scholarly journals Extracellular small RNAs: what, where, why?

2012 ◽  
Vol 40 (4) ◽  
pp. 886-890 ◽  
Author(s):  
Anna M. Hoy ◽  
Amy H. Buck
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Cell Communication ◽  
Cell Types ◽  
Free Form ◽  
Proper Function ◽  
Developmental Systems ◽  
Regulate Gene Expression ◽  
Extracellular Mirnas ◽  
A Cell

miRNAs (microRNAs) are a class of small RNA that regulate gene expression by binding to mRNAs and modulating the precise amount of proteins that get expressed in a cell at a given time. This form of gene regulation plays an important role in developmental systems and is critical for the proper function of numerous biological pathways. Although miRNAs exert their functions inside the cell, these and other classes of RNA are found in body fluids in a cell-free form that is resistant to degradation by RNases. A broad range of cell types have also been shown to secrete miRNAs in association with components of the RISC (RNA-induced silencing complex) and/or encapsulation within vesicles, which can be taken up by other cells. In the present paper, we provide an overview of the properties of extracellular miRNAs in relation to their capacity as biomarkers, stability against degradation and mediators of cell–cell communication.

scholarly journals Mechanism of Stochastic Resonance in a Quorum Sensing Network Regulated by Small RNAs

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Ya-nan Zhu ◽  
Jianwei Shen ◽  
Yong Xu
Keyword(s):  
Quorum Sensing ◽  
Stochastic Resonance ◽  
Small Rna ◽  
Small Rnas ◽  
Cell Communication ◽  
The Other ◽  
Important Process ◽  
Positive Role ◽  
Bacterial Quorum Sensing ◽  
Bacterial Quorum

Bacterial quorum sensing (QS) is an important process of cell communication and more and more attention is paid to it. Moreover, the noises are ubiquitous in nature and often play positive role. In this paper, we investigate how the noise enhances the QS though the stochastic resonance (SR) and explain the mechanism of SR in this quorum sensing network. In addition, we also discuss the interaction between the small RNA and the other genes in this network and discover the biological importance.

scholarly journals Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci

2017 ◽  
Author(s):  
Seth Polydore ◽  
Michael J. Axtell
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Small Rna ◽  
Small Rnas ◽  
Rna Seq ◽  
Triple Mutant ◽  
Physiological Mechanisms ◽  
Protein Coding ◽  
Regulate Gene Expression ◽  
Rna Biogenesis

SummaryPlant small RNAs regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that aren’t. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs and other hairpin-derived sRNAs. In this study, we produced and analyzed small RNA-seq libraries from rdr1/rdr2/rdr6 triple mutant plants. Only a small fraction of all sRNA loci were RDR1/RDR2/RDR6-independent; most of these were microRNA loci or associated with predicted hairpin precursors. We found 58 previously annotated microRNA loci that were reliant on RDR1, −2, or −6 function, casting doubt on their classification. We also found 38 RDR1/2/6-independent small RNA loci that are not MIRNAs or otherwise hairpin-derived, and did not fit into other known paradigms for small RNA biogenesis. These 38 small RNA-producing loci have novel biogenesis mechanisms, and are frequently located in the vicinity of protein-coding genes. Altogether, our analysis suggest that these 38 loci represent one or more new types of small RNAs in Arabidopsis thaliana.Significance StatementSmall RNAs regulate gene expression in plants and are produced through a variety of previously-described mechanisms. Here, we examine a set of previously undiscovered small RNA-producing loci that are produced by novel mechanisms.

scholarly journals ICELLNET: a transcriptome-based framework to dissect intercellular communication

2020 ◽  
Author(s):  
Floriane Noël ◽  
Lucile Massenet-Regad ◽  
Irit Carmi-Levy ◽  
Antonio Cappuccio ◽  
Maximilien Grandclaudon ◽  
...  
Keyword(s):  
Cell Population ◽  
Cell Communication ◽  
Cell Types ◽  
Receptor Expression ◽  
Global Integration ◽  
Cancer Associated Fibroblast ◽  
Receptor Interactions ◽  
Biological Interpretation ◽  
A Cell ◽  
Multiple Cell

AbstractCell-to-cell communication can be inferred from ligand-receptor expression in cell transcriptomic datasets. However, important challenges remain: 1) global integration of cell-to-cell communication, 2) biological interpretation, and 3) application to individual cell population transcriptomic profiles. We developed ICELLNET, a transcriptomic-based framework integrating: 1) an original expert-curated database of ligand-receptor interactions accounting for multiple subunits expression, 2) quantification of communication scores, 3) the possibility to connect a cell population of interest with 31 reference human cell types (BioGPS), and 4) three visualization modes to facilitate biological interpretation. We applied ICELLNET to uncover different communication in breast cancer associated fibroblast (CAF) subsets. ICELLNET also revealed autocrine IL-10 as a switch to control human dendritic cell communication with up to 12 other cell types, four of which were experimentally validated. In summary, ICELLNET is a global, versatile, biologically validated, and easy-to-use framework to dissect cell communication from single or multiple cell-based transcriptomic profile(s).

scholarly journals MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data

2020 ◽  
Vol 21 (5) ◽  
pp. 1754 ◽  
Author(s):  
Enrico Gaffo ◽  
Michele Bortolomeazzi ◽  
Andrea Bisognin ◽  
Piero Di Battista ◽  
Federica Lovisa ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Cell Types ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Sequencing Data ◽  
Research Findings ◽  
Human Blood Cell ◽  
And Function ◽  
Comprehensive Study

MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function.

scholarly journals A structural perspective on the mechanisms of quorum sensing activation in bacteria

2015 ◽  
Vol 87 (4) ◽  
pp. 2189-2203 ◽  
Author(s):  
CAROLINA LIXA ◽  
AMANDA MUJO ◽  
CRISTIANE D. ANOBOM ◽  
ANDERSON S. PINHEIRO
Keyword(s):  
Gene Expression ◽  
Quorum Sensing ◽  
Rational Design ◽  
Three Dimensional ◽  
Cell Communication ◽  
Dependent Manner ◽  
Regulate Gene Expression ◽  
Wide Range ◽  
A Cell ◽  
Regulate Gene

Bacteria are able to synchronize the population behavior in order to regulate gene expression through a cell-to-cell communication mechanism called quorum sensing. This phenomenon involves the production, detection and the response to extracellular signaling molecules named autoinducers, which directly or indirectly regulate gene expression in a cell density-dependent manner. Quorum sensing may control a wide range of biological processes in bacteria, such as bioluminescence, virulence factor production, biofilm formation and antibiotic resistance. The autoinducers are recognized by specific receptors that can either be membrane-bound histidine kinase receptors, which work by activating cognate cytoplasmic response regulators, or cytoplasmic receptors acting as transcription factors. In this review, we focused on the cytosolic quorum sensing regulators whose three-dimensional structures helped elucidate their mechanisms of action. Structural studies of quorum sensing receptors may enable the rational design of inhibitor molecules. Ultimately, this approach may represent an effective alternative to treat infections where classical antimicrobial therapy fails to overcome the microorganism virulence.

Biophotons, hallucinogens, and fluorescence

2011 ◽  
Vol 26 (S2) ◽  
pp. 1202-1202
Author(s):  
F. Grass
Keyword(s):  
Thermal Noise ◽  
Signal To Noise Ratio ◽  
Cell Communication ◽  
Cell Types ◽  
Ambient Light ◽  
A Cell ◽  
Inner Diameter ◽  
Different Cell Types ◽  
Light Guidance ◽  
Baby Hamster Kidney Cells

Several experiments show that there is a cell to cell communicaton by light in different cell types. The most convincing experiment shows that baby hamster kidney cells can communicate their spatial orientation through a glass film, this can only happen by photon signals. If so, it can be assumed that the cells with the highest differentiation, the neurons also use this mechanism. The nervous system would have excellent conditions for a cell to cell communication by light. Neurons are large, metabolically very active (lightproducing) cells with wide arborisation, contain little pigment and are protected from ambient light by bone and connective tissue. Signal to noise ratio should be high for photon signals. It has been shown that light can be propagated along the axis tracts. Also the hollow microtubules (neurofibrillae) could act as light guiding structures. According to Jibu et al. their inner diameter of 15 nm is ideal for light guidance free of thermal noise and loss. Other findings that may be of importance in this context, are the strong flurescence properties of the major hallucinogens: LSD, bufetonine, dimethyl-tryptamine, psilocybine, psilocin, iboguanin, harmine, cannabidinol and mescaline. Furthermore it has been shown that hallucinogenic properties of these substances have a direct correlation to their fluorescence properties and their readyness to donate electrons. As hypothesis we propose that the fluorescence interacts physically with the proposed Biophoton mediated cell to cell communication thus producing hallucinations. This would be an easy and plausible explanation for the strong hallucinogenic properties of these fluorescent substances.

scholarly journals FunRes: resolving tissue-specific functional cell states based on a cell–cell communication network model

2020 ◽  
Author(s):  
Sascha Jung ◽  
Kartikeya Singh ◽  
Antonio del Sol
Keyword(s):  
Communication Network ◽  
Communication Networks ◽  
Cell Communication ◽  
Cell Types ◽  
Computational Method ◽  
Tissue Specific ◽  
Great Utility ◽  
A Cell ◽  
Cell Cell

Abstract The functional specialization of cell types arises during development and is shaped by cell–cell communication networks determining a distribution of functional cell states that are collectively important for tissue functioning. However, the identification of these tissue-specific functional cell states remains challenging. Although a plethora of computational approaches have been successful in detecting cell types and subtypes, they fail in resolving tissue-specific functional cell states. To address this issue, we present FunRes, a computational method designed for the identification of functional cell states. FunRes relies on scRNA-seq data of a tissue to initially reconstruct the functional cell–cell communication network, which is leveraged for partitioning each cell type into functional cell states. We applied FunRes to 177 cell types in 10 different tissues and demonstrated that the detected states correspond to known functional cell states of various cell types, which cannot be recapitulated by existing computational tools. Finally, we characterize emerging and vanishing functional cell states in aging and disease, and demonstrate their involvement in key tissue functions. Thus, we believe that FunRes will be of great utility in the characterization of the functional landscape of cell types and the identification of dysfunctional cell states in aging and disease.

scholarly journals Large differences in small RNA composition between human biofluids

2018 ◽  
Author(s):  
Paula M. Godoy ◽  
Nirav R. Bhakta ◽  
Andrea J. Barczak ◽  
Hakan Cakmak ◽  
Susan Fisher ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Cellular Communication ◽  
Rna Seq ◽  
Extracellular Rna ◽  
Disease Biomarkers ◽  
Rna Biology ◽  
Extracellular Mirnas ◽  
Rna Fragments ◽  
Highly Correlated

SUMMARYExtracellular miRNAs and other small RNAs are implicated in cellular communication and may be useful as disease biomarkers. We systematically compared small RNAs in 12 human biofluid types using RNA-seq. miRNAs and tRNA-derived RNAs (tDRs) accounted for the majority of mapped reads in all biofluids, but the ratio of miRNA to tDR reads varied from 72 in plasma to 0.004 in bile. miRNA levels were highly correlated across all biofluids but levels of some miRNAs differed markedly between biofluids. tDR populations differed extensively between biofluids. Y RNA fragments were seen in all biofluids and accounted for >10% of reads in blood plasma, serum, and CSF. Reads mapping exclusively to piRNAs were very rare except in seminal plasma. These results demonstrate extensive differences in small RNAs between human biofluids and provide a useful resource for investigating extracellular RNA biology and developing biomarkers.

scholarly journals miRNAs as Influencers of Cell–Cell Communication in Tumor Microenvironment

Cells ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 220 ◽  
Author(s):  
Ilaria Conti ◽  
Gabriele Varano ◽  
Carolina Simioni ◽  
Ilaria Laface ◽  
Daniela Milani ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Cell Communication ◽  
Altered Expression ◽  
Regulate Gene Expression ◽  
Small Noncoding Rnas ◽  
Physiological Processes ◽  
Extracellular Mirnas ◽  
Obesity And Cancer ◽  
Posttranscriptional Level

microRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level, inducing the degradation of the target mRNA or translational repression. MiRNAs are involved in the control of a multiplicity of biological processes, and their absence or altered expression has been associated with a variety of human diseases, including cancer. Recently, extracellular miRNAs (ECmiRNAs) have been described as mediators of intercellular communication in multiple contexts, including tumor microenvironment. Cancer cells cooperate with stromal cells and elements of the extracellular matrix (ECM) to establish a comfortable niche to grow, to evade the immune system, and to expand. Within the tumor microenvironment, cells release ECmiRNAs and other factors in order to influence and hijack the physiological processes of surrounding cells, fostering tumor progression. Here, we discuss the role of miRNAs in the pathogenesis of multicomplex diseases, such as Alzheimer’s disease, obesity, and cancer, focusing on the contribution of both intracellular miRNAs, and of released ECmiRNAs in the establishment and development of cancer niche. We also review growing evidence suggesting the use of miRNAs as novel targets or potential tools for therapeutic applications.

scholarly journals Microbe-Host Communication by Small RNAs in Extracellular Vesicles: Vehicles for Transkingdom RNA Transportation

2019 ◽  
Vol 20 (6) ◽  
pp. 1487 ◽  
Author(s):  
Heon-Jin Lee
Keyword(s):  
Extracellular Vesicles ◽  
Small Rnas ◽  
Cell Communication ◽  
Cell Types ◽  
Eukaryotic Cells ◽  
Biological Research ◽  
Interspecies Communication ◽  
Microbe Interactions ◽  
Multiple Cell ◽  
Host Microbe Interactions

Extracellular vesicles (EVs) are evolutionary well-conserved nano-sized membranous vesicles that are secreted by both prokaryotic and eukaryotic cells. Recently, they have gained great attention for their proposed roles in cell-to-cell communication, and as biomarkers for human disease. In particular, small RNAs (sRNAs) contained within EVs have been considered as candidate interspecies-communication molecules, due to their demonstrated capacity to modulate gene expression in multiple cell types and species. While research into this field is in its infancy, elucidating the mechanisms that underlie host–microbe interactions and communications promises to impact many fields of biological research, including human health and medicine. Thus, this review discussed the results of recent studies that have examined the ways in which EVs and sRNAs mediate ‘microbe–host’ and ‘host–microbe’ interspecies communication.

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