scholarly journals siRNA-mediated de novo silencing of Ac/Ds transposons is initiated by alternative transposition in maize

2020 ◽  
Author(s):  
Dafang Wang ◽  
Jianbo Zhang ◽  
Tao Zuo ◽  
Damon Lisch ◽  
Meixia Zhao ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Defense Mechanisms ◽  
De Novo ◽  
Inverted Repeats ◽  
Small Interfering Rnas ◽  
Major Fraction ◽  
First Case ◽  
Transposon Silencing ◽  
Alternative Transposition ◽  
Eukaryotic Genomes

AbstractAlthough Transposable Elements (TEs) comprise a major fraction of many higher eukaryotic genomes, most TEs are silenced by host defense mechanisms. The means by which otherwise active TEs are recognized and silenced remains poorly understood. Here we analyzed two independent cases of spontaneous silencing of the active maize Ac/Ds transposon system. This silencing was initiated by Alternative Transposition (AT), a type of aberrant transposition event that engages the termini of two nearby separate TEs. AT during DNA replication can generate Composite Insertions (CIs) that contain inverted duplications of the transposon sequences. We show that the inverted duplications of two CIs are transcribed to produce dsRNAs that trigger the production of two distinct classes of siRNAs: a 24-nt class complementary to the TE terminal inverted repeats (TIRs) and non-coding sub-terminal regions, and a 21-22 nt class corresponding to the TE transcribed regions. Plants containing these siRNA-generating CIs exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. This study documents the first case of TE silencing attributable to transposon self-initiated AT and may represent a general initiating mechanism for silencing of DNA transposons.Article summaryTransposable Elements (TEs) are often silenced by their hosts, but how TEs are initially recognized for silencing remains unclear. Here we describe two independent loci that induce de novo heritable silencing of maize Ac/Ds transposons. Plants containing these loci produce dsRNA and Ac-homologous small interfering RNAs, and exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. We show that these loci comprise inverted duplications of TE sequences generated by Alternative Transposition coupled with DNA re-replication. This study documents the first case of transposon silencing induced by AT and may represent a general initiating mechanism for TE silencing.

scholarly journals Small RNA-Mediated De Novo Silencing of Ac/Ds Transposons Is Initiated by Alternative Transposition in Maize

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 393-406 ◽  
Author(s):  
Dafang Wang ◽  
Jianbo Zhang ◽  
Tao Zuo ◽  
Meixia Zhao ◽  
Damon Lisch ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
De Novo ◽  
Inverted Repeats ◽  
Small Interfering Rnas ◽  
Major Fraction ◽  
First Case ◽  
Transposon Silencing ◽  
Alternative Transposition ◽  
Interfering Rna ◽  
Eukaryotic Genomes

Although transposable elements (TEs) comprise a major fraction of many higher eukaryotic genomes, most TEs are silenced by host defense mechanisms. The means by which otherwise active TEs are recognized and silenced remains poorly understood. Here we analyzed two independent cases of spontaneous silencing of the active maize Ac/Ds transposon system. This silencing is initiated by alternative transposition, a type of aberrant transposition event that engages the termini of two nearby separate TEs. Alternative transposition during DNA replication can generate Composite Insertions that contain inverted duplications of the transposon sequences. We show that the inverted duplications of two Composite Insertions are transcribed to produce double-stranded RNAs that trigger the production of two distinct classes of small interfering RNAs: a 24-nt class complementary to the TE terminal inverted repeats and noncoding subterminal regions, and a 21- to 22-nt class corresponding to the TE transcribed regions. Plants containing these small interfering RNA-generating Composite Insertions exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. Further, we demonstrate that Composite Insertions can heritably silence otherwise active elements in trans. This study documents the first case of transposon silencing induced by alternative transposition and may represent a general initiating mechanism for silencing of DNA transposons.

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 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 Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes

2020 ◽  
Vol 48 (12) ◽  
pp. 6685-6698 ◽  
Author(s):  
Xinyan Zhang ◽  
Meixia Zhao ◽  
Donald R McCarty ◽  
Damon Lisch
Keyword(s):  
Transposable Elements ◽  
Rna Polymerase Ii ◽  
De Novo ◽  
Open Chromatin ◽  
Passive Targeting ◽  
Site Distribution ◽  
Highly Expressed Genes ◽  
Negative Impacts ◽  
Integration Strategies ◽  
Eukaryotic Genomes

Abstract Transposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic genomes and by selection following integration. Here, we compare TE target site distribution in host genomes using multiple de novo transposon insertion datasets in both plants and animals and compare them in the context of genome-wide transcriptional landscapes. We showcase two distinct types of transcription-associated TE targeting strategies that suggest a process of convergent evolution among eukaryotic TE families. The integration of two precision-targeting elements are specifically associated with initiation of RNA Polymerase II transcription of highly expressed genes, suggesting the existence of novel mechanisms of precision TE targeting in addition to passive targeting of open chromatin. We also highlight two features that can facilitate TE survival and rapid proliferation: tissue-specific transposition and minimization of negative impacts on nearby gene function due to precision targeting.

scholarly journals Software Evaluation for De Novo Detection of Transposons

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

Abstract 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 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 Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin H.-C. Wei ◽  
Lauren Gibilisco ◽  
Doris Bachtrog
Keyword(s):  
Y Chromosome ◽  
Early Development ◽  
Defense Mechanisms ◽  
De Novo ◽  
Genome Integrity ◽  
Selfish Dna ◽  
Mutational Burden ◽  
Y Chromosomes ◽  
Genome Wide ◽  
Eukaryotic Genomes

Abstract Large portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity in Drosophila. Repeat-rich Y chromosomes can act as reservoirs for TEs (‘toxic’ Y effect), and incomplete epigenomic defenses during early development can lead to deleterious TE mobilization. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different ages. Zygotic TE expression is elevated in male embryos relative to females in both species, mostly due to expression of Y-linked TEs. Interestingly, male-biased TE expression diminishes across development in D. pseudoobscura, but remains elevated in D. miranda, the species with the younger and larger Y chromosome. The repeat-rich Y of D. miranda still contains many actively transcribed genes, which compromise the formation of silencing heterochromatin. Elevated TE expression results in more de novo insertions of repeats in males compared to females. This lends support to the idea that the ‘toxic’ Y chromosome can create a mutational burden in males when genome-wide defense mechanisms are compromised, and suggests a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA.

scholarly journals Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males

2020 ◽  
Author(s):  
Kevin H.-C. Wei ◽  
Lauren Gibilisco ◽  
Doris Bachtrog
Keyword(s):  
Y Chromosome ◽  
Early Development ◽  
Defense Mechanisms ◽  
De Novo ◽  
Genome Integrity ◽  
Selfish Dna ◽  
Mutational Burden ◽  
Y Chromosomes ◽  
Genome Wide ◽  
Eukaryotic Genomes

AbstractLarge portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity in Drosophila. Repeat-rich Y chromosomes can act as reservoirs for TEs (‘toxic’ Y effect), and incomplete epigenomic defenses during early development can lead to deleterious TE mobilization. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different age. Zygotic TE expression is elevated in male embryos relative to females in both species, mostly due to expression of Y-linked TEs. Interestingly, male-biased TE misexpression diminishes across development in D. pseudoobscura, but remains elevated in D. miranda, the species with the younger and larger Y chromosome. The repeat-rich Y of D. miranda still contains many actively transcribed genes, which compromise the formation of silencing heterochromatin. Elevated TE expression results in more de novo insertions of repeats in males compared to females. This lends support to the idea that the ‘toxic’ Y chromosome can create a mutational burden in males when genome-wide defense mechanisms are compromised, and suggests a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA.

scholarly journals Endovascular repair of de novo post-stenotic aortic coarctation aneurysms with complex collateral supply: two cases with long and medium term follow-up

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Omar Abdel-Hadi ◽  
John Thomson ◽  
Simon J. McPherson
Keyword(s):  
Stent Graft ◽  
Endovascular Repair ◽  
Aortic Coarctation ◽  
De Novo ◽  
Aortic Aneurysms ◽  
Medium Term ◽  
First Case ◽  
Case Presentations ◽  
Selective Embolisation

Abstract Purpose To report the technical details and outcomes of the endovascular repair of two cases of de novo post-stenotic aortic coarctation aneurysms complicated by complex collateral supply. Case presentations Two patients with thoracic aortic aneurysms complicated by complex aneurysm sac collaterals distal to a previously untreated thoracic aortic coarctation have been treated at our institution. Open surgical intervention was deemed to carry a high risk of haemorrhage due to the degree and complexity of arterial collateralisation. In the first case, selective embolisation of collateral vasculature was performed prior to successful exclusion of the aneurysm with a thoracic endovascular stent-graft and then balloon-expandable stent dilatation of the coarctation stenosis. In the second case, the additional technique of using a jailed sheath within the aneurysm sac allowed for selective embolisation of previously inconspicuous collaterals after deployment of the stent-graft and stent combination. Results Technical success was achieved in both patients with successful occlusion of the aneurysm, with no recorded complications or aneurysm sac perfusion in the long and medium term follow up periods respectively. Conclusion De novo post stenotic aortic coarctation aneurysms are rare. Endovascular repair is a safe and durable technique that provides a less invasive alternative to open surgical repair. The use of a jailed sheath allows for complete selective embolisation of complex collaterals avoiding a type II aneurysm endoleak.

Enhanced accumulation of pinosylvin stilbenes and related gene expression in Pinus strobus after infection of pine wood nematode

2021 ◽  
Author(s):  
Hwan-Su Hwang ◽  
Jung Yeon Han ◽  
Yong Eui Choi
Keyword(s):  
Transcription Factors ◽  
Defense Mechanisms ◽  
De Novo ◽  
Pinus Strobus ◽  
Pine Wilt Disease ◽  
Monomethyl Ether ◽  
Bursaphelenchus Xylophilus ◽  
Nematicidal Activity ◽  
Dependent Manner ◽  
Pine Wood

Abstract Pine wood nematodes (PWNs: Bursaphelenchus xylophilus) infect pine trees and cause serious pine wilt disease. Eastern white pine (Pinus strobus) has resistance to PWN. However, the detailed defense mechanisms of P. strobus against PWN are not well known. When P. strobus plants were infected with PWNs, the accumulation of stilbenoids, dihydropinosylvin monomethyl ether (DPME) and pinosylvin monomethyl ether (PME), were increased remarkably. DPME and PME had the high nematicidal activity. Interestingly, the nematicidal activity of the two compounds was resulted in a developmental stage-dependent manner. PME was more toxic to adult PWNs than juveniles, whereas DPME was found more toxic to juvenile PWNs than the adults. The genes involved in PME and DPME biosynthesis such as phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), pinosylvin synthase (STS), and pinosylvin O-methyltransferase (PMT) were isolated using de novo sequencing of the transcriptome in P. strobus. In addition, transcription factors (bHLH, MYB and WRKY) related to stilbene biosynthesis were isolated. qPCR analyses of the selected genes (PAL, 4CL, STS, and PMT) including transcription factors (bHLH, MYB and WRKY) revealed that the expression level of the selected genes highly enhanced after PWN infection. Our results suggest that pinosylvin-type stilbenoid biosynthesis is highly responsive to PWN infection and plays an important role in PWN resistance of P. strobus trees.

scholarly journals Pustular Rash in Crohn’s Patient on Ustekinumab Raises Concern for Drug-Induced Paradoxical Psoriasis

2021 ◽  
pp. 662-666
Author(s):  
Mitra Barahimi ◽  
Scott Lee ◽  
Kindra Clark-Snustad
Keyword(s):  
Side Effect ◽  
De Novo ◽  
Pustular Psoriasis ◽  
Initial Weight ◽  
Drug Induced ◽  
Clinical Recurrence ◽  
Potential Side Effect ◽  
First Case ◽  
Tnf Antagonist ◽  
Subcorneal Pustular Dermatosis

We report the case of a 51-year-old male with Crohn’s disease (CD) who developed a reproducible pustular rash after ustekinumab (UST) administration. The patient first presented with a pustular rash on his hands, body, extremities, and scalp starting 5 weeks after his initial weight-based UST induction. The rash resolved spontaneously, then recurred 4 weeks after his first subcutaneous maintenance dose of UST 90 mg. Biopsy of the affected area demonstrated subcorneal pustular dermatosis (SPD). UST was discontinued and the rash resolved. Unfortunately, the patient experienced clinical recurrence of CD, and given prior failure of multiple CD medications, UST was restarted with premedication. Two weeks after UST re-induction, the rash recurred, though less severe. Given improvement in CD symptoms, UST was continued and the rash managed with topical corticosteroids. This is the first case of drug-induced SPD associated with UST. One case report has previously described de novo pustular psoriasis associated with UST in a patient with CD and enteropathic arthritis. Notably, SPD and pustular psoriasis can be histologically indistinguishable. The development of a paradoxical psoriasiform rash is thought to be one of the few dose and duration dependent side effects of TNF-antagonist therapy but has not previously been established as a side effect of UST. This case demonstrates a new potential side effect of UST.

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