scholarly journals The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora

2017 ◽  
Vol 9 (10) ◽  
pp. 2911-2920 ◽  
Author(s):  
Robert Horvath ◽  
Tanja Slotte
Keyword(s):  
Transposable Elements ◽  
Small Rna ◽  
Purifying Selection ◽  
Epigenetic Silencing

scholarly journals A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6080
Author(s):  
Clicia Grativol ◽  
Flavia Thiebaut ◽  
Sara Sangi ◽  
Patricia Montessoro ◽  
Walaci da Silva Santos ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Small Rna ◽  
Genome Assembly ◽  
Inverted Repeat ◽  
Small Rnas ◽  
Distribution Patterns ◽  
Plant Genomes ◽  
Sugarcane Genome

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.

scholarly journals Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

2017 ◽  
Author(s):  
Samuel H. Lewis ◽  
Kaycee A. Quarles ◽  
Yujing Yang ◽  
Melanie Tanguy ◽  
Lise Frézal ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Small Rna ◽  
Rna Silencing ◽  
Individual Species ◽  
Rna Molecules ◽  
Horseshoe Crabs ◽  
Silencing Pathways ◽  
Pirna Pathway ◽  
Interference Mechanism

AbstractIn animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were likely present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and mRNAs are common among arthropods. The presence of an RNA-dependent RNA polymerase in chelicerates (horseshoe crabs, spiders, scorpions) suggests that arthropods originally used a plant-like RNA interference mechanism to silence TEs. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.

scholarly journals The role of siRNAs in genome stability maintaining in the bread wheat introgression lines

2020 ◽  
Vol 26 ◽  
pp. 108-113
Author(s):  
A. G. Navalikhina ◽  
M. Z. Antonyuk ◽  
T. K. Ternovska
Keyword(s):  
Transposable Elements ◽  
Bread Wheat ◽  
Small Rna ◽  
Genome Stability ◽  
Molecular Mechanisms ◽  
Wheat Variety ◽  
Introgression Lines ◽  
Key Factor ◽  
Methylation Patterns

Aim. Deviations of the siRNAs levels from the parental ones in the plants with hybrid genomes are associated with the activation of transposable elements (TE). This, in turn, lead to the further genome rearrangements. Introgression lines Triticum aestivum / Amblyopyrum muticum are cytologically stable, however, there are visible signs of genetic and (or) epigenetic restructuring that are still going on. Molecular mechanisms of these processes are the subject of our study. Methods. The levels of siRNAs in the plant lemmas were determined by small RNA-seq. Reads of the small RNA libraries were aligned to the repeats to find siRNA sequences. Results. Introgression lines (ILs) and parental amphidiploid have variable levels of siRNAs regulating MITE and CACTA transposable elements, compared with the parental bread wheat variety. For twelve TE sequences, majority of which are CACTA elements, decrease in the levels of siRNAs in ILs and amphidiploid, compared to the wheat, is statistically significant. Decreased siRNAs levels could lead to the activation of corresponding TE classes. Conclusions. Variation of siRNA levels in ILs and amphidiploid can be the key factor that cause rearrangements in their genomes. These include activation of TEs, changes in DNA methylation patterns, and gene expression variation. Therefore, detected changes in siRNA levels can be the molecular mechanisms of the processes that occur in studied hybrid genomes. Keywords: siRNA, transposable elements, amphidiploid, introgression lines.

Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

2021 ◽  
pp. gr.275658.121
Author(s):  
Yuyun Zhang ◽  
Zijuan Li ◽  
Yu'e Zhang ◽  
Kande Lin ◽  
Yuan Peng ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Network ◽  
Sequence Similarity ◽  
Purifying Selection ◽  
Wheat Genome ◽  
Specific Gene ◽  
High Sequence Similarity ◽  
Wheat Genome Evolution

More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.

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