scholarly journals Identification and characterization of microRNAs from in vitro-grown pear shoots infected with Apple stem grooving virus in response to high temperature using small RNA sequencing

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Juan Liu ◽  
XueJiao Zhang ◽  
FangPeng Zhang ◽  
Ni Hong ◽  
GuoPing Wang ◽  
...  
Keyword(s):  
High Temperature ◽  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Apple Stem Grooving Virus ◽  
Apple Stem ◽  
Identification And Characterization

scholarly journals Identification and characterization of microRNAs in maize endosperm response to exogenous sucrose using small RNA sequencing

Genomics ◽  
2016 ◽  
Vol 108 (5-6) ◽  
pp. 216-223 ◽  
Author(s):  
Huanhuan Huang ◽  
Jiao Long ◽  
Lanjie Zheng ◽  
Yangping Li ◽  
Yufeng Hu ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Maize Endosperm ◽  
Identification And Characterization

scholarly journals Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato

PLoS ONE ◽  
2020 ◽  
Vol 15 (5) ◽  
pp. e0233076 ◽  
Author(s):  
Jagesh Kumar Tiwari ◽  
Tanuja Buckseth ◽  
Rasna Zinta ◽  
Aastha Saraswati ◽  
Rajesh Kumar Singh ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Nitrogen Stress ◽  
Small Rna Sequencing ◽  
Genome Wide ◽  
Low Nitrogen Stress ◽  
Identification And Characterization ◽  
Low Nitrogen

scholarly journals Small RNA Sequencing Identifies PIWI-Interacting RNAs Deregulated in Glioblastoma—piR-9491 and piR-12488 Reduce Tumor Cell Colonies In Vitro

2021 ◽  
Vol 11 ◽  
Author(s):  
Michael Bartos ◽  
Frantisek Siegl ◽  
Alena Kopkova ◽  
Lenka Radova ◽  
Jan Oppelt ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Genome Stability ◽  
Molecular Mechanisms ◽  
Prognostic Biomarker ◽  
Independent Set ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Tumor Patients

Glioblastoma (GBM) is the most frequently occurring primary malignant brain tumor of astrocytic origin. To change poor prognosis, it is necessary to deeply understand the molecular mechanisms of gliomagenesis and identify new potential biomarkers and therapeutic targets. PIWI-interacting RNAs (piRNAs) help in maintaining genome stability, and their deregulation has already been observed in many tumors. Recent studies suggest that these molecules could also play an important role in the glioma biology. To determine GBM-associated piRNAs, we performed small RNA sequencing analysis in the discovery set of 19 GBM and 11 non-tumor brain samples followed by TaqMan qRT-PCR analyses in the independent set of 77 GBM and 23 non-tumor patients. Obtained data were subsequently bioinformatically analyzed. Small RNA sequencing revealed 58 significantly deregulated piRNA molecules in GBM samples in comparison with non-tumor brain tissues. Deregulation of piR-1849, piR-9491, piR-12487, and piR-12488 was successfully confirmed in the independent groups of patients and controls (all p < 0.0001), and piR-9491 and piR-12488 reduced GBM cells’ ability to form colonies in vitro. In addition, piR-23231 was significantly associated with the overall survival of the GBM patients treated with Stupp regimen (p = 0.007). Our results suggest that piRNAs could be a novel promising diagnostic and prognostic biomarker in GBM potentially playing important roles in gliomagenesis.

scholarly journals Identification of microRNAs in the West Nile virus vector Culex tarsalis

2021 ◽  
Author(s):  
Sultan Asad ◽  
Ahmed M Mehdi ◽  
Sujit Pujhari ◽  
Claudia Rueckert ◽  
Gregory D Ebel ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Cell Line ◽  
Rna Sequencing ◽  
Small Rna ◽  
The United States ◽  
Small Rna Sequencing ◽  
Culex Tarsalis ◽  
Sequencing Data ◽  
West Nile

Background: microRNAs (miRNAs) represent a group of small non-coding RNAs that are crucial gene regulators of important biological functions including development and pathogen defense in most living organisms. Presently, there is a lack of availability of information regarding the miRNAs in the mosquito Culex tarsalis, which is one of the most important vectors of West Nile virus (WNV) in the United States. We used small RNA sequencing data and in vitro and in vivo experiments to identify and validate the presence of a repertoire of miRNAs in Cx. tarsalis mosquitoes. Results: Using bioinformatic approaches we analyzed small RNA sequencing data from the Cx. tarsalis CT embryonic cell line to discover 86 miRNAs. Consistent with other mosquitoes such as Aedes albopictus and Cx. quinquefasciatus, mi-184 was found to be the most abundant miRNA in Cx tarsalis. We also identified an additional 20 novel miRNAs from the recently sequenced Cx. tarsalis genome, for a total of 106 miRNAs identified in this study. The presence of selected miRNAs was biologically validated in both cell line and adult Cx. tarsalis mosquitoes using RT-qPCR and sequencing. Conclusions: Cx. tarsalis is an important vector of many medically important pathogens including WNV and Western Equine encephalitis. Here we report a detailed insight into the miRNA population in Cx. tarsalis mosquitoes. These results will open new avenues of research deciphering the role of miRNAs in different Cx. tarsalis biological events such as development, metabolism, immunity and pathogen infection.

scholarly journals Identification of CNS Injury-Related microRNAs as Novel Toll-Like Receptor 7/8 Signaling Activators by Small RNA Sequencing

Cells ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 186 ◽  
Author(s):  
Thomas Wallach ◽  
Max Wetzel ◽  
Paul Dembny ◽  
Ori Staszewski ◽  
Christina Krüger ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Cns Injury ◽  
Critical Feature ◽  
Systematic Screening ◽  
Extracellular Mirnas ◽  
The Media ◽  
Molecular Patterns

Toll-like receptors (TLRs) belong to pattern recognition receptors, which respond to danger signals such as pathogen-associated molecular patterns or damage-associated molecular patterns. Upon TLR activation in microglia, the major immune cells in the brain, distinct signaling cascades trigger the production of inflammatory molecules, being a critical feature in neuroinflammation and neurodegenerative processes. Recently, individual microRNAs (miRNAs) were shown to act as endogenous TLR ligands. Here, we conducted systematic screening for miRNAs as potential TLR7/8 ligands by small RNA sequencing of apoptotic neurons and their corresponding supernatants. Several miRNA species were identified in both supernatants and injured neurons, and 83.3% of the media-enriched miRNAs activated murine and/or human TLR7/8 expressed in HEK293-derived TLR reporter cells. Among the detected extracellular miRNAs, distinct miRNAs such as miR-340-3p and miR-132-5p induced cytokine and chemokine release from microglia and triggered neurotoxicity in vitro. Taken together, our systematic study establishes miRNAs released from injured neurons as new TLR7/8 activators, which contribute to inflammatory and neurodegenerative responses in the central nervous system (CNS).

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