scholarly journals TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
◽  
Tyler A. Elliott ◽  
Tony Heitkam ◽  
Robert Hubley ◽  
Hadi Quesneville ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Classification Systems ◽  
Large Collection ◽  
Functional Roles ◽  
Unique Biology ◽  
Software Classification ◽  
Twitter Account ◽  
Novices And Experts ◽  
Eukaryotic Genomes

AbstractTransposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into their unique biology has driven the creation of a large collection of databases, software, classification systems, and annotation guidelines. The diversity of available TE-related methods and resources raises compatibility concerns and can be overwhelming to researchers and communicators seeking straightforward guidance or materials. To address these challenges, we have initiated a new resource, TE Hub, that provides a space where members of the TE community can collaborate to document and create resources and methods. The space consists of (1) a website organized with an open wiki framework, https://tehub.org, (2) a conversation framework via a Twitter account and a Slack channel, and (3) bi-monthly Hub Update video chats on the platform’s development. In addition to serving as a centralized repository and communication platform, TE Hub lays the foundation for improved integration, standardization, and effectiveness of diverse tools and protocols. We invite the TE community, both novices and experts in TE identification and analysis, to join us in expanding our community-oriented resource.

scholarly journals A Field Guide to Eukaryotic Transposable Elements

2020 ◽  
Vol 54 (1) ◽  
pp. 539-561 ◽  
Author(s):  
Jonathan N. Wells ◽  
Cédric Feschotte
Keyword(s):  
Genetic Variation ◽  
Transposable Elements ◽  
Dna Sequences ◽  
Genetic Factors ◽  
Mobile Dna ◽  
Substantial Fraction ◽  
Evolutionary Origins ◽  
Unique Biology ◽  
Dramatic Variation ◽  
Eukaryotic Genomes

Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic behavior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species.

scholarly journals Transposable Elements and Teleost Migratory Behaviour

2021 ◽  
Vol 22 (2) ◽  
pp. 602
Author(s):  
Elisa Carotti ◽  
Federica Carducci ◽  
Adriana Canapa ◽  
Marco Barucca ◽  
Samuele Greco ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Environmental Changes ◽  
Chromosomal Rearrangements ◽  
Quantitative Difference ◽  
Regulatory Elements ◽  
Phylogenetic Position ◽  
Migratory Behaviour ◽  
Relative Contribution ◽  
Migratory Routes ◽  
Eukaryotic Genomes

Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.

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 Software Evaluation for de novo Detection of Transposons

2021 ◽  
Author(s):  
Matias Rodriguez ◽  
Wojciech Makałowski
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
De Novo ◽  
Simulated Data ◽  
Genomic Sequences ◽  
Software Evaluation ◽  
Easy Task ◽  
Eukaryotic Genomes

AbstractTransposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.

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 Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shujun Ou ◽  
Weija Su ◽  
Yi Liao ◽  
Kapeel Chougule ◽  
Jireh R. A. Agda ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Animal Species ◽  
Performance Metrics ◽  
De Novo ◽  
Terminal Inverted Repeat ◽  
Miniature Inverted Transposable Elements ◽  
Sensitivity Specificity ◽  
Genomic Regions ◽  
Assembly Algorithms ◽  
Eukaryotic Genomes

Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. Results We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. Conclusions The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA.

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 Roles of Transposable Elements in the Different Layers of Gene Expression Regulation

2019 ◽  
Vol 20 (22) ◽  
pp. 5755 ◽  
Author(s):  
Denise Drongitis ◽  
Francesco Aniello ◽  
Laura Fucci ◽  
Aldo Donizetti
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Gene Expression Regulation ◽  
Regulation Of Gene Expression ◽  
Chromatin Modification ◽  
Essential Element ◽  
Protein Translation ◽  
Expression Regulation ◽  
Molecular Processes ◽  
Eukaryotic Genomes

The biology of transposable elements (TEs) is a fascinating and complex field of investigation. TEs represent a substantial fraction of many eukaryotic genomes and can influence many aspects of DNA function that range from the evolution of genetic information to duplication, stability, and gene expression. Their ability to move inside the genome has been largely recognized as a double-edged sword, as both useful and deleterious effects can result. A fundamental role has been played by the evolution of the molecular processes needed to properly control the expression of TEs. Today, we are far removed from the original reductive vision of TEs as “junk DNA”, and are more convinced that TEs represent an essential element in the regulation of gene expression. In this review, we summarize some of the more recent findings, mainly in the animal kingdom, concerning the active roles that TEs play at every level of gene expression regulation, including chromatin modification, splicing, and protein translation.

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