plant small RNAs
235 views | +0 today
Follow
Your new post is loading...
Your new post is loading...
Scooped by Saima Shahid
Scoop.it!

Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs

Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs | plant small RNAs | Scoop.it
Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial.
more...
No comment yet.
Scooped by Saima Shahid
Scoop.it!

Newly identified small-RNA pathway defends genome against the enemy within

Newly identified small-RNA pathway defends genome against the enemy within | plant small RNAs | Scoop.it
Reproductive cells, such as an egg and sperm, join to form stem cells that can mature into any tissue type. But how do reproductive cells arise? We humans are born with all of the reproductive cells that we will ever produce.
more...
No comment yet.
Rescooped by Saima Shahid from fundoshi TOPICS: Plant biology, cell biology, and more
Scoop.it!

Nature : miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

Nature : miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis | plant small RNAs | Scoop.it
In plants, post-transcriptional gene silencing (PTGS) is mediated by DICER-LIKE 1 (DCL1)-dependent microRNAs (miRNAs), which also trigger 21-nucleotide secondary short interfering RNAs (siRNAs) via RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), DCL4 and ARGONAUTE 1 (AGO1), whereas transcriptional gene silencing (TGS) of transposons is mediated by 24-nucleotide heterochromatic (het)siRNAs, RDR2, DCL3 and AGO4 (ref. 4). Transposons can also give rise to abundant 21-nucleotide /`epigenetically activated/' small interfering RNAs (easiRNAs) in DECREASED DNA METHYLATION 1 (ddm1) and DNA METHYLTRANSFERASE 1 (met1) mutants, as well as in the vegetative nucleus of pollen grains and in dedifferentiated plant cell cultures. Here we show that easiRNAs in Arabidopsis thaliana resemble secondary siRNAs, in that thousands of transposon transcripts are specifically targeted by more than 50 miRNAs for cleavage and processing by RDR6. Loss of RDR6, DCL4 or DCL1 in a ddm1 background results in loss of 21-nucleotide easiRNAs and severe infertility, but 24-nucleotide hetsiRNAs are partially restored, supporting an antagonistic relationship between PTGS and TGS. Thus miRNA-directed easiRNA biogenesis is a latent mechanism that specifically targets transposon transcripts, but only when they are epigenetically reactivated during reprogramming of the germ line. This ancient recognition mechanism may have been retained both by transposons to evade long-term heterochromatic silencing and by their hosts for genome defence.

Via fundoshi
more...
fundoshi's curator insight, April 17, 2014 6:23 AM

「植物では、転写後遺伝子サイレンシング(PTGS)はDICER-LIKE 1( DCL1 )依存性マイクロRNA(miRNA)によって行われ、このmiRNAはRNA-DEPENDENT RNA POLYMERASE 6(RDR6)、DCL4、ARGONAUTE 1(AGO1)を介して21ヌクレオチド長の二次型短鎖干渉RNA(siRNA)も生じさせる。一方、トランスポゾンの転写型遺伝子サイレンシング (TGS)には、24ヌクレオチド長のヘテロクロマチン(het)siRNA、 RDR2 、 DCL3 、 AGO4 が関わっている。 DECREASED DNA METHYLATION 1 ( ddm1 )と DNA METHYLTRANSFERASE 1 ( met1 )変異体や花粉粒の栄養核、および脱分化した植物培養細胞ではトランスポゾンから21ヌクレオチド長の「エピジェネティックに活性化された」短鎖干渉RNA(easiRNA)も大量に生じることがある。今回我々はシロイヌナズナ( Arabidopsis thaliana )のeasiRNAが二次型siRNAに似ており、そのため何千ものトランスポゾン転写産物が50以上のmiRNAの特異的な標的となり、 RDR6 による切断とプロセシングを受けることを明らかにした。 ddm1 という条件下で RDR6 、 DCL4 または DCL1 を欠失させると21ヌクレオチド長のeasiRNAが失われ、重度の不稔になるが、24ヌクレオチド長のhetsiRNAは部分的に復活することから、 PTGSとTGSの間には競合関係があることが裏付けられた。従ってmiRNAが誘導するeasiRNA生合成は、トランスポゾン転写産物を特異的に標的 とする潜在的な機構だが、生殖系列の再プログラミングの際に限ってエピジェネティックに再活性化される。この古い認識機構は、トランスポゾンの側としては ヘテロクロマチン化による長期的なサイレンシングを回避するために、宿主の側ではゲノムを守るために、保持されてきたのかもしれない。」

Rescooped by Saima Shahid from Plant Biology Teaching Resources (Higher Education)
Scoop.it!

Plant Cell: mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

Plant Cell: mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat | plant small RNAs | Scoop.it

"Allohexaploid common wheat (Triticum aestivum) arose as a hybrid between allo-tetraploid Triticum turgidum and diploid Aegilops tauschii and is known to out-compete its progenitors in a number of traits, including broader adaptability to various conditions and enhanced resis- tance to biotic and abiotic stresses. It is also possible to create newly synthesized wheat allopolyploids, as hybridizations between species may be followed by spontaneous chromosome doubling. These nascent allohexaploid wheat lines, which also show heterosis and adaptive traits (see figure), may to some extent recapitulate the original genetic status of ancient wheat hybrids.

Li et al. (2014) apply this notion to an analysis of nascent allohexaploid wheat in comparison with its progenitor lines and common wheat."
Via Mary Williams
more...
No comment yet.
Rescooped by Saima Shahid from Plant Biology Teaching Resources (Higher Education)
Scoop.it!

Nature: miRNAs trigger widespread epigenetically activated siRNAs ...

Nature: miRNAs trigger widespread epigenetically activated siRNAs ... | plant small RNAs | Scoop.it
This ancient recognition mechanism may have been retained both by transposons to evade long-term heterochromatic silencing and by their hosts for genome defence.

Via Mary Williams
more...
Scooped by Saima Shahid
Scoop.it!

Sea Anemone is Genetically Half Animal, Half Plant « Homolog.us ...

Sea Anemone is Genetically Half Animal, Half Plant « Homolog.us ... | plant small RNAs | Scoop.it
This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, ...
more...
No comment yet.
Rescooped by Saima Shahid from AnnBot
Scoop.it!

Video: Striga avoids infection into other Orobanchaceae plant (2013)

via @KenShirasu http://twitter.com/KenShirasu ;


Via Kamoun Lab @ TSL, Annals of Botany: Plant Science Research
more...
Scooped by Saima Shahid
Scoop.it!

Gene Silencing with Small RNAs — Peter Waterhouse, ISS2013

Professor Peter Waterhouse from the School of Molecular Bioscience at the University of Sydney, speaking to students at ISS2013: Nanoscience — Sydney, Austra...
more...
No comment yet.
Scooped by Saima Shahid
Scoop.it!

Webinar - Degradome Sequencing for Plant microRNA Target Identification

Presenter Name: Dr. Qi Zhu - MicroRNAs (miRNAs) are endogenous small noncoding RNAs that play crucial roles in the post-transcriptional regulation of gene ex...
more...
No comment yet.
Rescooped by Saima Shahid from Plant Breeding and Genomics News
Scoop.it!

PLOS ONE: The Hot Pepper (Capsicum annuum) MicroRNA Transcriptome Reveals Novel and Conserved Targets: A Foundation for Understanding MicroRNA Functional Roles in Hot Pepper

PLOS ONE: The Hot Pepper (Capsicum annuum) MicroRNA Transcriptome Reveals Novel and Conserved Targets: A Foundation for Understanding MicroRNA Functional Roles in Hot Pepper | plant small RNAs | Scoop.it

MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nt in length which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, miRNAs and their target genes remain largely unknown in hot pepper (Capsicum annuum), one of the most important crops cultivated worldwide. Here, we employed high-throughput sequencing technology to identify miRNAs in pepper extensively from 10 different libraries, including leaf, stem, root, flower, and six developmental stage fruits. Based on a bioinformatics pipeline, we successfully identified 29 and 35 families of conserved and novel miRNAs, respectively. Northern blot analysis was used to validate further the expression of representative miRNAs and to analyze their tissue-specific or developmental stage-specific expression patterns. Moreover, we computationally predicted miRNA targets, many of which were experimentally confirmed using 5′ rapid amplification of cDNA ends analysis. One of the validated novel targets of miR-396 was a domain rearranged methyltransferase, the major de novomethylation enzyme, involved in RNA-directed DNA methylation in plants. This work provides the first reliable draft of the pepper miRNA transcriptome. It offers an expanded picture of pepper miRNAs in relation to other plants, providing a basis for understanding the functional roles of miRNAs in pepper.


Via Plant Breeding and Genomics News
more...
No comment yet.
Rescooped by Saima Shahid from Plant Breeding and Genomics News
Scoop.it!

Genome Biology | Abstract | Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids

Background

Recent genome-wide studies have suggested that in addition to genetic variation, epigenetic variation may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal model system for the study of epigenetic variation in hybrids, given the significant heterotic performance of the plant, the well-known complexity of the genome, and the rich history of epigenetic studies using this organism. However, integrated comparative transcriptomic and epigenomic analyses in different organs of maize hybrids remain largely unexplored.

Methods

We generated integrated maps of transcriptomes and epigenomes from shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different organs and genotypes.

Results

Whereas histone modifications varied both between organs and between genotypes, DNA-methylation patterns were more distinguishable between genotypes than between organs. Histone modifications were associated with transcriptomic divergence between organs and between hybrids and parents. Further, genes that were upregulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, small interfering RNAs (siRNAs) of 22 and 24 nucleotides long were shown to be derived from distinct transposable elements, and for different transposable elements in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species.

Conclusions

These results suggest that despite variation in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different organs of maize hybrids.


Via Plant Breeding and Genomics News
more...
No comment yet.
Rescooped by Saima Shahid from TAL effector science
Scoop.it!

PLOS ONE: Targeting Human MicroRNA Genes Using Engineered Tal-Effector Nucleases (TALENs)

PLOS ONE: Targeting Human MicroRNA Genes Using Engineered Tal-Effector Nucleases (TALENs) | plant small RNAs | Scoop.it

(suggested by Tom Schreiber, thx)

Hu et al, 2013

MicroRNAs (miRNAs) have quickly emerged as important regulators of mammalian physiology owing to their precise control over the expression of critical protein coding genes.

Despite significant progress in our understanding of how miRNAs function in mice, there remains a fundamental need to be able to target and edit miRNA genes in the human genome. Here, we report a novel approach to disrupting human miRNA genes ex vivo using engineered TAL-effector (TALE) proteins to function as nucleases (TALENs) that specifically target and disrupt human miRNA genes. We demonstrate that functional TALEN pairs can be designed to enable disruption of miRNA seed regions, or removal of entire hairpin sequences, and use this approach to successfully target several physiologically relevant human miRNAs including miR-155*, miR-155, miR-146a and miR-125b.

This technology will allow for a substantially improved capacity to study the regulation and function of miRNAs in human cells, and could be developed into a strategic means by which miRNAs can be targeted therapeutically during human disease.


Via dromius
more...
No comment yet.
Scooped by Saima Shahid
Scoop.it!

Plant microRNAs: key regulators of root architecture and biotic interactions | MycorWeb Plant-Microbe Interactions

Plant microRNAs: key regulators of root architecture and biotic interactions | MycorWeb Plant-Microbe Interactions | plant small RNAs | Scoop.it
Plants have evolved a remarkable faculty of adaptation to deal with various and changing environmental conditions.
more...
No comment yet.
Scooped by Saima Shahid
Scoop.it!

Elicitation of hypersensitive responses in Nicotiana glutinosa by the suppressor of RNA silencing protein P0 from poleroviruses - Wang - 2014 - Molecular Plant Pathology - Wiley Online Library

Elicitation of hypersensitive responses in Nicotiana glutinosa by the suppressor of RNA silencing protein P0 from poleroviruses - Wang - 2014 - Molecular Plant Pathology - Wiley Online Library | plant small RNAs | Scoop.it
Plant disease resistance (R) proteins that confer resistance to viruses recognize viral gene products with diverse functions, including viral suppressors of RNA silencing (VSRs). The P0 protein from poleroviruses is a VSR that targets the ARGONAUTE1 (AGO1) protein for degradation, thereby disrupting RNA silencing and antiviral defences. Here, we report resistance against poleroviruses in Nicotiana glutinosa directed against Turnip yellows virus (TuYV) and Potato leafroll virus (PLRV). The P0 proteins from TuYV (P0Tu), PLRV (P0PL) and Cucurbit aphid-borne yellows virus (P0CA) were found to elicit a hypersensitive response (HR) in N. glutinosa accession TW59, whereas other accessions recognized P0PL only. Genetic analysis showed that recognition of P0Tu by a resistance gene designated RPO1 (Resistance to POleroviruses 1) is inherited as a dominant allele. Expression of P0 from a Potato virus X (PVX) expression vector transferred recognition to the recombinant virus on plants expressing RPO1, supporting P0 as the unique Polerovirus factor eliciting resistance. The induction of HR required a functional P0 protein, as P0Tu mutants with substitutions in the F-box motif that abolished VSR activity were unable to elicit HR. We surmised that the broad P0 recognition seen in TW59 and the requirement for the F-box protein motif could indicate detection of P0-induced AGO1 degradation and disruption of RNA silencing; however, other viral silencing suppressors, including the PVX P25 that also causes AGO1 degradation, failed to elicit HR in N. glutinosa. Investigation of P0 elicitation of RPO1 could provide insight into P0 activities within the cell that trigger resistance.
more...
No comment yet.
Scooped by Saima Shahid
Scoop.it!

RNA‐directed DNA methylation requires stepwise binding of silencing factors to long non‐coding RNA - Böhmdorfer - 2014 - The Plant Journal

RNA‐directed DNA methylation requires stepwise binding of silencing factors to long non‐coding RNA - Böhmdorfer - 2014 - The Plant Journal | plant small RNAs | Scoop.it
more...
No comment yet.
Rescooped by Saima Shahid from Plant Pathogenomics
Scoop.it!

Science: Genomic-scale exchange of mRNA between a parasitic plant and its hosts (2014)

Science: Genomic-scale exchange of mRNA between a parasitic plant and its hosts (2014) | plant small RNAs | Scoop.it

Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.


Via Kamoun Lab @ TSL
more...
Arjen ten Have's curator insight, April 10, 2017 6:22 PM
Sharing stuff is key yo any interaction. The higher the mutual dependency, the more partners will share. What I do not have clear yet is whether pathogenic relationships will differ substantially from mutualistic ones. miRNA has been shown in plant pathogen relationships, but I can also envisage these in a mutualistic symbiosis. Quite a conundrum. But that' s what  plant-pathogen relations are about anyway.
Scooped by Saima Shahid
Scoop.it!

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs - Komiya - 2014 - The Plant Journal - Wiley Online Library

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs - Komiya - 2014 - The Plant Journal - Wiley Online Library | plant small RNAs | Scoop.it
Rice germline-specific Argonaute MEL1 protein binds phasiRNAs generated from more than 700 lincRNAs http://t.co/GOH6K0Y9qQ @ThePlantJournal
more...
No comment yet.
Scooped by Saima Shahid
Scoop.it!

Watch What Plants Talk About Online | Video: Full Episode | Nature | PBS

Watch What Plants Talk About Online | Video: Full Episode | Nature | PBS | plant small RNAs | Scoop.it
Plants are smarter and much more interactive than we thought! This film that explores the fascinating world of plants and plant behavior. Watch online.
more...
No comment yet.
Rescooped by Saima Shahid from AnnBot
Scoop.it!

PHD Comics: The Very Dead Caterpillar - 2 Minute Thesis

PHD Comics: The Very Dead Caterpillar - 2 Minute Thesis | plant small RNAs | Scoop.it
Link to Piled Higher and Deeper

Via Eve Emshwiller, Annals of Botany: Plant Science Research
more...
Eve Emshwiller's curator insight, July 19, 2013 11:09 AM

Jorge Cham (@PHDComics) illustrates a great 2 minute summary of a PhD disseration on plant defense.  Includes genetic diversity from teosinte, the wild ancestor of maize/corn.  I will definitely be showing this to classes!

Annals of Botany: Plant Science Research's curator insight, July 20, 2013 4:46 AM

Eve Emshwiller's insight:        

Jorge Cham (@PHDComics) illustrates a great 2 minute summary of a PhD disseration on plant defense.  Includes genetic diversity from teosinte, the wild ancestor of maize/corn.  I will definitely be showing this to classes!

Abigail Rumsey's comment, July 22, 2013 4:25 AM
That looks scarily like my undergrad revision notes, except with better artwork! It must have worked because I actually remember the jasmonate and everything.
Rescooped by Saima Shahid from Computational biology
Scoop.it!

Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways

RT @aemonten: [Report] Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways http://t.co/wTysUyLgtP

Via Asela Wijeratne
more...
No comment yet.
Scooped by Saima Shahid
Scoop.it!

PLOS ONE: A New Algorithm for Integrated Analysis of miRNA ...

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. It has been proposed that miRNAs play an important role in cancer development and progression. Their ability to affect multiple gene pathways by targeting ...
more...
No comment yet.
Rescooped by Saima Shahid from PlantBioInnovation
Scoop.it!

Introns of plant pri-miRNAs enhance miRNA biogenesis

Introns of plant pri-miRNAs enhance miRNA biogenesis | plant small RNAs | Scoop.it
EMBO reports encourages and publishes articles that report novel findings of wide biological significance in the areas of development, immunology, neuroscience, plant biology, structural biology, genomic & computational biology, genome stability &...

Via Biswapriya Biswavas Misra
more...
Biswapriya Biswavas Misra's curator insight, May 31, 2013 1:20 PM

Plant MIR genes are independent transcription units that encode long primary miRNA precursors, which usually contain introns. For two miRNA genes, MIR163 and MIR161, we show that introns are crucial for the accumulation of proper levels of mature miRNA. Removal of the intron in both cases led to a drop-off in the level of mature miRNAs. We demonstrate that the stimulating effects of the intron mostly reside in the 5′ss rather than on a genuine splicing event. Our findings are biologically significant as the presence of functional splice sites in the MIR163 gene appears mandatory for pathogen-triggered accumulation of miR163 and proper regulation of at least one of its targets.

Rescooped by Saima Shahid from Plant-Microbe Interaction
Scoop.it!

Comprehensive Protein-Based Artificial MicroRNA Screens for Effective Gene Silencing in Plants

Comprehensive Protein-Based Artificial MicroRNA Screens for Effective Gene Silencing in Plants | plant small RNAs | Scoop.it

Artificial microRNA (amiRNA) approaches offer a powerful strategy for targeted gene manipulation in any plant species. However, the current unpredictability ofamiRNA efficacy has limited broad application of this promising technology. To address this, we developed epitope-tagged protein-based amiRNA (ETPamir) screens, in which target mRNAs encoding epitope-tagged proteins were constitutively or inducibly coexpressed in protoplasts with amiRNA candidates targeting single or multiple genes. This design allowed parallel quantification of target proteins and mRNAs to define amiRNA efficacy and mechanism of action, circumventing unpredictable amiRNA expression/processing and antibody unavailability. Systematic evaluation of 63 amiRNAs in 79 ETPamir screens for 16 target genes revealed a simple, effective solution for selecting optimal amiRNAsfrom hundreds of computational predictions, reaching ∼100% gene silencing in plant cells and null phenotypes in transgenic plants. Optimal amiRNAspredominantly mediated highly specific translational repression at 5′ coding regions with limited mRNA decay or cleavage. Our screens were easily applied to diverse plant species, including Arabidopsis thaliana, tobacco (Nicotiana benthamiana), tomato (Solanum lycopersicum), sunflower (Helianthus annuus),Catharanthus roseus, maize (Zea mays) and rice (Oryza sativa), and effectively validated predicted natural miRNA targets. These screens could improve plant research and crop engineering by making amiRNA a more predictable and manageable genetic and functional genomic technology.


Via Guogen Yang
more...
No comment yet.