Genetics ofUstilago violacea. XXXIV. Genetic Evidence for a Transposable Element Functioning during Mitosis and Two Transposable Elements Functioning during Meiosis

1998 ◽  
Vol 159 (6) ◽  
pp. 1018-1022 ◽  
Author(s):  
E. D. Garber ◽  
M. Ruddat
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Genetic Evidence

scholarly journals Transcriptome analyses reveal tau isoform-driven changes in transposable element and gene expression

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0251611
Author(s):  
Jennifer Grundman ◽  
Brian Spencer ◽  
Floyd Sarsoza ◽  
Robert A. Rissman
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Transposable Elements ◽  
Transposable Element ◽  
Progressive Supranuclear Palsy ◽  
Rna Sequencing ◽  
Amyloid Beta ◽  
Specific Level ◽  
Tau Isoforms ◽  
Tau Isoform

Alternative splicing of the gene MAPT produces several isoforms of tau protein. Overexpression of these isoforms is characteristic of tauopathies, which are currently untreatable neurodegenerative diseases. Though non-canonical functions of tau have drawn interest, the role of tau isoforms in these diseases has not been fully examined and may reveal new details of tau-driven pathology. In particular, tau has been shown to promote activation of transposable elements—highly regulated nucleotide sequences that replicate throughout the genome and can promote immunologic responses and cellular stress. This study examined tau isoforms’ roles in promoting cell damage and dysregulation of genes and transposable elements at a family-specific and locus-specific level. We performed immunofluorescence, Western blot and cytotoxicity assays, along with paired-end RNA sequencing on differentiated SH-SY5Y cells infected with lentiviral constructs of tau isoforms and treated with amyloid-beta oligomers. Our transcriptomic findings were validated using publicly available RNA-sequencing data from Alzheimer’s disease, progressive supranuclear palsy and control human samples from the Accelerating Medicine’s Partnership for AD (AMP-AD). Significance for biochemical assays was determined using Wilcoxon ranked-sum tests and false discovery rate. Transcriptome analysis was conducted through DESeq2 and the TEToolkit suite available from the Hammell lab at Cold Spring Harbor Laboratory. Our analyses show overexpression of different tau isoforms and their interactions with amyloid-beta in SH-SY5Y cells result in isoform-specific changes in the transcriptome, with locus-specific transposable element dysregulation patterns paralleling those seen in patients with Alzheimer’s disease and progressive supranuclear palsy. Locus-level transposable element expression showed increased dysregulation of L1 and Alu sites, which have been shown to drive pathology in other neurological diseases. We also demonstrated differences in rates of cell death in SH-SY5Y cells depending on tau isoform overexpression. These results demonstrate the importance of examining tau isoforms’ role in neurodegeneration and of further examining transposable element dysregulation in tauopathies and its role in activating the innate immune system.

scholarly journals LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq

2019 ◽  
Vol 35 (19) ◽  
pp. 3839-3841 ◽  
Author(s):  
Artem Babaian ◽  
I Richard Thompson ◽  
Jake Lever ◽  
Liane Gagnier ◽  
Mohammad M Karimi ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Test Data ◽  
Source Code ◽  
Supplementary Information ◽  
Transcriptional Networks ◽  
Supplementary Data ◽  
Rna Seq ◽  
Transcriptional Initiation ◽  
Instruction Manual

Abstract Summary Transposable elements (TEs) influence the evolution of novel transcriptional networks yet the specific and meaningful interpretation of how TE-derived transcriptional initiation contributes to the transcriptome has been marred by computational and methodological deficiencies. We developed LIONS for the analysis of RNA-seq data to specifically detect and quantify TE-initiated transcripts. Availability and implementation Source code, container, test data and instruction manual are freely available at www.github.com/ababaian/LIONS. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 336 ◽  
Author(s):  
Justin P. Blumenstiel
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Horizontal Transfer ◽  
Evolutionary Dynamics ◽  
Evolutionary Strategies ◽  
Species Boundaries ◽  
Life Stages ◽  
School Work

Transposable elements (TEs) can be maintained in sexually reproducing species even if they are harmful. However, the evolutionary strategies that TEs employ during proliferation can modulate their impact. In this review, I outline the different life stages of a TE lineage, from birth to proliferation to extinction. Through their interactions with the host, TEs can exploit diverse strategies that range from long-term coexistence to recurrent movement across species boundaries by horizontal transfer. TEs can also engage in a poorly understood phenomenon of TE resurrection, where TE lineages can apparently go extinct, only to proliferate again. By determining how this is possible, we may obtain new insights into the evolutionary dynamics of TEs and how they shape the genomes of their hosts.

On the evolution and population genetics of hybrid-dysgenesis-causing transposable elements in Drosophila

1986 ◽  
Vol 312 (1154) ◽  
pp. 205-215 ◽  
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Populations ◽  
Element Composition ◽  
Hybrid Dysgenesis ◽  
Evolutionary Significance ◽  
Genetic Elements ◽  
Transposable Genetic Elements

Much has been learned about transposable genetic elements in Drosophila , but questions still remain, especially concerning their evolutionary significance. Three such questions are considered here, (i) Has the behaviour of transposable elements been most influenced by natural selection at the level of the organism, the population, or the elements themselves? (ii) How did the elements originate in the genome of the species? (iii) Why are laboratory stocks different from natural populations with respect to their transposable element composition? No final answers to these questions are yet available, but by focusing on the two families of hybrid dysgenesis-causing elements, the P and I factors, we can draw some tentative conclusions.

scholarly journals Transposable Element Loads in a Bacterial Symbiont of Weevils Are Extremely Variable

2008 ◽  
Vol 74 (24) ◽  
pp. 7832-7834 ◽  
Author(s):  
Kevin M. Dougherty ◽  
Gordon R. Plague
Keyword(s):  
Homologous Recombination ◽  
Transposable Elements ◽  
Transposable Element ◽  
Insertion Sequence ◽  
Bacterial Symbiont ◽  
Genomic Variation ◽  
Bacterial Endosymbiont

ABSTRACT Not only are transposable elements profuse in the bacterial endosymbiont of maize weevils, but we found that their quantities also vary ∼10-fold among individual weevils. Because multicopy elements can facilitate homologous recombination, this insertion sequence (IS) load variability suggests that these essentially asexual bacteria may exhibit substantial intraspecific genomic variation.

scholarly journals The transposable elements of the Drosophila serrata reference panel

2020 ◽  
Author(s):  
Zachary Tiedeman ◽  
Sarah Signor
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Copy Number ◽  
Genetic Background ◽  
Natural Populations ◽  
Inbred Lines ◽  
Transposable Element Insertion ◽  
Defense Systems ◽  
Drosophila Serrata ◽  
Transposable Element Copy

AbstractTransposable elements are an important element of the complex genomic ecosystem, proving to be both adaptive and deleterious - repressed by the piRNA system and fixed by selection. Transposable element insertion also appears to be bursty – either due to invasion of new transposable elements that are not yet repressed, de-repression due to instability of organismal defense systems, stress, or genetic variation in hosts. Here, we characterize the transposable element landscape in an important model Drosophila, D. serrata, and investigate variation in transposable element copy number between genotypes and in the population at large. We find that a subset of transposable elements are clearly related to elements annotated in D. melanogaster and D. simulans, suggesting they spread between species more recently than other transposable elements. We also find that transposable elements do proliferate in particular genotypes, and that often if an individual is host to a proliferating transposable element, it is host to more than one proliferating transposable element. In addition, if a transposable element is active in a genotype, it is often active in more than one genotype. This suggests that there is an interaction between the host and the transposable element, such as a permissive genetic background and the presence of potentially active transposable element copies. In natural populations an active transposable element and a permissive background would not be held in association as in inbred lines, suggesting the magnitude of the burst would be much lower. Yet many of the inbred lines have actively proliferating transposable elements suggesting this is an important mechanism by which transposable elements maintain themselves in populations.

scholarly journals Transposable element mobilization in interspecific yeast hybrids

2020 ◽  
Author(s):  
Caiti Smukowski Heil ◽  
Kira Patterson ◽  
Angela Shang-Mei Hickey ◽  
Erica Alcantara ◽  
Maitreya J. Dunham
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Regulation System ◽  
Ty Elements ◽  
Genomic Shock ◽  
Transposition Rate ◽  
Order Of Magnitude ◽  
Element Movement ◽  
Species Specific

AbstractBarbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements. This hypothesis is based on the idea that regulation of transposable element movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of transposable elements in Saccharomyces cerevisiae x Saccharomyces uvarum interspecific yeast hybrids. S. cerevisiae have a small number of active long terminal repeat (LTR) retrotransposons (Ty elements), while their distant relative S. uvarum have lost the Ty elements active in S. cerevisiae. While the regulation system of Ty elements is known in S. cerevisiae, it is unclear how Ty elements are regulated in other Saccharomyces species, and what mechanisms contributed to the loss of most classes of Ty elements in S. uvarum. Therefore, we first assessed whether transposable elements could insert in the S. uvarum sub-genome of a S. cerevisiae x S. uvarum hybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and non-randomly in the S. uvarum genome. We then used an in vivo reporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can facilitate the introduction of transposable elements across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of transposable elements suggested by the genomic shock theory.

scholarly journals Transposable Elements in Maize the?Activator-Dissociation (Ac-Ds) System

1984 ◽  
Vol 37 (6) ◽  
pp. 307 ◽  
Author(s):  
E A Howard ◽  
E S Dennis
Keyword(s):  
Zea Mays ◽  
Transposable Elements ◽  
Transposable Element ◽  
Chromosomal Location ◽  
Lower Eukaryotes ◽  
Element System ◽  
Controlling Element ◽  
Series Of Experiments ◽  
Higher Eukaryotes ◽  
Living Organisms

Although unstable mutants in maize (Zea mays) were described as early as 1914 (Emerson 1914, 1917, 1929; Rhoades 1936, 1938), the first explanation of such mutants in terms of transposable DNA was provided by Barbara McClintock's elegant series of experiments on the activator-dissociation (Ac-Ds) controlling-element system of maize (McClintock 1947,1948, 1951). McClintock demonstrated genetically thatAc and Ds were short regions of DNA which could move (transpose) from one chromosomal location to another. McClintock also established that Ds could transpose only in response to the action of Ac (i.e. both elements were required in the same nucleus for Ds transposition), and that Ac could transpose autonomously (i.e. in the absence of Ds). A total of eight transposable element systems have been recognized in maize, the best characterized of which are Ac(Mp)Ds, Spm and Robertson's mutator (reviewed in Fedoroff 1983; Nevers et al. 1984). All but Robertson's mutator occur as two-element systems, similar to Ac-Ds. Transposable elements have now been shown to be widespread in living organisms-occurring in prokaryotes and lower eukaryotes as well as other higher eukaryotes, including animals.

scholarly journals Expansion of a single transposable element family is associated with genome-size increase and radiation in the genus Hydra

2019 ◽  
Vol 116 (46) ◽  
pp. 22915-22917 ◽  
Author(s):  
Wai Yee Wong ◽  
Oleg Simakov ◽  
Diane M. Bridge ◽  
Paulyn Cartwright ◽  
Anthony J. Bellantuono ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Genome Size ◽  
Focal Point ◽  
Size Increase ◽  
Single Family ◽  
Evolutionary Patterns ◽  
Transposable Element Family ◽  
Chicken Repeat ◽  
Long Interspersed Nuclear Elements

Transposable elements are one of the major contributors to genome-size differences in metazoans. Despite this, relatively little is known about the evolutionary patterns of element expansions and the element families involved. Here we report a broad genomic sampling within the genus Hydra, a freshwater cnidarian at the focal point of diverse research in regeneration, symbiosis, biogeography, and aging. We find that the genome of Hydra is the result of an expansion event involving long interspersed nuclear elements and in particular a single family of the chicken repeat 1 (CR1) class. This expansion is unique to a subgroup of the genus Hydra, the brown hydras, and is absent in the green hydra, which has a repeat landscape similar to that of other cnidarians. These features of the genome make Hydra attractive for studies of transposon-driven genome expansions and speciation.

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