scholarly journals Using Small RNA Deep Sequencing Data to Detect Human Viruses

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Fang Wang ◽  
Yu Sun ◽  
Jishou Ruan ◽  
Rui Chen ◽  
Xin Chen ◽  
...  
Keyword(s):  
Small Rna ◽  
B Cell Lymphoma ◽  
Clinical Samples ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Detection And Identification ◽  
Small Rna Deep Sequencing ◽  
Human Viruses ◽  
First Time ◽  
Hiv 1

Small RNA sequencing (sRNA-seq) can be used to detect viruses in infected hosts without the necessity to have any prior knowledge or specialized sample preparation. The sRNA-seq method was initially used for viral detection and identification in plants and then in invertebrates and fungi. However, it is still controversial to use sRNA-seq in the detection of mammalian or human viruses. In this study, we used 931 sRNA-seq runs of data from the NCBI SRA database to detect and identify viruses in human cells or tissues, particularly from some clinical samples. Six viruses including HPV-18, HBV, HCV, HIV-1, SMRV, and EBV were detected from 36 runs of data. Four viruses were consistent with the annotations from the previous studies. HIV-1 was found in clinical samples without the HIV-positive reports, and SMRV was found in Diffuse Large B-Cell Lymphoma cells for the first time. In conclusion, these results suggest the sRNA-seq can be used to detect viruses in mammals and humans.

scholarly journals Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 267
Author(s):  
Axel J. Giudicatti ◽  
Ariel H. Tomassi ◽  
Pablo A. Manavella ◽  
Agustin L. Arce
Keyword(s):  
Small Rna ◽  
Stress Responses ◽  
Cellular Localization ◽  
Mirna Biogenesis ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Extensive Analysis ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Argonaute 1

MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs.

scholarly journals Somatic transposition in the Drosophila intestine occurs in active chromatin and is associated with tumor suppressor gene inactivation

2020 ◽  
Author(s):  
Katarzyna Siudeja ◽  
Marius van den Beek ◽  
Nick Riddiford ◽  
Benjamin Boumard ◽  
Annabelle Wurmser ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Small Rna ◽  
Suppressor Gene ◽  
Somatic Tissue ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Active Chromatin ◽  
Tumor Suppressor Gene Inactivation ◽  
Somatic Transposition

AbstractTransposable elements (TEs) play a significant role in evolution by contributing to genetic variation through germline insertional activity. However, how TEs act in somatic cells and tissues is not well understood. Here, we address the prevalence of transposition in a somatic tissue, exploiting the Drosophila midgut as a model system. Using whole-genome sequencing of in vivo clonally expanded gut tissue, we map hundreds of high-confidence somatic TE integration sites genome-wide. We show that somatic retrotransposon insertions are associated with inactivation of the tumor suppressor Notch, likely contributing to neoplasia formation. Moreover, by applying Oxford Nanopore long-read sequencing technology, as well as by mapping germline TE activity, we provide evidence suggesting tissue-specific differences in retrotransposition. By comparing somatic TE insertional activity with transcriptomic and small RNA sequencing data, we demonstrate that transposon mobility cannot be simply predicted by whole tissue TE expression levels or by small RNA pathway activity. Finally, we reveal that somatic TE insertions in the adult fly intestine are found preferentially in genic regions and open, transcriptionally active chromatin. Together, our findings provide clear evidence of ongoing somatic transposition in Drosophila and delineate previously unknown underlying features of somatic TE mobility in vivo.

2181The prothrombotic transcriptome of reticulated platelets

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
D Bongiovanni ◽  
G Santamaria ◽  
M Klug ◽  
D Santovito ◽  
A Felicetta ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Platelet Activation ◽  
Small Rna ◽  
Peripheral Blood ◽  
Cardiovascular Events ◽  
Platelet Reactivity ◽  
Gene Set Enrichment Analysis ◽  
Small Rna Sequencing ◽  
Reticulated Platelets ◽  
First Time

Abstract Introduction Reticulated platelets (RPs) are young, hyper-reactive platelets that are larger and contain significantly more RNA compared to older mature platelets. High levels of RPs in peripheral blood are predictors of an insufficient response to dual antiplatelet therapy in cardiovascular patients and of adverse cardiovascular events also in non-cardiac patients. However, the mechanisms underlying these correlations remains widely unknown and the biology of RPs has not been investigated yet. Purpose We aimed to compare for the first time the transcriptomic profiles of RPs and mature platelets (MPs). Methods RPs and MPs from peripheral blood of healthy donors were identified and isolated using FACS/Sorting based on their RNA-content. Immediately after sorting, RNA was extracted and quality, concentration and integrity was assessed with the Tapestation 4200 platform (Agilent). Total- and small-RNA libraries were prepared, multiplexed and sequenced on a NextSeq 500 Illumina platform Results Total-RNA-sequencing revealed 1744 differentially expressed genes (670 downregulated 1074 upregulated) in RPs compared to MPs (Figure 1A, B). In particular, transcripts for the collagen receptor GP6, thromboxane receptor A2 (TBXA2R), thrombin receptor PAR4 (F2RL3) and ATP receptor P2RX1 were significantly enriched in RPs, whereas several RNA regulators as the ribonuclease PARN, the RISC-component TNRC6A and the splicing factor LUC7L3 were downregulated in RPs. Gene ontology analysis revealed an enrichment of relevant biological categories in RPs including platelet activation and blood coagulation (Figure 1C). Gene Set Enrichment Analysis showed an enrichment of several activation pathways like thrombin, thromboxane and GPIIb/IIIa signaling in RPs. Small-RNA-sequencing reported 9 miRNAs significantly downregulated in RPs with targets involved in platelet reactivity. Figure 1 Conclusions This study represents the first comparative transcriptome analysis of RPs and MPs and reports for the first time a differential enrichment of transcripts involved in platelet activation. The clear upregulation of prothrombotic signaling in RPs could explain, at least in part, their hyper-activity and their correlation with cardiovascular events in different pathological settings (trancripts enriched in RPs: Figure 1D). Acknowledgement/Funding German Society of Cardiology (DGK Nr.102018) ESC First conctact initiative grant 2018

scholarly journals Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 429 ◽  
Author(s):  
Cecilia Osunmakinde ◽  
Ramganesh Selvarajan ◽  
Timothy Sibanda ◽  
Bhekie Mamba ◽  
Titus Msagati
Keyword(s):  
Treatment Plant ◽  
Viral Metagenomics ◽  
Clinical Samples ◽  
Environmental Matrices ◽  
African Countries ◽  
Entire Genome ◽  
Detection And Identification ◽  
Key Issues ◽  
Environmental Milieu ◽  
Human Viruses

There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.

scholarly journals Characterizing the cancer-associated microbiome with small RNA sequencing data

2020 ◽  
Vol 522 (3) ◽  
pp. 776-782
Author(s):  
Wei-Hao Lee ◽  
Kai-Pu Chen ◽  
Kai Wang ◽  
Hsuan-Cheng Huang ◽  
Hsueh-Fen Juan
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Sequencing Data

scholarly journals miRquant 2.0: an Expanded Tool for Accurate Annotation and Quantification of MicroRNAs and their isomiRs from Small RNA-Sequencing Data

2016 ◽  
Vol 13 (5) ◽  
Author(s):  
Matthew Kanke ◽  
Jeanette Baran-Gale ◽  
Jonathan Villanueva ◽  
Praveen Sethupathy
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Cell Types ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
Additional Information ◽  
Disease States ◽  
Non Coding Rnas ◽  
The Rich

SummarySmall non-coding RNAs, in particular microRNAs, are critical for normal physiology and are candidate biomarkers, regulators, and therapeutic targets for a wide variety of diseases. There is an ever-growing interest in the comprehensive and accurate annotation of microRNAs across diverse cell types, conditions, species, and disease states. Highthroughput sequencing technology has emerged as the method of choice for profiling microRNAs. Specialized bioinformatic strategies are required to mine as much meaningful information as possible from the sequencing data to provide a comprehensive view of the microRNA landscape. Here we present miRquant 2.0, an expanded bioinformatics tool for accurate annotation and quantification of microRNAs and their isoforms (termed isomiRs) from small RNA-sequencing data. We anticipate that miRquant 2.0 will be useful for researchers interested not only in quantifying known microRNAs but also mining the rich well of additional information embedded in small RNA-sequencing data.

scholarly journals Evidence for human microRNA-offset RNAs in small RNA sequencing data

2009 ◽  
Vol 25 (18) ◽  
pp. 2298-2301 ◽  
Author(s):  
D. Langenberger ◽  
C. Bermudez-Santana ◽  
J. Hertel ◽  
S. Hoffmann ◽  
P. Khaitovich ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Sequencing Data
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