scholarly journals Small RNA Mobility: Spread of RNA Silencing Effectors and its Effect on Developmental Processes and Stress Adaptation in Plants

2019 ◽  
Vol 20 (17) ◽  
pp. 4306 ◽  
Author(s):  
Chiara Pagliarani ◽  
Giorgio Gambino
Keyword(s):  
Small Rnas ◽  
Rna Silencing ◽  
Physiological Responses ◽  
Noncoding Rnas ◽  
Environmental Cues ◽  
Physiological Changes ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Small Noncoding Rnas ◽  
Surrounding Environment

Plants are exposed every day to multiple environmental cues, and tight transcriptome reprogramming is necessary to control the balance between responses to stress and processes of plant growth. In this context, the silencing phenomena mediated by small RNAs can drive transcriptional and epigenetic regulatory modifications, in turn shaping plant development and adaptation to the surrounding environment. Mounting experimental evidence has recently pointed to small noncoding RNAs as fundamental players in molecular signalling cascades activated upon exposure to abiotic and biotic stresses. Although, in the last decade, studies on stress responsive small RNAs increased significantly in many plant species, the physiological responses triggered by these molecules in the presence of environmental stresses need to be further explored. It is noteworthy that small RNAs can move either cell-to-cell or systemically, thus acting as mobile silencing effectors within the plant. This aspect has great importance when physiological changes, as well as epigenetic regulatory marks, are inspected in light of plant environmental adaptation. In this review, we provide an overview of the categories of mobile small RNAs in plants, particularly focusing on the biological implications of non-cell autonomous RNA silencing in the stress adaptive response and epigenetic modifications.

scholarly journals Deciphering the tRNA-derived small RNAs: origin, development, and future

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Bowen Liu ◽  
Jinling Cao ◽  
Xiangyun Wang ◽  
Chunlei Guo ◽  
Yunxia Liu ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Small Rnas ◽  
Molecular Mechanisms ◽  
Noncoding Rnas ◽  
Transfer Rna ◽  
Action Mechanism ◽  
Chemical Modifications ◽  
Future Directions ◽  
Small Noncoding Rnas ◽  
New Biomarkers

AbstractTransfer RNA (tRNA)-derived small RNAs (tsRNAs), a novel category of small noncoding RNAs, are enzymatically cleaved from tRNAs. Previous reports have shed some light on the roles of tsRNAs in the development of human diseases. However, our knowledge about tsRNAs is still relatively lacking. In this paper, we review the biogenesis, classification, subcellular localization as well as action mechanism of tsRNAs, and discuss the association between chemical modifications of tRNAs and the production and functions of tsRNAs. Furthermore, using immunity, metabolism, and malignancy as examples, we summarize the molecular mechanisms of tsRNAs in diseases and evaluate the potential of tsRNAs as new biomarkers and therapeutic targets. At the same time, we compile and introduce several resource databases that are currently publicly available for analyzing tsRNAs. Finally, we discuss the challenges associated with research in this field and future directions.

The multitasking abilities of MATE transporters in plants

2019 ◽  
Vol 70 (18) ◽  
pp. 4643-4656 ◽  
Author(s):  
Neha Upadhyay ◽  
Debojyoti Kar ◽  
Bhagyashri Deepak Mahajan ◽  
Sanchali Nanda ◽  
Rini Rahiman ◽  
...  
Keyword(s):  
Climatic Conditions ◽  
Membrane Transporters ◽  
Aluminium Tolerance ◽  
Environmental Cues ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Xenobiotic Detoxification ◽  
Almost All ◽  
Sessile Organisms ◽  
Structure And Functions

Abstract As sessile organisms, plants constantly monitor environmental cues and respond appropriately to modulate their growth and development. Membrane transporters act as gatekeepers of the cell regulating both the inflow of useful materials as well as exudation of harmful substances. Members of the multidrug and toxic compound extrusion (MATE) family of transporters are ubiquitously present in almost all forms of life including prokaryotes and eukaryotes. In bacteria, MATE proteins were originally characterized as efflux transporters conferring drug resistance. There are 58 MATE transporters in Arabidopsis thaliana, which are also known as DETOXIFICATION (DTX) proteins. In plants, these integral membrane proteins are involved in a diverse array of functions, encompassing secondary metabolite transport, xenobiotic detoxification, aluminium tolerance, and disease resistance. MATE proteins also regulate overall plant development by controlling phytohormone transport, tip growth processes, and senescence. While most of the functional characterizations of MATE proteins have been reported in Arabidopsis, recent reports suggest that their diverse roles extend to numerous other plant species. The wide array of functions exhibited by MATE proteins highlight their multitasking ability. In this review, we integrate information related to structure and functions of MATE transporters in plants. Since these transporters are central to mechanisms that allow plants to adapt to abiotic and biotic stresses, their study can potentially contribute to improving stress tolerance under changing climatic conditions.

scholarly journals Dysregulation of a family of short noncoding RNAs, tsRNAs, in human cancer

2016 ◽  
Vol 113 (18) ◽  
pp. 5071-5076 ◽  
Author(s):  
Yuri Pekarsky ◽  
Veronica Balatti ◽  
Alexey Palamarchuk ◽  
Lara Rizzotto ◽  
Dario Veneziano ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Rnas ◽  
Northern Blot Analysis ◽  
Human Cancer ◽  
Noncoding Rnas ◽  
Lymphocytic Leukemia ◽  
P Element ◽  
Human Leukemia ◽  
Hematopoietic Malignancies ◽  
Small Noncoding Rnas

Chronic lymphocytic leukemia (CLL) is the most common human leukemia, and transgenic mouse studies indicate that activation of the T-cell leukemia/lymphoma 1 (TCL1) oncogene is a contributing event in the pathogenesis of the aggressive form of this disease. While studying the regulation of TCL1 expression, we identified the microRNA cluster miR-4521/3676 and discovered that these two microRNAs are associated with tRNA sequences and that this region can produce two small RNAs, members of a recently identified class of small noncoding RNAs, tRNA-derived small RNAs (tsRNAs). We further proved that miR-3676 and miR-4521 are tsRNAs using Northern blot analysis. We found that, like ts-3676, ts-4521 is down-regulated and mutated in CLL. Analysis of lung cancer samples revealed that both ts-3676 and ts-4521 are down-regulated and mutated in patient tumor samples. Because tsRNAs are similar in nature to piRNAs [P-element–induced wimpy testis (Piwi)-interacting small RNAs], we investigated whether ts-3676 and ts-4521 can interact with Piwi proteins and found these two tsRNAs in complexes containing Piwi-like protein 2 (PIWIL2). To determine whether other tsRNAs are involved in cancer, we generated a custom microarray chip containing 120 tsRNAs 16 bp or more in size. Microarray hybridization experiments revealed tsRNA signatures in CLL and lung cancer, indicating that, like microRNAs, tsRNAs may have an oncogenic and/or tumor-suppressor function in hematopoietic malignancies and solid tumors. Thus, our results show that tsRNAs are dysregulated in human cancer.

scholarly journals Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 232 ◽  
Author(s):  
Lorena Pantano ◽  
Francisco Pantano ◽  
Eulalia Marti ◽  
Shannan Ho Sui
Keyword(s):  
Gene Regulation ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rnas ◽  
Model Organisms ◽  
Visualization Tool ◽  
Rna Seq ◽  
Small Noncoding Rnas ◽  
Different Types ◽  
Genomic Locations

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease.

scholarly journals Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 232
Author(s):  
Lorena Pantano ◽  
Francisco Pantano ◽  
Eulalia Marti ◽  
Shannan Ho Sui
Keyword(s):  
Gene Regulation ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rnas ◽  
Model Organisms ◽  
Visualization Tool ◽  
Rna Seq ◽  
Small Noncoding Rnas ◽  
Different Types ◽  
Genomic Locations

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease .

scholarly journals A review on chitosan: a new solution for combating abiotic stresses in agriculture

2020 ◽  
Vol 7 (2) ◽  
pp. 81-84
Author(s):  
Prajwal P. Dongare ◽  
Prashant R. Shingote ◽  
Narsing D. Parlawar
Keyword(s):  
Abiotic Stresses ◽  
Organic Molecule ◽  
Physiological Responses ◽  
Biochemical Properties ◽  
Wide Spread ◽  
Biotic And Abiotic Stresses ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Naturally Occurring ◽  
Hydrolysis Of

Chitosan is a second most abundant naturally occurring polysaccharide after cellulose derived from chitin which commercially produced from seafood shells, fungi (Aspergillus and mucus) and also from algae by alkaline deacetylation of chitin. It is bio adhesive, biocompatible, biodegradable, organic molecule. Chitosan has wide spread application in agriculture. Chitosan acts as bio-stimulant which upon application to plants stimulates photosynthetic rate, enhances antioxidant production, increases tolerance to biotic and abiotic stresses. Chitosan causes hydrolysis of peptidoglycan of microbes resulting to death of microbes. Recent studies have shown that chitosan induces mechanisms in plants against various biotic and abiotic stresses and helps in formation of barriers that enhances plant's productivity.This paper takes a closer look at the genesis, structural alteration and physiological responses of chitosan foliar applications on plants.As, Abiotic stresses is an important multidimensional environment stresses that damage plant’s physiology, biochemical propertIes and Molecular traits. Chitosan help to combat abiotic and biotic stresses.

scholarly journals DANSR: A Tool for the Detection of Annotated and Novel Small RNAs

2022 ◽  
Vol 8 (1) ◽  
pp. 9
Author(s):  
Jin Zhang ◽  
Abdallah M. Eteleeb ◽  
Emily B. Rozycki ◽  
Matthew J. Inkman ◽  
Amy Ly ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Biologically Relevant ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas ◽  
Rna Analysis ◽  
Length Range

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.

Identification of target genes of microRNAs in retinoic acid-induced neuronal differentiation

2005 ◽  
Vol 77 (1) ◽  
pp. 313-318 ◽  
Author(s):  
Hiroaki Kawasaki ◽  
Kazunari Taira
Keyword(s):  
Retinoic Acid ◽  
Neuronal Differentiation ◽  
Small Rnas ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Messenger Rnas ◽  
Regulate Gene Expression ◽  
Small Noncoding Rnas ◽  
Translational Level ◽  
Regulate Gene

MicroRNAs (miRNAs) are phylogenetically widespread, small noncoding RNAs of 18–25 nucleotides in length, and are expressed in animals and plants. These small RNAs can regulate gene expression at the translational level through interactions with their target messenger RNAs, and have a role in the development of Caenorhabditis elegans, plants, and mammals. Although more than 200 miRNAs have been found in mammals, it is not easy to identify their targets. We investigated the target genes of miRNAs and analyzed the function of these miRNAs during retinoic acid (RA)-induced neuronal differentiation.

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