSTRACT Retroviruses and retrotransposons insert into the host genome with no obvious sequence specificity. We examined the target sites of the retroelement ZAM by sequencing each host-ZAM junction in the genome ofDrosophila melanogaster. Our overall data provide compelling evidence that ZAM integration machinery recognizes and leads to ZAM insertion into the sequence 5′-GCGCGCg-3′. This unique property of ZAM will facilitate the development of new tools to study the integration process of retroelements.

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9

Fukuda, Kei, and Yoichi Shinkai. "SETDB1-Mediated Silencing of Retroelements." Viruses 12, no. 6 (May 30, 2020): 596. http://dx.doi.org/10.3390/v12060596.

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SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) is a protein lysine methyltransferase and methylates histone H3 at lysine 9 (H3K9). Among other H3K9 methyltransferases, SETDB1 and SETDB1-mediated H3K9 trimethylation (H3K9me3) play pivotal roles for silencing of endogenous and exogenous retroelements, thus contributing to genome stability against retroelement transposition. Furthermore, SETDB1 is highly upregulated in various tumor cells. In this article, we describe recent advances about how SETDB1 activity is regulated, how SETDB1 represses various types of retroelements such as L1 and class I, II, and III endogenous retroviruses (ERVs) in concert with other epigenetic factors such as KAP1 and the HUSH complex and how SETDB1-mediated H3K9 methylation can be maintained during replication.

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10

Buchatskyi, L. P. "Endogenous retroelemens of fish and molluscs." Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv 18, no. 1-2 (January 29, 2021): 34–43. http://dx.doi.org/10.7124/visnyk.utgis.18.1-2.1353.

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Aim. Analysis of scientific literature sources devoted to the study of retroelements of fish and mollusks. Results. It is shown that endogenous retroelements are widespread both among fish and mollusks. Endogenous retroviruses of fish, like exogenous ones, are also widespread, but their total number in the genomes of fish is much less than in other vertebrates. The Steamer retroelement, the presence of which is associated with the development of tumors in molluscs, can be transmitted horizontally between these invertebrates. In addition, it is able to pass into organisms of other types of aquatic animals, including vertebrates, sea urchins and corals. Conclusions. The study of the retroelements of fish and molluscs, as the most ancient organisms, makes it possible to more fully trace the stages of evolution of aquatic animals. It was shown that retroelements of fish and molluscs play an important role in the development of antiviral defense in vertebrates. The low cost of mollusks and well-developed methods of their cultivation put these invertebrates at the forefront as model systems for studying the molecular mechanisms of tumor processes in vertebrates and humans.Keywords: retroelements, fish, molluscs, tumors.

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11

Dosay-Akbulut, Mine. "Intron and Its Splicing Mechanism and Their Connection with Human Disease." Bangladesh Journal of Medical Science 15, no. 3 (November 3, 2016): 307–12. http://dx.doi.org/10.3329/bjms.v15i3.24527.

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In the maturation mechanism of a messenger RNA, splicing play an important role with removing the noncoding introns and ligating the coding exons. Alternative splicing (AS) gives an extra difficulty to this mechanism and to the regulation of gene expression. The possible disturbing in the alternative RNA splicing mechanism can be a reason to several diseases like cancers and neurodegenerative disorders. Intronless genes (IGs) are seen in almost 3% of the human genome. Functionality of IGs has an important role in signal transduction genes and related regulatory proteins. This diversity can be reason to IG-associated diseases, especially neuropathies, developmental disorders, and cancer. The retroelements can be seen in almost half of the human genome. The known informations indicate that insertion of retroelement into exons and introns of genes promote different types of genetic disease, including cancer. The retroelement connected mutagenesis cause to fifty different types of human disease. The molecular informations and bioinformatic analyses can be used to explain the connection with splicing mutations and genetic mechanisms of several different human disease and understanding of this mechanism play an important role in the formation of treatment programme against to these diseases.Bangladesh Journal of Medical Science Vol.15(3) 2016 p.307-312

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12

Chiu, Ya-Lin, and Warner C. Greene. "APOBEC3G: an intracellular centurion." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1517 (November 13, 2008): 689–703. http://dx.doi.org/10.1098/rstb.2008.0193.

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The intrinsic antiretroviral factor APOBEC3G (A3G) is highly active against HIV-1 and other retroviruses. In different cell types, A3G is expressed in high-molecular-mass (HMM) RNA–protein complexes or low-molecular-mass (LMM) forms displaying different biological activities. In resting CD4 T cells, a LMM form of A3G potently restricts HIV-1 infection soon after virion entry. However, when T cells are activated, LMM A3G is recruited into HMM complexes that include Staufen-containing RNA granules. These complexes are probably nucleated by the induced expression of Alu/hY retroelement RNAs that accompany T-cell activation. HMM A3G sequesters these retroelement RNAs away from the nuclear long interspersed nuclear element-derived enzymes required for Alu/hY retrotransposition. Human immunodeficiency virus (HIV) exploits this ‘window of opportunity’ provided by the loss of LMM A3G in activated CD4 T cells to productively infect these cells. During HIV virion formation, newly synthesized LMM A3G is preferentially encapsidated but only under conditions where Vif is absent and thus not able to target A3G for proteasome-mediated degradation. Together, these findings highlight the discrete functions of the different forms of A3G. LMM A3G opposes the external threat posed by exogenous retroviruses, while HMM A3G complexes oppose the internal threat posed by the retrotransposition of select types of retroelements.

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13

Löber, Ulrike, Matthew Hobbs, Anisha Dayaram, Kyriakos Tsangaras, Kiersten Jones, David E. Alquezar-Planas, Yasuko Ishida, et al. "Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion." Proceedings of the National Academy of Sciences 115, no. 34 (August 6, 2018): 8609–14. http://dx.doi.org/10.1073/pnas.1807598115.

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Endogenous retroviruses (ERVs) are proviral sequences that result from colonization of the host germ line by exogenous retroviruses. The majority of ERVs represent defective retroviral copies. However, for most ERVs, endogenization occurred millions of years ago, obscuring the stages by which ERVs become defective and the changes in both virus and host important to the process. The koala retrovirus, KoRV, only recently began invading the germ line of the koala (Phascolarctos cinereus), permitting analysis of retroviral endogenization on a prospective basis. Here, we report that recombination with host genomic elements disrupts retroviruses during the earliest stages of germ-line invasion. One type of recombinant, designated recKoRV1, was formed by recombination of KoRV with an older degraded retroelement. Many genomic copies of recKoRV1 were detected across koalas. The prevalence of recKoRV1 was higher in northern than in southern Australian koalas, as is the case for KoRV, with differences in recKoRV1 prevalence, but not KoRV prevalence, between inland and coastal New South Wales. At least 15 additional different recombination events between KoRV and the older endogenous retroelement generated distinct recKoRVs with different geographic distributions. All of the identified recombinant viruses appear to have arisen independently and have highly disrupted ORFs, which suggests that recombination with existing degraded endogenous retroelements may be a means by which replication-competent ERVs that enter the germ line are degraded.

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14

Levin, H. L. "A novel mechanism of self-primed reverse transcription defines a new family of retroelements." Molecular and Cellular Biology 15, no. 6 (June 1995): 3310–17. http://dx.doi.org/10.1128/mcb.15.6.3310.

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Retroviruses and long terminal repeat (LTR)-containing retrotransposons initiate reverse transcription by using a specific tRNA primer than anneals to the primer-binding site of the retroelement transcript. Sequences from a large number of retroviruses and LTR-containing retrotransposons had indicated that the role of tRNAs in priming reverse transcription is universal among these LTR-containing retroelements. Data presented here strongly support the surprising conclusion that Tf1, a highly active LTR-containing retrotransposon isolated from Schizosaccharomyces pombe, undergoes a novel self-priming process that requires hybridization between the primer-binding site and the first 11 bases of the Tf1 transcript. Single-base mutations in these regions block transposition and reverse transcription, while compensatory mutations that reestablish complementarily rescue both defects. In addition, the sequence of the minus-strand RNA primer of reverse transcription was consistent with its being derived from the 5' end of the Tf1 transcript. Evidence that this mechanism defines a new family of retroelements is presented.

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15

Nikitin, Daniil, Andrew Garazha, Maxim Sorokin, Dmitry Penzar, Victor Tkachev, Alexander Markov, Nurshat Gaifullin, Pieter Borger, Alexander Poltorak, and Anton Buzdin. "Correction: Nikitin, D., et al. Retroelement—Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution. Cells 2019, 8, 130." Cells 8, no. 8 (August 5, 2019): 832. http://dx.doi.org/10.3390/cells8080832.

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In the article ‘Retroelement—Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution,’ a number of transcription factor binding sites (TFBS) mapped on all retroelement classes were incorrectly calculated as sum of TFBS numbers separately mapped on LINEs, SINEs and LTR retrotransposons/endogenous retroviruses (LR/ERVs) [...]

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16

Mroczek, Rebecca J., and R. Kelly Dawe. "Distribution of Retroelements in Centromeres and Neocentromeres of Maize." Genetics 165, no. 2 (October 1, 2003): 809–19. http://dx.doi.org/10.1093/genetics/165.2.809.

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AbstractFluorescent in situ hybridization was used to examine the distribution of six abundant long terminal repeat (LTR) retroelements, Opie, Huck, Cinful-1, Prem-2/Ji, Grande, and Tekay/Prem-1 on maize pachytene chromosomes. Retroelement staining in euchromatin was remarkably uniform, even when we included the structurally polymorphic abnormal chromosome 10 (Ab10) in our analysis. This uniformity made it possible to use euchromatin as a control for quantitative staining intensity measurements in other regions of the genome. The data show that knobs, known to function as facultative neocentromeres when Ab10 is present, tend to exclude retroelements. A notable exception is Cinful-1, which accumulates in TR-1 knob arrays. Staining for each of the six retroelements was also substantially reduced in centromeric satellite arrays to an average of 30% of the staining in euchromatin. This contrasted with two previously described centromere-specific retrotransposable (CR) elements that were readily detected in centromeres. We suggest that retroelements are relatively rare in centromeres because they interrupt the long satellite arrays thought to be required for efficient centromere function. CR elements may have evolved mutualistic relationships with their plant hosts: they are known to interact with the kinetochore protein CENH3 and appear to accumulate in clusters, leaving long satellite arrays intact.

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17

Lim, Ai Khim, Liheng Tao, and Toshie Kai. "piRNAs mediate posttranscriptional retroelement silencing and localization to pi-bodies in the Drosophila germline." Journal of Cell Biology 186, no. 3 (August 3, 2009): 333–42. http://dx.doi.org/10.1083/jcb.200904063.

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Nuage, a well-conserved perinuclear organelle found in germline cells, is thought to mediate retroelement repression in Drosophila melanogaster by regulating the production of Piwi-interacting RNAs (piRNAs). In this study, we present evidence that the nuage–piRNA pathway components can be found in cytoplasmic foci that also contain retroelement transcripts, antisense piRNAs, and proteins involved in messenger RNA (mRNA) degradation. These mRNA degradation proteins, decapping protein 1/2 (DCP1/2), Me31B (maternal expression at 31B), and pacman (PCM), are normally thought of as components of processing bodies. In spindle-E (spn-E) and aubergine (aub) mutants that lack piRNA production, piRNA pathway proteins no longer overlap the mRNA degradation proteins. Concomitantly, spn-E and aub mutant ovaries show an accumulation of full-length retroelement transcripts and prolonged stabilization of HeT-A mRNA, supporting the role of piRNAs in mediating posttranscriptional retroelement silencing. HeT-A mRNA is derepressed in mRNA degradation mutants twin, dcp1, and ski3, indicating that these enzymes also aid in removing full-length transcripts and/or decay intermediates.

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18

Shimamoto, Tadashi, Mihoko Kobayashi, Tomofusa Tsuchiya, Sumio Shinoda, Hideyuki Kawakami, Sumiko Inouye, and Masayori Inouye. "A retroelement in Vibrio cholerae." Molecular Microbiology 34, no. 3 (November 1999): 631–32. http://dx.doi.org/10.1046/j.1365-2958.1999.01531.x.

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19

Kingsman, Alan J., and Susan M. Kingsman. "Ty: A retroelement moving forward." Cell 53, no. 3 (May 1988): 333–35. http://dx.doi.org/10.1016/0092-8674(88)90151-1.

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20

Lamb, Jonathan C., and James A. Birchler. "Retroelement Genome Painting: Cytological Visualization of Retroelement Expansions in the Genera Zea and Tripsacum." Genetics 173, no. 2 (April 2, 2006): 1007–21. http://dx.doi.org/10.1534/genetics.105.053165.

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21

Cheng, Zhi-Jun, and Minoru Murata. "A Centromeric Tandem Repeat Family Originating From a Part of Ty3/gypsy-Retroelement in Wheat and Its Relatives." Genetics 164, no. 2 (June 1, 2003): 665–72. http://dx.doi.org/10.1093/genetics/164.2.665.

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AbstractFrom a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that ∼250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity (∼53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

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22

Jiang, Di. "Hitching a ride with a retroelement." Science 373, no. 6557 (August 19, 2021): 866.3–866. http://dx.doi.org/10.1126/science.373.6557.866-c.

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23

Perlman, P. S. "MOLECULAR BIOLOGY: Ring Around the Retroelement." Science 303, no. 5655 (January 9, 2004): 182–84. http://dx.doi.org/10.1126/science.1093514.

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Simon, Anna J., Barrett R. Morrow, and Andrew D. Ellington. "Retroelement-Based Genome Editing and Evolution." ACS Synthetic Biology 7, no. 11 (September 26, 2018): 2600–2611. http://dx.doi.org/10.1021/acssynbio.8b00273.

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25

Lee, Ja-Rang, and Heui-Soo Kim. "Radiation-induced retroelement-mediated genomic instability." Biotechnology and Bioprocess Engineering 17, no. 3 (June 2012): 439–45. http://dx.doi.org/10.1007/s12257-012-0008-3.

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Becker, Kristina, Marlen Braune, Natalya Benderska, Emanuele Buratti, Francisco Baralle, Carmen Villmann, Stefan Stamm, Volker Eulenburg, and Cord-Michael Becker. "A Retroelement Modifies Pre-mRNA Splicing." Journal of Biological Chemistry 287, no. 37 (July 10, 2012): 31185–94. http://dx.doi.org/10.1074/jbc.m112.375691.

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dos Santos Costa, Maria, Hallana Cristina Menezes da Silva, Simone Cardoso Soares, Ramon Marin Favarato, Eliana Feldberg, Ana Lúcia Silva Gomes, Roberto Ferreira Artoni, and Daniele Aparecida Matoso. "A Perspective of Molecular Cytogenomics, Toxicology, and Epigenetics for the Increase of Heterochromatic Regions and Retrotransposable Elements in Tambaqui (Colossoma macropomum) Exposed to the Parasiticide Trichlorfon." Animals 12, no. 15 (July 31, 2022): 1945. http://dx.doi.org/10.3390/ani12151945.

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Rex retroelements are the best-known transposable elements class and are broadly distributed through fish and also individual genomes, playing an important role in their evolutionary dynamics. Several agents can stress these elements; among them, there are some parasitic compounds such as the organochlorophosphate Trichlorfon. Consequently, knowing that the organochlorophosphate Trichlorfon is indiscriminately used as an antiparasitic in aquaculture, the current study aimed to analyze the effects of this compound on the activation of the Transposable Elements (TEs) Rex1, Rex3, and Rex6 and the structure of heterochromatin in the mitotic chromosomes of the tambaqui (Colossoma macropomum). For this, two concentrations of the pesticide were used: 30% (0.261 mg/L) and 50% (0.435 mg/L) of the recommended LC50–96 h concentration (0.87 mg/L) for this fish species. The results revealed a dispersed distribution for Rex1 and Rex6 retroelements. Rex3 showed an increase in both marking intensity and distribution, as well as enhanced chromosomal heterochromatinization. This probably happened by the mediation of epigenetic adaptive mechanisms, causing the retroelement mobilization to be repressed. However, this behavior was most evident when Trichlorfon concentrations and exposure times were the greatest, reflecting the genetic flexibility necessary for this species to successfully adapt to environmental changes.

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Cloutier, Alison, Timothy B. Sackton, Phil Grayson, Michele Clamp, Allan J. Baker, and Scott V. Edwards. "Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone." Systematic Biology 68, no. 6 (April 23, 2019): 937–55. http://dx.doi.org/10.1093/sysbio/syz019.

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Abstract Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

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Ustyugova, Svetlana V., Anna L. Amosova, Yuri B. Lebedev, and Eugene D. Sverdlov. "Cell line fingerprinting using retroelement insertion polymorphism." BioTechniques 38, no. 4 (April 2005): 561–65. http://dx.doi.org/10.2144/05384st02.

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Brennan, Michael T., and Jean-Luc C. Mougeot. "Alu retroelement-associated autoimmunity in Sjögren's syndrome." Oral Diseases 22, no. 5 (March 10, 2016): 345–47. http://dx.doi.org/10.1111/odi.12462.

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P�lissier, T., S. Tutois, J. M. Deragon, S. Tourmente, S. Genestier, and G. Picard. "Athila, a new retroelement from Arabidopsis thaliana." Plant Molecular Biology 29, no. 3 (November 1995): 441–52. http://dx.doi.org/10.1007/bf00020976.

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Staplin, William R., and Joseph A. Knezetic. "BVL-1–like VL30 promoter sustains long-term expression in erythroid progenitor cells." Blood 101, no. 5 (March 1, 2003): 1798–800. http://dx.doi.org/10.1182/blood-2002-07-2105.

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Congenital blood disorders are common and yet clinically challenging globin disorders. Gene therapy continues to serve as a potential therapeutic method to treat these disorders. While tremendous advances have been made in vivo, gene delivery protocols and vector prototypes still require optimization. Alternativecis-acting promoter elements derived from VL30 retroelements have been effective in expressing tissue-specific transgene expression in vivo in nonerythroid cells. VL30 promoter elements were isolated from ELM-I-1 erythroid progenitor cells upon erythropoietin (epo) treatment. These promoters were inserted into a VL30-derived expression vector and reintroduced into the ELM-I-1 cells. β-Galactosidase reporter gene activity from the ELM 5 clone, a BVL-1–like VL30 promoter, was capable of expressing sustained levels of the transgene expression over a 16-week assay period. These findings delineate the potential utility of these retroelement promoters as transcriptionally active, erythroid-specific, long terminal repeat (LTR) components for current globin vector constructs.

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Cohen, Carla J., Rita Rebollo, Sonja Babovic, Elizabeth L. Dai, Wendy P. Robinson, and Dixie L. Mager. "Placenta-specific Expression of the Interleukin-2 (IL-2) Receptor β Subunit from an Endogenous Retroviral Promoter." Journal of Biological Chemistry 286, no. 41 (August 24, 2011): 35543–52. http://dx.doi.org/10.1074/jbc.m111.227637.

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The long terminal repeat (LTR) sequences of endogenous retroviruses and retroelements contain promoter elements and are known to form chimeric transcripts with nearby cellular genes. Here we show that an LTR of the THE1D retroelement family has been domesticated as an alternative promoter of human IL2RB, the gene encoding the β subunit of the IL-2 receptor. The LTR promoter confers expression specifically in the placental trophoblast as opposed to its native transcription in the hematopoietic system. Rather than sequence-specific determinants, DNA methylation was found to regulate transcription initiation and splicing efficiency in a tissue-specific manner. Furthermore, we detected the cytoplasmic signaling domain of the IL-2Rβ protein in the placenta, suggesting that IL-2Rβ undergoes preferential proteolytic cleavage in this tissue. These findings implicate novel functions for this cytokine receptor subunit in the villous trophoblast and reveal an intriguing example of ancient LTR exaptation to drive tissue-specific gene expression.

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Das, Rasel, Tadashi Shimamoto, and Md Arifuzzaman. "A Novel msDNA (Multicopy Single-Stranded DNA) Strain Present inYersinia frederikseniiATCC 33641 Contig01029 Enteropathogenic Bacteria with the Genomic Analysis of It's Retron." Journal of Pathogens 2011 (2011): 1–6. http://dx.doi.org/10.4061/2011/693769.

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Retron is a retroelement that encodes msDNA (multicopy single-stranded DNA) which was significantly found mainly in Gram-negative pathogenic bacteria. We screenedYersinia frederikseniiATCC 33641 contig01029 for the presence of retroelement by using bioinformatics tools and characterized a novel retron-Yf79 on the chromosome that encodes msDNA-Yf79. In this study, we perceived that, the codon usage of retron-Yf79 were noteworthy different from those of theY. frederikseniigenome. It demonstrates that, the retron-Yf79 was a foreign DNA element and integrated into this organism genome during their evolution. In addition to this, we have observed a transposase gene which is located just downstream of retron-Yf79. So, the enzyme might be responsible for the transposition of this novel retron element.

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Carducci, Federica, Maria Assunta Biscotti, Mariko Forconi, Marco Barucca, and Adriana Canapa. "An intriguing relationship between teleost Rex3 retroelement and environmental temperature." Biology Letters 15, no. 9 (September 4, 2019): 20190279. http://dx.doi.org/10.1098/rsbl.2019.0279.

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The movement and accumulation of transposable elements (TEs) exert a great influence on the host genome, e.g. determining architecture and genome size, providing a substrate for homologous recombination and DNA rearrangements. TEs are also known to be responsive and susceptible to environmental changes. However, the correlation between environmental conditions and the sequence evolution of TEs is still an unexplored field of research. Among vertebrates, teleosts represent a successful group of animals adapted to a wide range of different environments and their genome is constituted by a rich repertoire of TEs. The Rex3 retroelement is a lineage-specific non-LTR retrotransposon and thus represents a valid candidate for performing comparative sequence analyses between species adapted to diverse temperature conditions. Partial reverse transcriptase sequences of the Rex3 retroelement belonging to 39 species of teleosts were investigated through phylogenetic analysis to evaluate whether the species' adaptation to different environments led to the evolution of different Rex3 temperature-related variants. Our findings highlight an intriguing behaviour of the analysed sequences, showing clustering of Rex3 sequences isolated from species living in cold waters (Arctic and Antarctic regions and cold waters of temperate regions) compared with those isolated from species living in warm waters. This is the first evidence to our knowledge of a correlation between environmental temperature and Rex3 retroelement evolution.

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Papamichos, Spyros I. "Endogenous Retroelement-Driven Expression of OCT4B mRNA Variants." Stem Cell Reviews and Reports 17, no. 3 (March 5, 2021): 1078–80. http://dx.doi.org/10.1007/s12015-021-10146-6.

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Jiang, Rays H. Y., and Francine Govers. "Nonneutral GC3 and Retroelement Codon Mimicry in Phytophthora." Journal of Molecular Evolution 63, no. 4 (September 4, 2006): 458–72. http://dx.doi.org/10.1007/s00239-005-0211-3.

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38

Kingsman, A. "Retroelement particles as purification, presentation and targeting vehicles." Trends in Biotechnology 9, no. 1 (January 1991): 303–9. http://dx.doi.org/10.1016/0167-7799(91)90100-v.

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Platt II, Roy N., and David A. Ray. "A non-LTR retroelement extinction in Spermophilus tridecemlineatus." Gene 500, no. 1 (May 2012): 47–53. http://dx.doi.org/10.1016/j.gene.2012.03.051.

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Castro-Diaz, Nathaly, Marc Friedli, and Didier Trono. "Drawing a fine line on endogenous retroelement activity." Mobile Genetic Elements 5, no. 1 (January 2, 2015): 1–6. http://dx.doi.org/10.1080/2159256x.2015.1006109.

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Guo, Huatao, Longping V. Tse, Angela W. Nieh, Elizabeth Czornyj, Steven Williams, Sabrina Oukil, Vincent B. Liu, and Jeff F. Miller. "Target Site Recognition by a Diversity-Generating Retroelement." PLoS Genetics 7, no. 12 (December 15, 2011): e1002414. http://dx.doi.org/10.1371/journal.pgen.1002414.

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GAO, X., and D. VOYTAS. "A eukaryotic gene family related to retroelement integrases." Trends in Genetics 21, no. 3 (March 2005): 133–37. http://dx.doi.org/10.1016/j.tig.2005.01.006.

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Rodriguez Almaraz, J., G. Guerra, G. Wendt, S. Chang, and S. S. Francis. "P10.09.B Retroelement expression in glioma tumors exhibits subtype specific patterns." Neuro-Oncology 24, Supplement_2 (September 1, 2022): ii50. http://dx.doi.org/10.1093/neuonc/noac174.174.

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Abstract Background There are ~3 million transposable elements in the human genome constituting about 42% of all basepairs. Retroelements (REs) are ~90% of the transposable elements present in the human genome. Active REs are considered highly mutagenic and have been implicated in multiple steps of cancer development and progression, as well as in neurologic diseases. RE activity has functional effects on the genome, including the maintenance of centromere and telomere integrity, and deleterious gene expression. Previous studies have shown that certain families of RE (HERVK, L1, Alu) are expressed in gliomas, however, their specific role as arbitrators of oncogenesis or promoters of the innate anti-tumor immune response remains uncertain. Moreover, it has been shown that a soluble form of PD-L1 (sPD-L1) that blocks its inhibitory activity is produced by exaptation of an intronic endogenous retroelement (LINE-2A) in the gene encoding PD-L1, highlighting the importance of REs as potential therapeutic targets. In this analysis we aim to identify the unique patterns of RE expression across major subtypes of glioma. Material and Methods We conducted a differential expression analysis of 49 RE families using RNA-seq data measured in glioma tumors from The Cancer Genome Atlas (TCGA). RE counts were produced using the software REDiscoverTE. Pairwise comparisons between glioma subtypes (defined by WHO2021) were done using in 625 tumor samples adjusting for age, sex and race. Results 10 of the 49 considered RE families exhibited significantly different (false discovery rate, FDR, <0.05) expression in at least one glioma subtype. Alu(Fold change, FC=1.5), RNA(FC=11.3), PiggyBac(FC=1.6), rRNA(FC=5.23) and Dong-R4(FC=1.8) were overexpressed in IDH-wildtype glioblastoma while Gypsy(FC=0.4) and CRP1(FC=0.26) were decreased in expression. scRNA (FC=2.7) were overexpressed in IDH-mutant oligodendroglioma compared to glioblastoma while Dong-R4 (FC = 0.53) showed decreased expression. LTR (FC=2.02) and tRNA-Deu (FC=1.46), showed increased expression in IDH-wildtype diffuse astrocytomas compared to IDH-mutant, 1p/19q-codeleted oligodendrogliomas while Gypsy (FC =0.41) showed decreased expression. Conclusion We have shown that expression of certain RE families within gliomas have subtype-specific patterns. While it is well established that RE expression is dysregulated in cancer, our analysis is the first at exploring a wide range of retroelements in the context of glioma by subtype. Given the important role of REs in transcriptional control, genomic instability, chromosomal rearrangements, and oncogenic activation, the identification of individual families and specific REs in glioma holds an intrinsic value to potential biomarkers and immunotherapy targets.

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Natali, L., S. Santini, T. Giordani, S. Minelli, P. Maestrini, P. G. Cionini, and A. Cavallini. "Distribution of Ty3-gypsy- and Ty1-copia-like DNA sequences in the genus Helianthus and other Asteraceae." Genome 49, no. 1 (January 1, 2006): 64–72. http://dx.doi.org/10.1139/g05-058.

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Two repeated DNA sequences, pHaS13 and pHaS211, which revealed similarity to the int gene of Ty3-gypsy retrotransposons and the RNAse-H gene of Ty1-copia retroelements, respectively, were surveyed in Asteraceae species and within the genus Helianthus. Southern analysis of the genome of selected Asteraceae that belong to different tribes showed that pHaS13- and pHaS211-related subfamilies of gypsy- and copia-like retroelements are highly redundant only in Helianthus and, to a lesser extent, in Tithonia, a Helianthus strict relative. However, under low stringency posthybridization washes, bands were observed in almost all the other Asteraceae tested when pHaS13 was used as a probe, and in several species when pHaS211 was hybridized. FISH analysis of pHaS13 or pHaS211 probes was performed in species in which labelling was observed in Southern hybridizations carried out under high stringency conditions (Helianthus annuus, Tithonia rotundifolia, Ageratum spp., Leontopodium spp., Senecio vulgaris for pHaS13, and H. annuus, Tithonia rotundifolia, and S. vulgaris for pHaS211). Scattered labelling was observed over all metaphase chromosomes, indicating a large dispersal of both Ty3-gypsy- and Ty1-copia-like retroelements. However, preferential localization of Ty3-gypsy-like sequences at centromeric chromosome regions was observed in all of the species studies but one, even in species in which pHaS13-related elements are poorly represented. Ty1-copia -like sequences showed preferential localization at the chromosome ends only in H. annuus. To study the evolution of gypsy- and copia-like retrotransposons in Helianthus, cladograms were built based on the Southern blot hybridization patterns of pHaS13 or pHaS211 sequences to DNA digests of several species of this genus. Both cladograms agree in splitting the genomes studied into annuals and perennials. Differences that occurred within the clades of perennial and annual species between gypsy- and copia-like retroelements indicated that these retrotransposons were differentially active during Helianthus speciation, suggesting that the evolution of the 2 retroelement families was, within limits, independent.Key words: Asteraceae, FISH, genome evolution, Helianthus, retrotransposons, Ty1-copia, Ty3-gypsy.

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Rose, Kevin M., Stephanie J. Spada, Rebecca Broeckel, Kristin L. McNally, Vanessa M. Hirsch, Sonja M. Best, and Fadila Bouamr. "From Capsids to Complexes: Expanding the Role of TRIM5α in the Restriction of Divergent RNA Viruses and Elements." Viruses 13, no. 3 (March 10, 2021): 446. http://dx.doi.org/10.3390/v13030446.

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An evolutionary arms race has been ongoing between retroviruses and their primate hosts for millions of years. Within the last century, a zoonotic transmission introduced the Human Immunodeficiency Virus (HIV-1), a retrovirus, to the human population that has claimed the lives of millions of individuals and is still infecting over a million people every year. To counteract retroviruses such as this, primates including humans have evolved an innate immune sensor for the retroviral capsid lattice known as TRIM5α. Although the molecular basis for its ability to restrict retroviruses is debated, it is currently accepted that TRIM5α forms higher-order assemblies around the incoming retroviral capsid that are not only disruptive for the virus lifecycle, but also trigger the activation of an antiviral state. More recently, it was discovered that TRIM5α restriction is broader than previously thought because it restricts not only the human retroelement LINE-1, but also the tick-borne flaviviruses, an emergent group of RNA viruses that have vastly different strategies for replication compared to retroviruses. This review focuses on the underlying mechanisms of TRIM5α-mediated restriction of retroelements and flaviviruses and how they differ from the more widely known ability of TRIM5α to restrict retroviruses.

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Nefedova, Lidia, and Alexander Kim. "Mechanisms of LTR‐Retroelement Transposition: Lessons from Drosophila melanogaster." Viruses 9, no. 4 (April 16, 2017): 81. http://dx.doi.org/10.3390/v9040081.

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Dalle Nogare, Damian E., Melody S. Clark, Greg Elgar, Ian G. Frame, and Russell T. M. Poulter. "Xena, a Full-Length Basal Retroelement from Tetraodontid Fish." Molecular Biology and Evolution 19, no. 3 (March 1, 2002): 247–55. http://dx.doi.org/10.1093/oxfordjournals.molbev.a004078.

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Bureau, Thomas E., Shawn E. White, and Susan R. Wessler. "Transduction of a cellular gene by a plant retroelement." Cell 77, no. 4 (May 1994): 479–80. http://dx.doi.org/10.1016/0092-8674(94)90210-0.

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Goering, Wolfgang, Teodora Ribarska, and Wolfgang A. Schulz. "Selective changes of retroelement expression in human prostate cancer." Carcinogenesis 32, no. 10 (August 8, 2011): 1484–92. http://dx.doi.org/10.1093/carcin/bgr181.

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Schumacher, April J., Guylaine Haché, Donna A. MacDuff, William L. Brown, and Reuben S. Harris. "The DNA Deaminase Activity of Human APOBEC3G Is Required for Ty1, MusD, and Human Immunodeficiency Virus Type 1 Restriction." Journal of Virology 82, no. 6 (January 9, 2008): 2652–60. http://dx.doi.org/10.1128/jvi.02391-07.

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ABSTRACT Human APOBEC3G and several other APOBEC3 proteins have been shown to inhibit the replication of a variety of retrotransposons and retroviruses. All of these enzymes can deaminate cytosines within single-strand DNA, but the overall importance of this conserved activity in retroelement restriction has been questioned by reports of deaminase-independent mechanisms. Here, three distinct retroelements, a yeast retrotransposon, Ty1, a murine endogenous retrovirus, MusD, and a lentivirus, human immunodeficiency virus type 1 (HIV-1), were used to evaluate the relative contributions of deaminase-dependent and -independent mechanisms. Although human APOBEC3G can restrict the replication of all three of these retroelements, APOBEC3G lacking the catalytic glutamate (E259Q) was clearly defective. This phenotype was particularly clear in experiments with low levels of APOBEC3G expression. In contrast, purposeful overexpression of APOBEC3G-E259Q was able to cause modest to severe reductions in the replication of Ty1, MusD, and HIV-1(ΔVif). The importance of these observations was highlighted by data showing that CEM-SS T-cell lines expressing near-physiologic levels of APOBEC3G-E259Q failed to inhibit the replication of HIV-1(ΔVif), whereas similar levels of wild-type APOBEC3G fully suppressed virus infectivity. Despite the requirement for DNA deamination, uracil DNA glycosylase did not modulate APOBEC3G-dependent restriction of Ty1 or HIV-1(ΔVif), further supporting prior studies indicating that the major uracil excision repair system of cells is not involved. In conclusion, the absolute requirement for the catalytic glutamate of APOBEC3G in Ty1, MusD, and HIV-1 restriction strongly indicates that DNA cytosine deamination is an essential part of the mechanism.

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