Mobile DNA最新文献

Background: LTR-retrotransposons (LTR-RT) are a major component of plant genomes and important drivers of genome evolution. Most LTR-RT copies in plant genomes are defective elements found as truncated copies, nested insertions or as part of more complex structures. The recent availability of highly contiguous plant genome assemblies based on long-read sequences now allows to perform detailed characterization of these complex structures and to evaluate their importance for plant genome evolution.

Results: The detailed analysis of two rice loci containing complex LTR-RT structures showed that they consist of tandem arrays of LTR copies sharing internal LTRs. Our analyses suggests that these LTR-RT tandems are the result of a single insertion and not of the recombination of two independent LTR-RT elements. Our results also suggest that gypsy elements may be more prone to form these structures. We show that these structures are highly polymorphic in rice and therefore have the potential to generate genetic variability. We have developed a computational pipeline (IDENTAM) that scans genome sequences and identifies tandem LTR-RT candidates. Using this tool, we have detected 266 tandems in a pangenome built from the genomes of 76 accessions of cultivated and wild rice, showing that tandem LTR-RT structures are frequent and highly polymorphic in rice. Running IDENTAM in the Arabidopsis, almond and cotton genomes showed that LTR-RT tandems are frequent in plant genomes of different size, complexity and ploidy level. The complexity of differentiating intra-element variations at the nucleotide level among haplotypes is very high, and we found that graph-based pangenomic methodologies are appropriate to resolve these structures.

Conclusions: Our results show that LTR-RT elements can form tandem arrays. These structures are relatively abundant and highly polymorphic in rice and are widespread in the plant kingdom. Future studies will contribute to understanding how these structures originate and whether the variability that they generate has a functional impact.

Background: LTR-retrotransposons are widely distributed among the eukaryote tree of life and have extensive impacts on genome evolution. Among the three canonical superfamilies, the Copia superfamily demonstrates the lowest abundances and repartitions among metazoans. To better understand their dynamics, we have conducted the first large-scale study of LTR-retrotransposon diversity in metazoans and we report on the diversity and distribution of the Copia elements.

Results: We have identified over than 2,300 Copia elements from 263 metazoan genomes. The sequences were annotated at the clade level based on the classification of their RT/RNaseH domain. Our results confirmed that Copia are scarce in metazoans. However, we observed a great variation in Copia abundance between taxa. Surprisingly, some genomes, had a record number of copies, especially in Squamata. In contrast, terrestrial Deuterostomia display a clear loss of Copia diversity leading to their disappearance in some taxa. Additionally, we identified 18 new clades, tripling the number of previously defined clades. By studying more than 50 widespread taxa, we believe that most metazoan Copia clades have now been identified. The most striking result is that environment appears to be related to Copia distribution. We defined two sets of clades characterizing marine or terrestrial taxa. This two-sided pattern could be partially explained by horizontal transfers within both environments.

Conclusions: This research enhances our understanding of transposable element evolution and emphasizes the influence of sharing the same ecological contexts on genomic diversity, and highlights the importance of annotating them at the clade level to characterize their evolutionary dynamics.

Background: Fungicide resistance poses a significant challenge to plant disease management and influences the evolutionary dynamics of fungal pathogens. Besides being important phytopathogens, Monilinia species have become a model for discovering many fundamental questions related to fungal pathosystems. In this study, DMI-propiconazole sensitivity was investigated in view of transposable element (TE) dynamics in M. fructicola and M. laxa.

Results: Propiconazole-sensitivity of 109 M. fructicola and 20 M. laxa isolates from different regions of Türkiye was assessed. Comprehensive TE identification within the species revealed that Class I elements were predominant, and TEs constituted approximately 9% of the genome for both M. fructicola and M. laxa, with a total of 15,327 and 10,710 TEs, respectively. An experimental evolution plan was developed for Monilinia that allows observing phenotypic and genotypic changes over successive generations under controlled selection pressures. Dynamic changes in TE content were discovered throughout the experimental evolution of M. fructicola under propiconazole pressure. With a net change of 187 TEs, the evolved strain showed an expansion of TE sequences, whereas different TE classes displayed diverse patterns of increase/decrease. Additionally, the presence of a nested TE upstream of the CYP51 gene was observed in less-sensitive M. fructicola isolates but absent in highly-sensitive ones. Gene expressions of CYP51 differed significantly between TE-containing and TE-lacking isolates, strongly supporting the contribution of this TE to fungicide resistance.

Conclusion: This study establishes a critical link between TEs and DMI fungicide resistance by associating a nested TE with reduced sensitivity to propiconazole. We introduce an innovative experimental evolution framework for studying genomic changes under selective pressure and provide a comprehensive characterization of Monilinia TEs. These findings significantly advance our understanding of molecular resistance mechanisms in fungal pathogens, offering insights for more effective disease management.

The horizontal transfer (HT) of the P-element is one of the best documented cases of the HT of a transposable element. The P-element invaded natural D. melanogaster populations between 1950 and 1980 following its HT from Drosophila willistoni, a species endemic to South and Central America. Subsequently, it spread in D. simulans populations between 2006 and 2014, following a HT from D. melanogaster. The geographic region where the spread into D. simulans occurred is unclear, as both involved species are cosmopolitan. The P-element differs between these two species by a single base substitution at site 2040, where D. melanogaster carries a 'G' and D. simulans carries an 'A'. It has been hypothesized that this base substitution was a necessary adaptation that enabled the spread of the P-element in D. simulans, potentially explaining the 30-50-year lag between the invasions of D. melanogaster and D. simulans. To test this hypothesis, we monitored the invasion dynamics of P-elements with both alleles in experimental populations of D. melanogaster and D. simulans. Our results indicate that the allele at site 2040 has a minimal impact on the invasion dynamics of the P-element and, therefore, was not necessary for the invasion of D. simulans. However, we found that the host species significantly influenced the invasion dynamics, with higher P-element copy numbers accumulating in D. melanogaster than in D. simulans. Finally, based on SNPs segregating in natural D. melanogaster populations, we suggest that the horizontal transfer of the P-element from D. melanogaster to D. simulans likely occurred around Tasmania.

Transposable elements (TEs) drive genome evolution and can affect gene expression through diverse mechanisms. In breast cancer, disrupted regulation of TE sequences may facilitate tumor-specific transcriptomic alterations. We examine 142,514 full-length isoforms derived from long-read RNA sequencing (LR-seq) of 30 breast samples to investigate the effects of TEs on the breast cancer transcriptome. Approximately half of these isoforms contain TE sequences, and these contribute to half of the novel annotated splice junctions. We quantify splicing of these LR-seq derived isoforms in 1,135 breast tumors from The Cancer Genome Atlas (TCGA) and 1,329 healthy tissue samples from the Genotype-Tissue Expression (GTEx), and find 300 TE-overlapping tumor-specific splicing events. Some splicing events are enriched in specific breast cancer subtypes - for example, a TE-driven transcription start site upstream of ERBB2 in HER2 + tumors, and several TE-mediated splicing events are associated with patient survival and poor prognosis. The full-length sequences we capture with LR-seq reveal thousands of isoforms with signatures of RNA editing, including a novel isoform belonging to RHOA; a gene previously implicated in tumor progression. We utilize our full-length isoforms to discover polymorphic TE insertions that alter splicing and validate one of these events in breast cancer cell lines. Together, our results demonstrate the widespread effects of dysregulated TEs on breast cancer transcriptomes and highlight the advantages of long-read isoform sequencing for understanding TE biology. TE-derived isoforms may alter the expression of genes important in cancer and can potentially be used as novel, disease-specific therapeutic targets or biomarkers.One sentence summary: Transposable elements generate alternative isoforms and alter post-transcriptional regulation in human breast cancer.

Tn7 family transposons are mobile genetic elements known for precise target site selection, with some co-opting CRISPR-Cas systems for RNA-guided transposition. We identified a novel group of Tn7-like transposons in Cyanobacteria that preferentially target CRISPR arrays, suggesting a new functional interaction between these elements and CRISPR-Cas systems. Using bioinformatics tools, we characterized their phylogeny, target specificity, and sub-specialization. The array-targeting elements are phylogenetically close to tRNA-targeting elements. The distinct target preference coincides with loss of a C-terminal region in the TnsD protein which is responsible for recognizing target sites when compared to closely related elements. Notably, elements are found integrated into a fixed position within CRISPR spacer regions, a behavior that might minimize negative impacts on the host defense system. These transposons were identified in both plasmid and genomic CRISPR arrays, indicating that their preferred target provides a means for both safe insertion in the host chromosome and a mechanism for dissemination. Attempts to reconstitute these elements in E. coli were unsuccessful, indicating possible dependence on native host factors. Our findings expand the diversity of interactions between Tn7-like transposons and CRISPR systems.

Background: Endogenous retroviruses (ERV) are traces of ancestral retroviral germline infections that constitute a significant portion of mammalian genomes and are classified as LTR-retrotransposons. The exploration of their dynamics and evolutionary history in ruminants remains limited, highlighting the need for a comprehensive and thorough investigation of the ERV landscape in the genomes of cattle, sheep and goat.

Results: Through a de novo bioinformatic analysis, we characterized 24 Class I and II ERV families across four reference assemblies of domestic and wild sheep and goats, and one assembly of cattle. Among these families, 13 are represented by consensus sequences identified in the five analyzed species, while eight are exclusive to small ruminants and three to cattle. The similarity-based approach used to search for the presence of these families in other ruminant species revealed multiple endogenization events over the last 40 million years and distinct evolutionary dynamics among species. The ERV annotation resulted in a high-resolution dataset of 100,534 ERV insertions across the five genomes, representing between 0.5 and 1% of their genomes. Solo-LTRs account for 83.2% of the annotated insertions demonstrating that most of the ERVs are relics of past events. Two Class II families showed higher abundance and copy conservation in small ruminants. One of them is closely related to circulating exogenous retroviruses and is represented by 22 copies sharing identical LTRs and 12 with complete coding capacities in the domestic goat.

Conclusions: Our results suggest the presence of two ERV families with recent transpositional activity in ruminant genomes, particularly in the domestic goat, illustrating distinct evolutionary dynamics among the analyzed species. This work highlights the ongoing influence of ERVs on genomic landscapes and call for further investigation of their evolutionary trajectories in these genomes.

Background: Both the expression and activities of LINE-1 (L1) retrotransposons are known to occur in numerous cell-types and are implicated in pathobiological contexts such as aging-related inflammation, autoimmunity, and in cancers. L1s encode two proteins that are translated from bicistronic transcripts. The translation product of ORF1 (ORF1p) has been robustly detected by immunoassays and shotgun mass spectrometry (MS). Yet, more sensitive detection methods would enhance the use of ORF1p as a clinical biomarker. In contrast, until now, no direct evidence of endogenous L1 ORF2 translation to protein (ORF2p) has been shown. Instead, assays for ORF2p have been limited to ectopic L1 ORF over-expression contexts and to indirect detection of endogenous ORF2p enzymatic activity, such as by the sequencing of de novo genomic insertions. Immunoassays for endogenous ORF2p have been problematic, producing apparent false positives due to cross-reactivities, and shotgun MS has not yielded reliable evidence of ORF2p peptides in biological samples.

Results: Here we present targeted mass spectrometry assays, selected and parallel reaction monitoring (SRM and PRM, respectively) to detect and quantify L1 ORF1p and ORF2p at their endogenous abundances. We were able to quantify ORF1p and ORF2p present in our samples down to a range in the low attomoles. Confident in our ability to affinity enrich ORF2p, we describe an interactome associated with endogenous ORF2-containing macromolecular assemblies.

Conclusions: This is the first assay to demonstrate sensitive and robust quantitation of endogenous ORF2p. The ability to assay ORF2p directly and quantitatively will improve our understanding of the developmental and diseased cell states where L1 expression and its activity naturally occur. The ability to simultaneously assay endogenous L1 ORF1p and ORF2p is an important step forward for L1 analytical biochemistry. Endogenous ORF2p interactomes can now be presented with confidence that ORF2p is among the enriched proteins.

Background: Piwi-interacting RNAs (piRNA)s are non-coding small RNAs that post-transcriptionally affect gene expression and regulation. Through complementary seed region binding with transposable elements (TEs), piRNAs protect the genome from transposition. A tool to link piRNAs with complementary TE targets will improve our understanding of the role of piRNAs in genome maintenance and gene regulation. Existing tools such as TEsmall can process sRNA-seq datasets to produce differentially expressed piRNAs, and piRScan developed for nematodes can link piRNAs and TEs but it requires knowledge about the target region of interest and works backwards.

Results: We developed FishPi to predict the pairings between piRNA and TEs for available genomes from zebrafish, medaka and tilapia, with full user customisation of parameters including orientation of piRNA, mismatches in the piRNA seed binding to TE and scored output lists of piRNA-TE matches. FishPi works with individual piRNAs or a list of piRNA sequences in fasta format. The software focuses on the piRNA-TE seed region and analyses reference TEs for piRNA complementarity. TE type is examined, counted and stored to a dictionary, with genomic loci recorded. Any updates to piRNA-TE binding rules can easily be incorporated by changing the seed-region options in the graphic user-interface. FishPi provides a graphic interface using tkinter for the user to input piRNA sequences to generate comprehensive reports on piRNA-TE interactions. FishPi can easily be adapted to genomes from other species and taxa opening the interpretation of piRNA functionality to a wide community.

Conclusions: Users will gain insight into genome mobility and FishPi will help further our understanding of the biological role of piRNAs and their interaction with TEs in a similar way that public databases have improved the access to and the understanding of the role of small RNAs.

Background: Messenger RNA 3' untranslated regions (3'UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA (AATAAA in DNA) is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3'UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy numbers. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands of Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may terminate transcript in some dog genes.

Results: Each of the dog's nine Can-SINE consensus sequences carry an average of three AATAAA PASs on their sense strands but zero on their antisense strands. Consistent with the idea that Can-SINEs can terminate transcripts, we find that sense-oriented Can-SINEs are approximately ten times more frequent at 3' ends of 3'UTRs compared to further upstream within 3'UTRs. Furthermore, the count of AATAAA PASs on head-to-tail SINE sequences differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3'UTR ends are likely to carry an AATAAA motif on the mRNA sense strand while those further upstream are not. We identified loci where Can-SINE insertion has truncated or altered a 3'UTR of the dog genome (dog 3'UTR) compared to the human ortholog. Dog 3'UTRs have peaks of AATAAA PAS frequency at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp length for target site duplications (TSDs). All dog Can-SINE types favor integration at TSDs beginning with A(4).

Conclusion: Dog Can-SINE retrotransposition has imported AATAAA PASs into gene transcripts and led to alteration of 3'UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3'UTR regions but are retained at the far downstream end of 3'UTRs, which we infer reflects their role as termination sequences for these transcripts.