scholarly journals Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Diego R. Gelsinger ◽  
Gherman Uritskiy ◽  
Rahul Reddy ◽  
Adam Munn ◽  
Katie Farney ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Microbial Community ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Field Experiments ◽  
Natural World ◽  
Community Level ◽  
Model Organisms ◽  
Rain Event ◽  
Expression Levels

ABSTRACT Regulatory small RNAs (sRNAs) play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been extensively studied in model organisms, but very little is known about the dynamics of sRNA synthesis and their roles in the natural environment. In this study, we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed in an extremophilic microbial community inhabiting halite nodules (salt rocks) in the Atacama Desert. For this, we built SnapT, a new sRNA annotation pipeline that can be applied to any microbial community. We found asRNAs with expression levels negatively correlated with that of their overlapping putative target and itsRNAs that were conserved and significantly differentially expressed between 2 sampling time points. We demonstrated that we could perform target prediction and correlate expression levels between sRNAs and predicted target mRNAs at the community level. Functions of putative mRNA targets reflected the environmental challenges members of the halite communities were subjected to, including osmotic adjustments to a major rain event and competition for nutrients. IMPORTANCE Microorganisms in the natural world are found in communities, communicating and interacting with each other; therefore, it is essential that microbial regulatory mechanisms, such as gene regulation affected by small RNAs (sRNAs), be investigated at the community level. This work demonstrates that metatranscriptomic field experiments can link environmental variation with changes in RNA pools and have the potential to provide new insights into environmental sensing and responses in natural microbial communities through noncoding RNA-mediated gene regulation.

scholarly journals Regulatory non-coding small RNAs are diverse and abundant in an extremophilic microbial community

2019 ◽  
Author(s):  
Diego R. Gelsinger ◽  
Gherman Uritskiy ◽  
Rahul Reddy ◽  
Adam Munn ◽  
Katie Farney ◽  
...  
Keyword(s):  
Small Rnas ◽  
Large Scale ◽  
Field Experiments ◽  
Target Prediction ◽  
Model Organisms ◽  
Natural Environments ◽  
Cellular Processes ◽  
Non Coding Rna ◽  
Domains Of Life ◽  
Gene Regulatory

ABSTRACTRegulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks) from the Atacama Desert with SnapT – a new sRNA annotation pipeline – we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs. The halite sRNAs were taxonomically diverse with the majority expressed by members of the Halobacteria. We found asRNAs with expression levels negatively correlated with that of their putative overlapping target, suggesting a potential gene regulatory mechanism. A number of itsRNAs were conserved and significantly differentially expressed (FDR<5%) between 2 sampling time points allowing for stable secondary structure modeling and target prediction. This work demonstrates that metatranscriptomic field experiments link environmental variation with changes in RNA pools and have the potential to provide new insights into environmental sensing and responses in natural microbial communities through non-coding RNA mediated gene regulation.

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 .

Roles of Regulatory RNAs in Nutritional Control

2020 ◽  
Vol 40 (1) ◽  
pp. 77-104
Author(s):  
Elizabeth M. McNeill ◽  
Kendal D. Hirschi
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Small Cell ◽  
Altered Expression ◽  
Nutritional Interventions ◽  
Metabolic Genes ◽  
Regulatory Rnas ◽  
Dietary Bioactive Compounds

Small RNAs (sRNAs), including microRNAs (miRNAs), are noncoding RNA (ncRNA) molecules involved in gene regulation. sRNAs play important roles in development; however, their significance in nutritional control and as metabolic modulators is still emerging. The mechanisms by which diet impacts metabolic genes through miRNAs remain an important area of inquiry. Recent work has established how miRNAs are transported in body fluids often within exosomes, which are small cell-derived vesicles that function in intercellular communication. The abundance of other recently identified ncRNAs and new insights regarding ncRNAs as dietary bioactive compounds could remodel our understanding about how foods impact gene expression. Although controversial, some groups have shown that dietary RNAs from plants and animals (i.e., milk) are functional in consumers. In the future, regulating sRNAs either directly through dietary delivery or indirectly by altered expression of endogenous sRNA may be part of nutritional interventions for regulating metabolism.

NEAT1 Is a Novel Oncogenic LncRNA and Correlated with miR-143 in Pediatric Oligodendrogliomas

2021 ◽  
Vol 56 (2) ◽  
pp. 133-139
Author(s):  
Secil Ak Aksoy ◽  
Melis Mutlu ◽  
Rabia Nur Balcin ◽  
Mevlut Ozgur Taskapilioglu ◽  
Cagla Tekin ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Expression Profiles ◽  
Prognostic Significance ◽  
Disease Free Survival ◽  
Pediatric Brain Tumors ◽  
Normal Brain ◽  
Diffuse Glioma ◽  
Expression Levels ◽  
Treatment Models ◽  
New Treatment

Introduction: The noncoding RNAs (ncRNAs) play a role in biological processes of various cancers including gliomas. The majority of these transcripts are uniquely expressed in differentiated tissues or specific glioma types. Pediatric oligodendroglioma (POG) is a rare subtype of diffuse glioma and accounts for <1% of pediatric brain tumors. Because histologically POG resembles adult OG, the same treatment is applied as adults. However, the significance in predicting outcomes in POG patients is unclear. In this study, we aimed to investigate the prognostic significance of expression ­profiles of microRNA (miRNA) and long noncoding RNA ­(LncRNA) in POGs. Methods: We investigated the levels of 13 known miRNAs and 6 LncRNAs in tumor samples from 9 patients with primary POG by using RT-PCR and analyzed their association with outcomes. Results: The expression levels of miR-21, miR-106a, miR-10b, and LncRNA NEAT1 were higher, and the expression level of miR-143 was lower in POG tissues compared with normal brain tissues (p = 0.006, p = 0.032, p = 0.034, p = 0.002, and p = 0.001, respectively). High levels of NEAT1 and low expression of miR-143 were associated with decreased probability of short disease-free survival (p = 0.018 and p = 0.022, respectively). Discussion: NEAT1 and miR-143 levels could serve as reciprocal prognostic predictors of disease progression in patients with POG. New treatment models to regulate the expression levels of NEAT1 and miR-143 will bring a new approach to the therapy of POG.

scholarly journals Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene

2021 ◽  
Vol 22 (6) ◽  
pp. 3234
Author(s):  
Juhyun Lee ◽  
Si-Eun Sung ◽  
Janghyun Lee ◽  
Jin Young Kang ◽  
Joon-Hwa Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Nmr Spectroscopy ◽  
Bacillus Cereus ◽  
Base Pair ◽  
Noncoding Rna ◽  
Hydrogen Exchange ◽  
Magnesium Ion ◽  
Fluoride Ion ◽  
Base Pair Opening

Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.

scholarly journals Antifungal Effect of Long Noncoding RNA 9708-1 in the Vulvovaginal Candidiasis Murine Model

2021 ◽  
Vol 186 (2) ◽  
pp. 177-188
Author(s):  
Ying Wu ◽  
Lisha Jiang ◽  
Lingling Zhang ◽  
Xia Liu ◽  
Lina Yan ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Basal Layer ◽  
Vulvovaginal Candidiasis ◽  
Control Group ◽  
Therapeutic Effects ◽  
Blank Control Group ◽  
Candida Spp ◽  
Expression Levels ◽  
Gene And Protein Expression

AbstractVulvovaginal candidiasis (VVC) caused by Candida spp. affects 70–75% of women at least once during their lives. We aim to elucidate the potential mechanism of VVC and investigate the therapeutic effects of long noncoding RNA 9708-1. Female BALB/c mice were randomized to four treatment groups, including the blank control group, VVC control group, vehicle control group and lncRNA 9708-1-overexpressed group. Mice were euthanized on Day 4, Day 7 and Day 14 after treatment. Colony-forming unit (CFU) was measured, and the inflammation was detected by hematoxylin and eosin (H&E). Gene and protein expression levels of lncRNA 9708-1 and FAK were determined by real-time PCR, Western blot and immunohistochemistry. The overexpression of lncRNA 9708-1 significantly decreased the fungal load from Day 4 to 7. H&E staining indicated that the impaired histological profiles were improved in lncRNA 9708-1-overexpressed group. LncRNA 9708-1 led to a significant increase in FAK level of vagina tissue which is expressed mainly in epithelial basal layer. This study suggests that lncRNA 9708-1 played a protective role on murine experimental VVC by upregulating the expression levels of FAK.

scholarly journals NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

Cell Reports ◽  
2013 ◽  
Vol 4 (2) ◽  
pp. 255-261 ◽  
Author(s):  
Shobbir Hussain ◽  
Abdulrahim A. Sajini ◽  
Sandra Blanco ◽  
Sabine Dietmann ◽  
Patrick Lombard ◽  
...  
Keyword(s):  
Small Rnas ◽  
Noncoding Rna

Effects of Community Versus Single Strain Inoculants on the Biocontrol of Salmonella and Microbial Community Dynamics in Alfalfa Sprouts†

2005 ◽  
Vol 68 (1) ◽  
pp. 40-48 ◽  
Author(s):  
ANABELLE MATOS ◽  
JAY L. GARLAND
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Community Level ◽  
Microbial Consortia ◽  
Single Strain ◽  
Acridine Orange Staining ◽  
Physiological Profiles ◽  
Alfalfa Sprouts ◽  
Alfalfa Seeds

Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that different modes of actions of single versus microbial consortia biocontrol treatments may be involved.

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