scholarly journals Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

2018 ◽  
Author(s):  
Ryan M. Allen ◽  
Shilin Zhao ◽  
Marisol A. Ramirez Solano ◽  
Danielle L. Michell ◽  
Yuhuan Wang ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Small Rnas ◽  
Bioinformatic Analysis ◽  
Significant Advance ◽  
Extracellular Rna ◽  
Individual Fragment ◽  
Bacterial Sources

AbstractTo comprehensively study extracellular small RNAs (sRNA) by sequencing (sRNA-seq), we developed a novel pipeline to overcome current limitations in analysis entitled, “Tools for Integrative Genome analysis of Extracellular sRNAs (TIGER)”. To demonstrate the power of this tool, sRNA-seq was performed on mouse lipoproteins, bile, urine, and liver samples. A key advance for the TIGER pipeline is the ability to analyze both host and non-host sRNAs at genomic, parent RNA, and individual fragment levels. TIGER was able to identify approximately 60% of sRNAs on lipoproteins, and >85% of sRNAs in liver, bile, and urine, a significant advance compared to existing software. Results suggest that the majority of sRNAs on lipoproteins are non-host sRNAs derived from bacterial sources in the microbiome and environment, specifically rRNA-derived sRNAs from Proteobacteria. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of extracellular RNA.

scholarly journals Equine Adipose-Derived Mesenchymal Stromal Cells Release Extracellular Vesicles Enclosing Different Subsets of Small RNAs

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Stefano Capomaccio ◽  
Katia Cappelli ◽  
Cinzia Bazzucchi ◽  
Mauro Coletti ◽  
Rodolfo Gialletti ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Extracellular Vesicles ◽  
Mesenchymal Stromal Cells ◽  
Stromal Cells ◽  
Small Rnas ◽  
Rna Binding ◽  
Bioinformatic Analysis ◽  
Protein Coding ◽  
Significant Enrichment ◽  
Pathway Analyses

Background. Equine adipose-derived mesenchymal stromal cells (e-AdMSC) exhibit attractive proregenerative properties strongly related to the delivery of extracellular vesicles (EVs) that enclose different kinds of molecules including RNAs. In this study, we investigated small RNA content of EVs produced by e-AdMSC with the aim of speculating on their possible biological role. Methods. EVs were obtained by ultracentrifugation of the conditioned medium of e-AdMSC of 4 subjects. Transmission electron microscopy and scanning electron microscopy were performed to assess their size and nanostructure. RNA was isolated, enriched for small RNAs (<200 nt), and sequenced by Illumina technology. After bioinformatic analysis with state-of-the-art pipelines for short sequences, mapped reads were used to describe EV RNA cargo, reporting classes, and abundances. Enrichment analyses were performed to infer involved pathways and functional categories. Results. Electron microscopy showed the presence of vesicles ranging in size from 30 to 300 nm and expressing typical markers. RNA analysis revealed that ribosomal RNA was the most abundant fraction, followed by small nucleolar RNAs (snoRNAs, 13.67%). Miscellaneous RNA (misc_RNA) reached 4.57% of the total where Y RNA, RNaseP, and vault RNA represented the main categories. miRNAs were sequenced at a lower level (3.51%) as well as protein-coding genes (1.33%). Pathway analyses on the protein-coding fraction revealed a significant enrichment for the “ribosome” pathway followed by “oxidative phosphorylation.” Gene Ontology analysis showed enrichment for terms like “extracellular exosome,” “organelle envelope,” “RNA binding,” and “small molecule metabolic process.” The miRNA target pathway analysis revealed the presence of “signaling pathways regulating pluripotency of stem cells” coherent with the source of the samples. Conclusion. We herein demonstrated that e-AdMSC release EVs enclosing different subsets of small RNAs that potentially regulate a number of biological processes. These findings shed light on the role of EVs in the context of MSC biology.

scholarly journals Whole genome sequence of Peribacillus sp. MUM 13 derived from mangrove forest in Malaysia

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Jodi Woan-Fei Law ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Mangrove Forest ◽  
Screening Program ◽  
Gene Clusters ◽  
Bioinformatic Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Chemical Structures ◽  
Pathogenic Microbes ◽  
Unique Chemical

Acting like mini-factories, microorganisms are a valuable source of naturalbioactive compounds of unique chemical structures. Peribacillus sp. MUM 13 was recoveredfrom the mangrove forest in Malaysia during a screening program for bioactive microbes.Whole genome analysis revealed that the genome size of MUM 13 as 4,649,225 bp (with G+ C content of 40.8 %). Bioinformatic analysis predicted the presence of lassopeptidebiosynthetic gene clusters within the genome of MUM 13, which indicates the bioactivepotential of the strain and calls for further experiments to explore the strain characteristics,particularly in combatting against pathogenic microbes.

scholarly journals The most common technologies and tools for functional genome analysis

2017 ◽  
Vol 24 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Evelina Gasperskaja ◽  
Vaidutis Kučinskas
Keyword(s):  
Functional Analysis ◽  
Human Genome ◽  
Genome Analysis ◽  
Bioinformatic Analysis ◽  
Genome Wide ◽  
Polymerase Chain ◽  
Scientific Results ◽  
The Right ◽  
Generation Sequencing ◽  
Functional Genome

Since the  sequence of the  human genome is complete, the  main issue is how to understand the information written in the DNA sequence. Despite numerous genome-wide studies that have already been performed, the challenge to determine the function of genes, gene products, and also their interaction is still open. As changes in the human genome are highly likely to cause pathological conditions, functional analysis is vitally important for human health. For many years there have been a  variety of technologies and tools used in functional genome analysis. However, only in the  past decade there has been rapid revolutionizing progress and improvement in high-throughput methods, which are ranging from traditional real-time polymerase chain reaction to more complex systems, such as next-generation sequencing or mass spectrometry. Furthermore, not only laboratory investigation, but also accurate bioinformatic analysis is required for reliable scientific results. These methods give an opportunity for accurate and comprehensive functional analysis that involves various fields of studies: genomics, epigenomics, proteomics, and interactomics. This is essential for filling the  gaps in the  knowledge about dynamic biological processes at both cellular and organismal level. However, each method has both advantages and limitations that should be taken into account before choosing the right method for particular research in order to ensure successful study. For this reason, the present review paper aims to describe the most frequent and widely-used methods for the comprehensive functional analysis.

scholarly journals High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2432
Author(s):  
Emiliya Navrotskaya ◽  
Elena Porotikova ◽  
Eugeniya Yurchenko ◽  
Zsuzsanna Nagyne Galbacs ◽  
Eva Varallyay ◽  
...  
Keyword(s):  
High Throughput ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Integrated Approach ◽  
High Viral Load ◽  
Bioinformatic Analysis ◽  
High Genetic Diversity ◽  
Krasnodar Krai ◽  
Raspberry Bushy Dwarf Virus ◽  
Virus Genomes

The use of high-throughput sequencing (HTS) technology has led to significant progress in the identification of many viruses and their genetic variants. In this study, we used the HTS platform to sequence small RNAs (sRNAs) of grapevine to study the virome. Isolation of RNA was performed using symptomatic grapevines collected from commercial vineyards in Krasnodar Krai in 2017–2018. To determine the viromes of vineyards, we used an integrated approach that included a bioinformatic analysis of the results of sRNA HTS and the molecular method RT-PCR, which made it possible to identify 13 viruses and 4 viroids. Grapevine leafroll-associated virus 4 (GLRaV-4), Grapevine Syrah Virus-1 (GSyV-1), Raspberry bushy dwarf virus (RBDV), Australian grapevine viroid (AGVd), and Grapevine yellow speckle viroid 2 (GYSVd-2) were identified for the first time in Russia. Out of 38 samples analyzed, 37 had mixed infections with 4–11 viruses, indicating a high viral load. Analysis of the obtained sequences of fragments of virus genomes made it possible to identify recombination events in GLRaV-1, GLRaV-2, GLRaV-3, GLRaV-4, GVT, GPGV, GRSPaV, GVA, and GFLV. The obtained results indicate a wide spread of the viruses and a high genetic diversity in the vineyards of Krasnodar Krai and emphasize the urgent need to develop and implement long-term strategies for the control of viral grapevine diseases.

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 Identification of tRNA-derived small RNAs and their potential roles in the hippocampus of nicotine exposure rats

2021 ◽  
Author(s):  
Jiali Shao ◽  
Yanxia Fei ◽  
Chen Su ◽  
Wangyuan Zou ◽  
Jinfeng Yang
Keyword(s):  
Small Rnas ◽  
Health Care Systems ◽  
Enrichment Analysis ◽  
Bioinformatic Analysis ◽  
Rat Hippocampus ◽  
Differentially Expressed ◽  
Exposure Model ◽  
Pathway Enrichment Analysis ◽  
Nicotine Exposure ◽  
Care Systems

Abstract Nicotine use is highly prevalent and brings a huge burden on individuals, society, health-care systems and economic development. The existing mechanisms underlying nicotine’ actions can’t illuminate all basic and clinical problems thoroughly. Transfer RNA-derived small RNAs (tsRNAs) is a novel class of small non-coding RNAs (sncRNAs), possessing potential regulatory functions in various diseases. However, the roles of tsRNAs in nicotine exposure have not been determined yet. In this study, firstly we established nicotine exposure model by subcutaneously injecting (sc.) with 0.5mg/kg of nicotine twice daily for 14 consecutive days, and conducted some behavioral observations (the pain threshold and body weight gains). Secondly, we identified the differentially expressed profiles of tsRNAs in rat hippocampus on saline or nicotine delivery conditions by using ncRNA-Seq, and then predicted the promising functions of the putative genes of the tsRNAs by bioinformatic method. The results shown that there were 26 differentially expressed tsRNAs (7 up-regulated and 19 down-regulated tsRNAs) (Fold change > 1.5; P < 0.05), of which the tRF-5 was the most common type. Eight tsRNAs were selected to validate the sequencing result by RT-qPCR. Then, based on the sequencing and RT-qPCR data, five candidate tsRNAs (tRF-1-T28-His-GTG-1, tRF-5c-Glu-CTC-1, tRF-5c-Glu-CTC-3, tRF-5c-Gly-GCC-2-M2, tRF-5c-Glu-TTC-4) were finally selected for further bioinformatic analysis. The GO and KEGG pathway enrichment analysis suggested that the five candidate tsRNAs might play regulatory roles through the cholinergic synapse pathways, dopaminergic synapse pathways, etc. In conclusion, our results indicated that tsRNAs were dysregulated in the rat hippocampus after nicotine exposure, and among them, tRF-5c-Glu-CTC-1 was the most promising one, which might lay a novel foundation for further research into nicotine’ actions.

scholarly journals Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing

2018 ◽  
Vol 64 (7) ◽  
pp. 1085-1095 ◽  
Author(s):  
Feng Li ◽  
Karolina Elżbieta Kaczor-Urbanowicz ◽  
Jie Sun ◽  
Blanca Majem ◽  
Hsien-Chun Lo ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Data Storage ◽  
Small Rna ◽  
Small Rnas ◽  
Rna Isolation ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Extracellular Rna ◽  
Library Construction ◽  
Rrna Depletion

Abstract BACKGROUND It was recently discovered that abundant and stable extracellular RNA (exRNA) species exist in bodily fluids. Saliva is an emerging biofluid for biomarker development for noninvasive detection and screening of local and systemic diseases. Use of RNA-Sequencing (RNA-Seq) to profile exRNA is rapidly growing; however, no single preparation and analysis protocol can be used for all biofluids. Specifically, RNA-Seq of saliva is particularly challenging owing to high abundance of bacterial contents and low abundance of salivary exRNA. Given the laborious procedures needed for RNA-Seq library construction, sequencing, data storage, and data analysis, saliva-specific and optimized protocols are essential. METHODS We compared different RNA isolation methods and library construction kits for long and small RNA sequencing. The role of ribosomal RNA (rRNA) depletion also was evaluated. RESULTS The miRNeasy Micro Kit (Qiagen) showed the highest total RNA yield (70.8 ng/mL cell-free saliva) and best small RNA recovery, and the NEBNext library preparation kits resulted in the highest number of detected human genes [5649–6813 at 1 reads per kilobase RNA per million mapped (RPKM)] and small RNAs [482–696 microRNAs (miRNAs) and 190–214 other small RNAs]. The proportion of human RNA-Seq reads was much higher in rRNA-depleted saliva samples (41%) than in samples without rRNA depletion (14%). In addition, the transfer RNA (tRNA)-derived RNA fragments (tRFs), a novel class of small RNAs, were highly abundant in human saliva, specifically tRF-4 (4%) and tRF-5 (15.25%). CONCLUSIONS Our results may help in selection of the best adapted methods of RNA isolation and small and long RNA library constructions for salivary exRNA studies.

scholarly journals Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

2018 ◽  
Vol 7 (1) ◽  
pp. 1506198 ◽  
Author(s):  
Ryan M. Allen ◽  
Shilin Zhao ◽  
Marisol A. Ramirez Solano ◽  
Wanying Zhu ◽  
Danielle L. Michell ◽  
...  
Keyword(s):  
Small Rnas ◽  
Bioinformatic Analysis

scholarly journals Identification of tRNA-Derived Small RNAs and their Potential Roles in the Hippocampus of Nicotine Exposure Rats

2021 ◽  
Author(s):  
Jiali Shao ◽  
Yanxia Fei ◽  
Chen Su ◽  
Wangyuan Zou ◽  
Jinfeng Yang
Keyword(s):  
Small Rnas ◽  
Health Care Systems ◽  
Enrichment Analysis ◽  
Bioinformatic Analysis ◽  
Rat Hippocampus ◽  
Differentially Expressed ◽  
Exposure Model ◽  
Pathway Enrichment Analysis ◽  
Nicotine Exposure ◽  
Care Systems

Abstract Nicotine use is highly prevalent and brings a huge burden on individuals, society, health-care systems and economic development. The existing mechanisms underlying nicotine’ actions can’t illuminate all basic and clinical problems thoroughly. Transfer RNA-derived small RNAs (tsRNAs) is a novel class of small non-coding RNAs (sncRNAs), possessing potential regulatory functions in various diseases. However, the roles of tsRNAs in nicotine exposure have not been determined yet. In this study, firstly we established nicotine exposure model by subcutaneously injecting (sc.) with 0.5mg/kg of nicotine twice daily for 14 consecutive days, and conducted some behavioral observations (the pain threshold and body weight gains). Secondly, we identified the differentially expressed profiles of tsRNAs in rat hippocampus on saline or nicotine delivery conditions by using ncRNA-Seq, and then predicted the promising functions of the putative genes of the tsRNAs by bioinformatic method. The results shown that there were 26 differentially expressed tsRNAs (7 up-regulated and 19 down-regulated tsRNAs) (Fold change > 1.5; P < 0.05), of which the tRF-5 was the most common type. Eight tsRNAs were selected to validate the sequencing result by RT-qPCR. Then, based on the sequencing and RT-qPCR data, five candidate tsRNAs (tRF-1-T28-His-GTG-1, tRF-5c-Glu-CTC-1, tRF-5c-Glu-CTC-3, tRF-5c-Gly-GCC-2-M2, tRF-5c-Glu-TTC-4) were finally selected for further bioinformatic analysis. The GO and KEGG pathway enrichment analysis suggested that the five candidate tsRNAs might play regulatory roles through the cholinergic synapse pathways, dopaminergic synapse pathways, etc. In conclusion, our results indicated that tsRNAs were dysregulated in the rat hippocampus after nicotine exposure, and among them, tRF-5c-Glu-CTC-1 was the most promising one, which might lay a novel foundation for further research into nicotine’ actions.

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