scholarly journals Miniature inverted-repeat transposable elements drive rapid microRNA diversification in angiosperms

2021 ◽  
Author(s):  
Zhonglong Guo ◽  
Zheng Kuang ◽  
Yihan Tao ◽  
Haotian Wang ◽  
Miaomiao Wan ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Small Rnas ◽  
De Novo ◽  
Arms Race ◽  
Plant Adaptation ◽  
Molecular Domestication ◽  
Transcription Process ◽  
Sporadic Cases ◽  
And Behavior

MicroRNAs (miRNAs) are rapidly evolving endogenous small RNAs programing organism function and behavior. Although models for miRNA origination have been proposed based on sporadic cases, the genomic mechanisms driving swift diversification of the miRNA repertoires in plants remain elusive. Here, by comprehensively analyzing 20 phylogenetically representative plant species, we identified miniature inverted-repeat transposable elements (MITEs) as the predominant genomic sources for de novo miRNAs in angiosperms. Our data illustrated a transposition-transcription process whereby properly sized MITEs transposed into active genic regions could be converted into new miRNAs, termed MITE-miRNAs, in as few as 20 generations. We showed that this molecular domestication mechanism leads to a possible evolutionary arms race between the MITEs and the host genomes that rapidly and continuously changes the miRNA repertoires. We found that the MITE-miRNAs are selected for targeting genes associated with plant adaptation and habitat expansion, thereby constituting a genomic innovation potentially underlying angiosperm megadiversity.

scholarly journals Small RNA Functions as a Trafficking Effector in Plant Immunity

2019 ◽  
Vol 20 (11) ◽  
pp. 2816 ◽  
Author(s):  
Chen Zhu ◽  
Ting Liu ◽  
Ya-Nan Chang ◽  
Cheng-Guo Duan
Keyword(s):  
Small Rna ◽  
Stress Responses ◽  
Small Rnas ◽  
Plant Immunity ◽  
Arms Race ◽  
Abiotic And Biotic Stress ◽  
Plant Adaptation ◽  
Cellular Processes ◽  
Challenging Environment ◽  
Rna Export

Small RNAs represent a class of small but powerful agents that regulate development and abiotic and biotic stress responses during plant adaptation to a constantly challenging environment. Previous findings have revealed the important roles of small RNAs in diverse cellular processes. The recent discovery of bidirectional trafficking of small RNAs between different kingdoms has raised many interesting questions. The subsequent demonstration of exosome-mediated small RNA export provided a possible tool for further investigating how plants use small RNAs as a weapon during the arms race between plant hosts and pathogens. This review will focus on discussing the roles of small RNAs in plant immunity in terms of three aspects: the biogenesis of extracellular small RNAs and the transportation and trafficking small RNA-mediated gene silencing in pathogens.

scholarly journals Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower

2019 ◽  
Vol 116 (35) ◽  
pp. 17578-17583 ◽  
Author(s):  
Delfina Gagliardi ◽  
Damian A. Cambiagno ◽  
Agustin L. Arce ◽  
Ariel H. Tomassi ◽  
Jorge I. Giacomelli ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Inverted Repeat ◽  
Small Rnas ◽  
Rna Silencing ◽  
De Novo ◽  
Epigenetic Modification ◽  
Regulatory Elements ◽  
Dynamic Regulation ◽  
Transposon Activity ◽  
De Novo Methylation

Transposable elements (TEs) are extremely abundant in complex plant genomes. siRNAs of 24 nucleotides in length control transposon activity in a process that involves de novo methylation of targeted loci. Usually, these epigenetic modifications trigger nucleosome condensation and a permanent silencing of the affected loci. Here, we show that a TE-derived inverted repeat (IR) element, inserted near the sunflower HaWRKY6 locus, dynamically regulates the expression of the gene by altering chromatin topology. The transcripts of this IR element are processed into 24-nt siRNAs, triggering DNA methylation on its locus. These epigenetic marks stabilize the formation of tissue-specific loops in the chromatin. In leaves, an intragenic loop is formed, blocking HaWRKY6 transcription. While in cotyledons (Cots), formation of an alternative loop, encompassing the whole HaWRKY6 gene, enhances transcription of the gene. The formation of this loop changes the promoter directionality, reducing IR transcription, and ultimately releasing the loop. Our results provide evidence that TEs can act as active and dynamic regulatory elements within coding loci in a mechanism that combines RNA silencing, epigenetic modification, and chromatin remodeling machineries.

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 MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Juan Manuel Crescente ◽  
Diego Zavallo ◽  
Marcelo Helguera ◽  
Leonardo Sebastián Vanzetti
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Large Genomes

scholarly journals Identification of De Novo Germline Mutations in the HRPT2 Gene in Two Apparently Sporadic Cases with Challenging Parathyroid Tumor Diagnoses

2011 ◽  
Vol 22 (1) ◽  
pp. 44-52 ◽  
Author(s):  
Branca Maria Cavaco ◽  
Rita Santos ◽  
Ana Félix ◽  
Davide Carvalho ◽  
José Manuel Lopes ◽  
...  
Keyword(s):  
De Novo ◽  
Germline Mutations ◽  
Parathyroid Tumor ◽  
Sporadic Cases ◽  
Hrpt2 Gene

scholarly journals Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis

2021 ◽  
Author(s):  
Jincheng Long ◽  
James Walker ◽  
Wenjing She ◽  
Billy Aldridge ◽  
Hongbo Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Small Rnas ◽  
Nurse Cell ◽  
De Novo ◽  
Epigenetic Inheritance ◽  
Genome Integrity ◽  
Nurse Cells ◽  
Male Germline ◽  
Methylation Patterns

AbstractThe plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and facilitates meiosis. Why reprogramming is limited to the germline and how specific genes are chosen is unknown. Here, we demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by germline-specific siRNAs transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) via activity of the tapetum-specific chromatin remodeler CLASSY3. Remarkably, tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Finally, we demonstrate that these nurse cell-derived siRNAs (niRNAs) silence germline transposons, thereby safeguarding genome integrity. Our results reveal that tapetal niRNAs are sufficient to reconstitute germline methylation patterns and drive extensive, functional methylation reprogramming analogous to piRNA-mediated reprogramming in animal germlines.

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.

Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution

2012 ◽  
Vol 124 (7) ◽  
pp. 1365-1373 ◽  
Author(s):  
Beery Yaakov ◽  
Elif Ceylan ◽  
Katherine Domb ◽  
Khalil Kashkush
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat
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