scholarly journals Robustness of Transposable Element regulation but no genomic shock observed in interspecific Arabidopsis hybrids

2018 ◽  
Author(s):  
Ulrike Göbel ◽  
Agustin Arce ◽  
Fei He ◽  
Alain Rico ◽  
Gregor Schmitz ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transposable Elements ◽  
Transposable Element ◽  
Parental Species ◽  
Strongly Correlated ◽  
Severe Dehydration ◽  
Genomic Context ◽  
Small Magnitude ◽  
F1 Hybrid ◽  
Genomic Shock

AbstractThe merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. We conclude that TE expression is globally robust to hybridization and that the term “genomic shock” is no longerappropriate to describe the anticipated consequences of merging divergent genomes in a hybrid.

scholarly journals Transposable element mobilization in interspecific yeast hybrids

2020 ◽  
Author(s):  
Caiti Smukowski Heil ◽  
Kira Patterson ◽  
Angela Shang-Mei Hickey ◽  
Erica Alcantara ◽  
Maitreya J. Dunham
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Regulation System ◽  
Ty Elements ◽  
Genomic Shock ◽  
Transposition Rate ◽  
Order Of Magnitude ◽  
Element Movement ◽  
Species Specific

AbstractBarbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements. This hypothesis is based on the idea that regulation of transposable element movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of transposable elements in Saccharomyces cerevisiae x Saccharomyces uvarum interspecific yeast hybrids. S. cerevisiae have a small number of active long terminal repeat (LTR) retrotransposons (Ty elements), while their distant relative S. uvarum have lost the Ty elements active in S. cerevisiae. While the regulation system of Ty elements is known in S. cerevisiae, it is unclear how Ty elements are regulated in other Saccharomyces species, and what mechanisms contributed to the loss of most classes of Ty elements in S. uvarum. Therefore, we first assessed whether transposable elements could insert in the S. uvarum sub-genome of a S. cerevisiae x S. uvarum hybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and non-randomly in the S. uvarum genome. We then used an in vivo reporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can facilitate the introduction of transposable elements across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of transposable elements suggested by the genomic shock theory.

scholarly journals Transposable element mobilization in interspecific yeast hybrids

2021 ◽  
Author(s):  
Caiti Smukowski Heil ◽  
Kira Patterson ◽  
Angela Shang-Mei Hickey ◽  
Erica Alcantara ◽  
Maitreya J Dunham
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Regulation System ◽  
Ty Elements ◽  
Genomic Shock ◽  
Transposition Rate ◽  
Order Of Magnitude ◽  
Element Movement ◽  
Species Specific

Abstract Barbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements. This hypothesis is based on the idea that regulation of transposable element movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of transposable elements in Saccharomyces cerevisiae x Saccharomyces uvarum interspecific yeast hybrids. S. cerevisiae have a small number of active long terminal repeat (LTR) retrotransposons (Ty elements), while their distant relative S. uvarum have lost the Ty elements active in S. cerevisiae. While the regulation system of Ty elements is known in S. cerevisiae, it is unclear how Ty elements are regulated in other Saccharomyces species, and what mechanisms contributed to the loss of most classes of Ty elements in S. uvarum. Therefore, we first assessed whether transposable elements could insert in the S. uvarum sub-genome of a S. cerevisiae x S. uvarum hybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and non-randomly in the S. uvarum genome. We then used an in vivo reporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can potentially facilitate the introduction of transposable elements across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of transposable elements suggested by the genomic shock theory.

scholarly journals Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anna Ullastres ◽  
Miriam Merenciano ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Populations ◽  
Regulatory Elements ◽  
Genomic Context ◽  
Specific Expression ◽  
Survival Capacity ◽  
Immune Related Genes

Abstract Background Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements. Results In this work, we use a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identify 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validate three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions is consistent with an increased survival to infection. Indeed, for one of the insertions, we show that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion is deleted from its native genomic context. Conclusions We show that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, transposable elements are likely to play a role in immune response in other organisms as well.

scholarly journals Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weitao Chen ◽  
Ming Zou ◽  
Yuefei Li ◽  
Shuli Zhu ◽  
Xinhui Li ◽  
...  
Keyword(s):  
De Novo ◽  
Parental Species ◽  
F1 Hybrids ◽  
Pelteobagrus Fulvidraco ◽  
F1 Hybrid ◽  
Short Reads ◽  
Final Assembly ◽  
Genome Complexity ◽  
Hybrid Genome ◽  
Silurus Asotus

AbstractGenome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

scholarly journals Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yan Xue ◽  
Zhenhui Zhong ◽  
C. Jake Harris ◽  
Javier Gallego-Bartolomé ◽  
Ming Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Arabidopsis Thaliana ◽  
Transposable Element ◽  
Zinc Finger ◽  
Protein Function ◽  
C Elegans ◽  
Eukaryotic Organisms

AbstractThe Microrchidia (MORC) family of ATPases are required for transposable element (TE) silencing and heterochromatin condensation in plants and animals, and C. elegans MORC-1 has been shown to topologically entrap and condense DNA. In Arabidopsis thaliana, mutation of MORCs has been shown to reactivate silent methylated genes and transposons and to decondense heterochromatic chromocenters, despite only minor changes in the maintenance of DNA methylation. Here we provide the first evidence localizing Arabidopsis MORC proteins to specific regions of chromatin and find that MORC4 and MORC7 are closely co-localized with sites of RNA-directed DNA methylation (RdDM). We further show that MORC7, when tethered to DNA by an artificial zinc finger, can facilitate the establishment of RdDM. Finally, we show that MORCs are required for the efficient RdDM mediated establishment of DNA methylation and silencing of a newly integrated FWA transgene, even though morc mutations have no effect on the maintenance of preexisting methylation at the endogenous FWA gene. We propose that MORCs function as a molecular tether in RdDM complexes to reinforce RdDM activity for methylation establishment. These findings have implications for MORC protein function in a variety of other eukaryotic organisms.

An Analysis of Microsatellite Loci in Arabidopsis thaliana: Mutational Dynamics and Application

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1475-1488
Author(s):  
V Vaughan Symonds ◽  
Alan M Lloyd
Keyword(s):  
Arabidopsis Thaliana ◽  
Microsatellite Loci ◽  
Current Knowledge ◽  
Flowering Plant ◽  
Allele Frequency Distribution ◽  
Strongly Correlated ◽  
Microsatellite Evolution ◽  
Stepwise Mutation ◽  
Mutation Pattern ◽  
Infinite Alleles Model

Abstract Microsatellite loci are among the most commonly used molecular markers. These loci typically exhibit variation for allele frequency distribution within a species. However, the factors contributing to this variation are not well understood. To expand on the current knowledge of microsatellite evolution, 20 microsatellite loci were examined for 126 accessions of the flowering plant, Arabidopsis thaliana. Substantial variability in mutation pattern among loci was found, most of which cannot be explained by the assumptions of the traditional stepwise mutation model or infinite alleles model. Here it is shown that the degree of locus diversity is strongly correlated with the number of contiguous repeats, more so than with the total number of repeats. These findings support a strong role for repeat disruptions in stabilizing microsatellite loci by reducing the substrate for polymerase slippage and recombination. Results of cluster analyses are also presented, demonstrating the potential of microsatellite loci for resolving relationships among accessions of A. thaliana.

scholarly journals Characterization of the Putative Transposase mRNA of Tag1, Which Is Ubiquitously Expressed in Arabidopsis and Can Be Induced by Agrobacterium-Mediated Transformation With dTag1 DNA

Genetics ◽  
1998 ◽  
Vol 149 (2) ◽  
pp. 693-701 ◽  
Author(s):  
Dong Liu ◽  
Nigel M Crawford
Keyword(s):  
Arabidopsis Thaliana ◽  
Transposable Element ◽  
Nuclear Localization ◽  
Nuclear Localization Signal ◽  
Transcript Levels ◽  
Agrobacterium Mediated Transformation ◽  
Transgenic Lines ◽  
Localization Signal ◽  
Transposase Mrna

Abstract Tag1 is an autonomous transposable element of Arabidopsis thaliana. Tag1 expression was examined in two ecotypes of Arabidopsis (Columbia and No-0) that were transformed with CaMV 35S-Tag1-GUS DNA. These ecotypes contain no endogenous Tag1 elements. A major 2.3-kb and several minor transcripts were detected in all major organs of the plants. The major transcript encoded a putative transposase of 84.2 kD with two nuclear localization signal sequences and a region conserved among transposases of the Ac or hAT family of elements. The abundance of Tag1 transcripts varied among transgenic lines and did not correlate with somatic excision frequency or germinal reversion rates, suggesting that factors other than transcript levels control Tag1 excision activity. In untransformed plants of the Landsberg ecotype, which contain two endogenous Tag1 elements, no Tag1 transcripts were detected. Agrobacterium-mediated transformation of these Landsberg plants with a defective 1.4-kb Tag1 element resulted in the appearance of full-length Tag1 transcripts from the endogenous elements. Transformation with control DNA containing no Tag1 sequences did not activate endogenous Tag1 expression. These results indicate that Agrobacterium-mediated transformation with dTag1 can activate the expression of Tag1.

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.

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