Genetic applications of transposable elements in eukaryotes

Genome ◽  
1994 ◽  
Vol 37 (4) ◽  
pp. 519-525 ◽  
Author(s):  
Chaoqiang Lai
Keyword(s):  
Gene Transfer ◽  
Molecular Biology ◽  
Transposable Elements ◽  
Gene Mapping ◽  
Transposable Element ◽  
Gene Cloning ◽  
Insertional Mutagenesis ◽  
Genetic Research ◽  
Potential Applications ◽  
Mapping Gene

Transposable elements have many potential applications in genetic research, including insertional mutagenesis, gene mapping, gene cloning, gene transfer within and between species, and identification of genes expressed in specific tissues at a particular time. All these genetic approaches are important in the study of molecular biology and evolution. As the number of known transposable element families increases and their properties are further documented, their utility as genetic research tools will become greater. The purpose of this article is to discuss the salient properties of transposable elements in eukaryotes and their applications to genetic research.Key words: transposable elements, mutagenesis, plants, Drosophila, genetic application.

Repetitive elements and their genetic applications in zebrafish

1997 ◽  
Vol 75 (5) ◽  
pp. 507-523 ◽  
Author(s):  
Zsuzsanna Izsvák ◽  
Zoltan Ivics ◽  
Perry B Hackett
Keyword(s):  
Insertional Mutagenesis ◽  
Repetitive Sequences ◽  
Genetic Research ◽  
Strain Differences ◽  
Gene Families ◽  
Repetitive Elements ◽  
Model Systems ◽  
Evolutionary Forces ◽  
Individual Strain ◽  
Potential Applications

Repetitive elements provide important clues about chromosome dynamics, evolutionary forces, and mechanisms for exchange of genetic information between organisms. Repetitive sequences, especially the mobile elements, have many potential applications in genetic research. DNA transposons and retroposons are routinely used for insertional mutagenesis, gene mapping, gene tagging, and gene transfer in several model systems. Once they are developed for the zebrafish, they will greatly facilitate the identification, mapping, and isolation of genes involved in development as well as the investigation of the evolutionary processes that have been shaping eukaryotic genomes. In this review repetitive elements are characterized in terms of their lengths and other physical properties, copy numbers, modes of amplification, and mobilities within a single genome and between genomes. Examples of how they can be used to screen genomes for species and individual strain differences are presented. This review does not cover repetitive gene families that encode well-studied products such as rRNAs, tRNAs, and the like.

Insertional mutagenesis in Bacillus subtilis: mechanism and use in gene cloning

Gene ◽  
1982 ◽  
Vol 19 (3) ◽  
pp. 277-284 ◽  
Author(s):  
B. Niaudet ◽  
A. Goze ◽  
S.D. Ehrlich
Keyword(s):  
Bacillus Subtilis ◽  
Gene Cloning ◽  
Insertional Mutagenesis

scholarly journals Truncated Non-Nuclear Transposable Elements in Grapevine: A Mini Review

2019 ◽  
Vol 50 (4) ◽  
pp. 219-227
Author(s):  
A.V. Milovanov ◽  
J. Tello ◽  
U.C.M. Anhalt ◽  
A. Forneck
Keyword(s):  
Gene Transfer ◽  
Mitochondrial Genome ◽  
Transposable Elements ◽  
Vitis Vinifera ◽  
In Silico ◽  
Gene Evolution ◽  
High Rate ◽  
Miniature Inverted Transposable Elements ◽  
High Level ◽  
Inner Region

Abstract In this mini-review we present insight to the non-nuclear transposable elements and in silico analysis of miniature inverted transposable elements (MITEs) in the grapevine mitochondrial genome. Here we report the identification of 17 truncated sequences in grapevine (Vitis vinifera L.) mitochondrial genome which expectedly belongs to the four ancient transposon families (hAT, Tc1Mariner, Mutator and PIF/Harbinger). Some sequences with a high rate of homology in chloroplast and nuclear genomes were also identified. Thus, it suggests the intercellular gene transfer between these three organelles. These partial sequences showed a high level of similitude with full MITE sequences, and they were found in their inner region, supporting their MITE origin. Further analysis revealed these sequences in other life kingdoms (including eubacteria and archaea), which indicates their ancient origin. Further research showed that 13 out of the 17 sequences are conserved domains of the genes where they are located, suggesting their contribution to gene evolution. Therefore, we suppose that more studies of nature, origin and functional meaning of these sequences and their fusion with genes are necessary. In the light of our observations it will be useful for further studies of V. vinifera genome organizing and systematics, as well as for other species.

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.

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