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Articles
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Citation: Mobile DNA 2022 13:32
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CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism thr...
Citation: Mobile DNA 2022 13:31 -
Generalized nuclear localization of retroelement transcripts
LINE-1s, Alus and SVAs are the only retrotransposition competent elements in humans. Their mobilization followed by insertional mutagenesis is often linked to disease. Apart from these rare integration events,...
Citation: Mobile DNA 2022 13:30 -
T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data
Despite the advent of Chromatin Immunoprecipitation Sequencing (ChIP-seq) having revolutionised our understanding of the mammalian genome’s regulatory landscape, many challenges remain. In particular, because ...
Citation: Mobile DNA 2022 13:29 -
Recurrent co-domestication of PIF/Harbinger transposable element proteins in insects
Transposable elements (TEs) are selfish DNA sequences capable of moving and amplifying at the expense of host cells. Despite this, an increasing number of studies have revealed that TE proteins are important c...
Citation: Mobile DNA 2022 13:28 -
The coevolution between APOBEC3 and retrotransposons in primates
Retrotransposons are genetic elements with the ability to replicate in the genome using reverse transcriptase: they have been associated with the development of different biological structures, such as the Cen...
Citation: Mobile DNA 2022 13:27 -
A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition
Transposable elements are ubiquitous and play a fundamental role in shaping genomes during evolution. Since excessive transposition can be mutagenic, mechanisms exist in the cells to keep these mobile elements...
Citation: Mobile DNA 2022 13:26 -
Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9
Krüppel Associated Box-containing Zinc Finger Proteins (KRAB-ZFPs), representing the largest superfamily of transcription factors in mammals, are predicted to primarily target and repress transposable elements...
Citation: Mobile DNA 2022 13:25 -
A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease
DNA transposons are ubiquitous components of eukaryotic genomes. A major group of them encode a DDD/E transposase and contain terminal inverted repeats (TIRs) of varying lengths. The Kolobok superfamily of DNA tr...
Citation: Mobile DNA 2022 13:24 -
Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns
Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and ...
Citation: Mobile DNA 2022 13:23 -
Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells
Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adapta...
Citation: Mobile DNA 2022 13:22 -
SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution
Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly under...
Citation: Mobile DNA 2022 13:21 -
Multiple horizontal transfers of a Helitron transposon associated with a parasitoid wasp
In a previous study we described a Helitron transposon that apparently became one of the segments in the symbiotic Cotesia vestalis bracovirus (CvBV) from the parasitoid wasp C. vestalis. We presented evidence th...
Citation: Mobile DNA 2022 13:20 -
Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria
ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory ge...
Citation: Mobile DNA 2022 13:19 -
Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin
Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome...
Citation: Mobile DNA 2022 13:18 -
Correction: Characterization of transposable elements within the Bemisia tabaci species complex
Citation: Mobile DNA 2022 13:17 -
Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants
Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing ...
Citation: Mobile DNA 2022 13:16 -
Correction: A beginner’s guide to manual curation of transposable elements
Citation: Mobile DNA 2022 13:15 -
Software evaluation for de novo detection of transposons
Transposable 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 tas...
Citation: Mobile DNA 2022 13:14 -
Subfamily-specific differential contribution of individual monomers and the tether sequence to mouse L1 promoter activity
The internal promoter in L1 5’UTR is critical for autonomous L1 transcription and initiating retrotransposition. Unlike the human genome, which features one contemporarily active subfamily, four subfamilies (A...
Citation: Mobile DNA 2022 13:13 -
Characterization of transposable elements within the Bemisia tabaci species complex
Whiteflies are agricultural pests that cause negative impacts globally to crop yields resulting at times in severe economic losses and food insecurity. The Bemisia tabaci whitefly species complex is the most dama...
Citation: Mobile DNA 2022 13:12 -
TE Density: a tool to investigate the biology of transposable elements
Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic vari...
Citation: Mobile DNA 2022 13:11 -
RNA sensor MDA5 suppresses LINE-1 retrotransposition by regulating the promoter activity of LINE-1 5′-UTR
Type 1 long interspersed elements, or LINE-1, are the only retroelements that replicate autonomously in human cells. The retrotransposition process of LINE-1 can trigger the activation of the innate immune sys...
Citation: Mobile DNA 2022 13:10 -
SETMAR, a case of primate co-opted genes: towards new perspectives
We carry out a review of the history and biological activities of one domesticated gene in higher primates, SETMAR, by discussing current controversies. Our purpose is to open a new outlook that will serve as ...
Citation: Mobile DNA 2022 13:9 -
The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms
CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, f...
Citation: Mobile DNA 2022 13:8 -
A beginner’s guide to manual curation of transposable elements
In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate ...
Citation: Mobile DNA 2022 13:7 -
Eco-evolutionary significance of domesticated retroelements in microbial genomes
Since the first discovery of reverse transcriptase in bacteria, and later in archaea, bacterial and archaeal retroelements have been defined by their common enzyme that coordinates diverse functions. Yet, evol...
Citation: Mobile DNA 2022 13:6 -
Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus
Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in...
Citation: Mobile DNA 2022 13:5 -
KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences
Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize ...
Citation: Mobile DNA 2022 13:4 -
The fifth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements
The fifth Japanese meeting on host–transposon interactions, titled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs),” was held online on August 26–27, 2021....
Citation: Mobile DNA 2022 13:3 -
Response from Varani et al. to “Comment on ‘the IS6 family, a clinically important group of insertion sequences including IS26’ by Ruth M. Hall”
The IS6 family of insertion sequences is a large but coherent group which was originally named to avoid confusion between a number of identical or nearly identical IS that were identified at about the same time a...
Citation: Mobile DNA 2022 13:2 -
Comment on “the IS6 family, a clinically important group of insertion sequences including IS26” by Varani and co-authors
The insertion sequence IS26 has long been known to play a major role in the recruitment of antibiotic resistance genes into the mobile resistance gene pool of Gram-negative bacteria and IS26 also plays a major ro...
Citation: Mobile DNA 2022 13:1 -
Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder
Retrotransposons have been implicated as causes of Mendelian disease, but their role in autism spectrum disorder (ASD) has not been systematically defined, because they are only called with adequate sensitivit...
Citation: Mobile DNA 2021 12:28 -
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotrans...
Citation: Mobile DNA 2021 12:27 -
A comparative analysis of L1 retrotransposition activities in human genomes suggests an ongoing increase in L1 number despite an evolutionary trend towards lower activity
LINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications fo...
Citation: Mobile DNA 2021 12:26 -
Chromosomal integration of Tn5253 occurs downstream of a conserved 11-bp sequence of the rbgA gene in Streptococcus pneumoniae and in all the other known hosts of this integrative conjugative element (ICE)
Tn5253, a composite Integrative Conjugative Element (ICE) of Streptococcus pneumoniae carrying tet(M) and cat resistance determinants, was found to (i) integrate at specific 83-bp integration site (attB), (ii) pr...
Citation: Mobile DNA 2021 12:25 -
Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, gen...
Citation: Mobile DNA 2021 12:24 -
Differential regulation of transposable elements (TEs) during the murine submandibular gland development
The submandibular gland (SG) is a relatively simple organ formed by three cell types: acinar, myoepithelial, and an intricate network of duct-forming epithelial cells, that together fulfills several physiologi...
Citation: Mobile DNA 2021 12:23 -
Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans
Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational ap...
Citation: Mobile DNA 2021 12:22 -
Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9
The autonomous retroelement Long Interspersed Element-1 (LINE-1) mobilizes though a copy and paste mechanism using an RNA intermediate (retrotransposition). Throughout human evolution, around 500,000 LINE-1 se...
Citation: Mobile DNA 2021 12:21 -
A 192 bp ERV fragment insertion in the first intron of porcine TLR6 may act as an enhancer associated with the increased expressions of TLR6 and TLR1
Toll-like receptors (TLRs) play important roles in building innate immune and inducing adaptive immune responses. Associations of the TLR genes polymorphisms with disease susceptibility, which are the basis of mo...
Citation: Mobile DNA 2021 12:20 -
Correction to: Upregulation of selected HERVW loci in multiple sclerosis
Citation: Mobile DNA 2021 12:19 -
Upregulation of selected HERVW loci in multiple sclerosis
Citation: Mobile DNA 2021 12:18 -
SINE jumping contributes to large-scale polymorphisms in the pig genomes
Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene a...
Citation: Mobile DNA 2021 12:17 -
TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation
Transposable 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 coll...
Citation: Mobile DNA 2021 12:16 -
melRNA-seq for Expression Analysis of SINE RNAs and Other Medium-Length Non-Coding RNAs
Small interspersed elements (SINEs) are transcribed by RNA polymerase III (Pol III) to produce RNAs typically 100–500 nucleotides in length. Although their RNA abundance can be evaluated by Northern blotting a...
Citation: Mobile DNA 2021 12:15 -
The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis
Transposable elements (TEs) are repetitive sequences of viral origin that compose almost half of the human genome. These elements are tightly controlled within cells, and if activated, they can cause changes i...
Citation: Mobile DNA 2021 12:14 -
Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing
Bacterial transposons propagate through either non-replicative (cut-and-paste) or replicative (copy-and-paste) pathways, depending on how the mobile element is excised from its donor source. In the well-charac...
Citation: Mobile DNA 2021 12:13 -
The unusual structure of the PiggyMac cysteine-rich domain reveals zinc finger diversity in PiggyBac-related transposases
Transposons are mobile genetic elements that colonize genomes and drive their plasticity in all organisms. DNA transposon-encoded transposases bind to the ends of their cognate transposons and catalyze their m...
Citation: Mobile DNA 2021 12:12 -
The IS6 family, a clinically important group of insertion sequences including IS26
The IS6 family of bacterial and archaeal insertion sequences, first identified in the early 1980s, has proved to be instrumental in the rearrangement and spread of multiple antibiotic resistance. Two IS, IS26 (fo...
Citation: Mobile DNA 2021 12:11