Identification of conserved miRNA molecules in einkorn wheat ( Triticum monococcum  subsp.  monococcum ) by using small RNA sequencing analysis

Grapevine Pinot gris virus (GPGV) is a putative causal agent of grapevine leaf mottling and deformation disease that has been reported worldwide throughout the grapevine-growing regions. Fifty-four grapevines collected from five Algerian grapevine-growing regions were tested for the presence of GPGV in phloem tissues. Eight of the tested grapevines were infected by GPGV. Viromes of two selected Vitis vinifera cv. Sabel grapevines infected by GPGV and showing virus-like symptoms were analyzed by small RNA sequencing. Phylogenetic analyses of the partial coding sequence (cds) of the RNA-dependent RNA polymerase (RdRp) domain showed that all Algerian GPGV isolates were grouped with some already-described asymptomatic isolates. This study provides the first survey of the occurrence of GPGV in Algeria. Moreover, Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine virus B, Grapevine rupestris vein feathering virus, Hop stunt viroid and Grapevine yellow speckle viroid 1 were detected in Algeria for the first time.

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Abstract 16544: Small Rna-sequencing Analysis of Circulating Proinflammatory Microrna Following Murine Myocardial Ischemia/reperfusion Injury

Circulation ◽

10.1161/circ.142.suppl_3.16544 ◽

2020 ◽

Vol 142 (Suppl_3) ◽

Author(s):

Yang Yang ◽

Sheng Wang ◽

Andrew Suen ◽

Briana K Shimada ◽

Lin Zou ◽

...

Keyword(s):

Reperfusion Injury ◽

Rna Sequencing ◽

Small Rna ◽

Ischemia Reperfusion Injury ◽

Ischemia Reperfusion ◽

Cdna Libraries ◽

Small Rna Sequencing ◽

Myocardial Inflammation ◽

Sequencing Analysis ◽

Plasma Rna

Introduction: Transient myocardial ischemic/reperfusion injury (I/R) leads to cellular RNA release into extracellular (ex) space. Ex-RNAs and certain uridine-rich miRNAs activate innate immune response via TLR7-MyD88 pathway. Systemic administration of RNase reduces myocardial inflammation and infarct size after I/R, suggesting a pivotal role of ex-RNA in I/R injury. However, the nature of plasma RNAs and their biological functions in inflammation are not well understood. Hypothesis: Multiple plasma miRNAs are elevated in response to myocardial I/R injury and some are proinflammatory. Methods: Myocardial I/R injury was created in C57BL/6 mice by thoracotomy and 45 min of left anterior descending (LAD) ligation followed by 4 h of reperfusion. Sham mice underwent same procedure without LAD ligation. Plasma RNA was extracted using Trizol LS with Cel-miR-39 as spiked-in and quantified by RNA Quant-it kits. The plasma RNA was used to create cDNA libraries for small RNA sequencing (Norgen, Canada). Three abundant miRNAs that were differentially expressed between sham and I/R groups were tested for their proinflammatory effect. Results: Myocardial I/R led to a marked increase in plasma troponin (392.1±324.6 vs. 17.9±9.9ng/ml, P<0.05) and RNA levels (163±129 vs. 81±40 ng/ml) as compared with sham mice ( Fig. A ). Plasma RNA-Seq revealed miRNA was the predominate biotype constituting of 85.7% and 79.2% of plasma RNA in sham and I/R mice, respectively ( Fig. B ). We validated three miRNA expressions using qRT-PCR and found miR191-5p, miR125a-5p, and miR125b-5p were substantially increased ( Fig. C ). When incubated with macrophage cultures, miR125a-5p and miR-125b-5p, but not miR-191-5p, induced a dose-dependent response in CXCL-2 and IL-6 productions ( Fig. D ). Conclusions: Myocardial I/R injury results in an increase in multiple miRNAs in plasma. miR125a-5p and miR125b-5p, but not miR-191-5p, are pro-inflammatory in macrophages.

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Integrated analyses of the transcriptome and small RNA of the hemiparasitic plant Monochasma savatieri before and after establishment of parasite-host association

BMC Plant Biology ◽

10.1186/s12870-021-02861-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lanlan Chen ◽

Qiaosheng Guo ◽

Zaibiao Zhu ◽

Hefang Wan ◽

Yuhao Qin ◽

...

Keyword(s):

Rna Sequencing ◽

Small Rna ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Sequencing Analysis ◽

Relationship Analysis ◽

Differentially Expressed Mirnas ◽

Before And After ◽

Aba Content ◽

Host Associations

Abstract Background Monochasma savatieri is a medicinal root hemiparasitic herb that extracts water and nutrients from the host plant via a haustorium. M. savatieri exhibits an enhanced growth after the establishment of parasite-host associations, but little is known about the molecular mechanism responsible. In this study, endogenous hormones, RNA sequencing and small RNA sequencing analysis were performed on M. savatieri before and after establishment of parasite-host associations. Results When grown with the host, decreased contents of jasmonic acid (JA) and indole-3-acetic acid (IAA) and increased abscisic acid (ABA) content were observed in M. savatieri with the established parasitic relationship. When grown with the host, 46,424 differentially expressed genes (DEGs) and 162 differentially expressed miRNAs (DEmiRs) were identified in the comparison between M. savatieri with the established parasitic relationship and without the established parasitic relationship. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these DEGs and targets of DEmiRs mostly participated in plant hormone signal transduction, starch and sucrose metabolism, carbohydrate metabolism, cell growth and death, and transport and catabolism. Furthermore, correlation analysis of mRNA and miRNA revealed that 10 miRNA-target pairs from novel_mir65, novel_mir40, novel_mir80, miR397-5p_1, novel_mir36, novel_mir25 and novel_mir17 may have important roles in regulating the parasitic development of M. savatieri. Conclusions Our study not only expands the understanding of enhanced growth in M. savatieri after the establishment of parasite-host associations, but also first provides abundant resources for future molecular and genetic studies in M. savatieri.

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

Frontiers in Oncology ◽

10.3389/fonc.2021.707017 ◽

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.

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Detection of circulating extracellular mRNAs by modified small RNA-sequencing analysis

10.1101/507681 ◽

2018 ◽

Author(s):

Kemal M. Akat ◽

Youngmin A. Lee ◽

Arlene Hurley ◽

Pavel Morozov ◽

Klaas E.A. Max ◽

...

Keyword(s):

Rna Sequencing ◽

Small Rna ◽

Hematopoietic Cells ◽

Small Rna Sequencing ◽

Additional Contribution ◽

Sequencing Analysis ◽

Sample Type ◽

Extracellular Rna ◽

Coronary Syndrome ◽

Ribonucleoprotein Complexes

AbstractExtracellular mRNAs (ex-mRNAs) potentially supersede extracellular miRNAs (ex-miRNAs) and other RNA classes as biomarkers. Here, we present a comprehensive extracellular RNA (exRNA) study in human blood circulation based on conventional small RNA-sequencing (sRNA-seq) and sRNA-seq after T4 polynucleotide kinase (PNK) end-treatment of total exRNA isolated from serum and platelet-poor EDTA, ACD, and heparin plasma. Applying strict criteria for read mapping and annotation, we found that compared to conventional sRNA-seq PNK-treatment increased the detection of informative ex-mRNAs reads up to 50-fold. Based on captured ex-mRNAs from healthy individuals, we concluded that the exRNA pool is dominated by hematopoietic cells and platelets, with additional contribution from the liver. About 60% of the 15- to 42-nt long reads originated from the coding sequences, in a pattern reminiscent of ribosome-profiling studies for high abundance transcripts. Blood sample type had a considerable influence on the exRNA profile. The number of detected distinct ex-mRNA transcripts ranged from on average ~350 to 1100 in the different plasma types. In serum, additional transcripts from neutrophils and hematopoietic cells increased this number to ~2300. For EDTA and ACD, in particular, we found evidence of destabilization of mRNA and non-coding RNA ribonucleoprotein complexes. In a proof-of-concept study, we compared patients with acute coronary syndrome (ACS) to healthy controls. The improved tissue resolution of ex-mRNAs after PNK-treatment enabled us to detect a neutrophil-signature in ACS that escaped detection in an ex-miRNA analysis. Thus, ex-mRNAs provide superior resolution for the study of exRNA changes in vivo and ex vivo. They can be readily studied by sRNA-seq after T4 PNK end-treatment.

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Small RNA Sequencing Analysis of miRNA Expression Reveals Novel Insihts into Root Formation under Root Restriction Cultivation in Grapevine (Vitis vinifera L.)

International Journal of Molecular Sciences ◽

10.3390/ijms21103513 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3513

Author(s):

Hui Li ◽

Zhen Gao ◽

Muhammad Salman Zahid ◽

Dongmei Li ◽

Hafiz Umer Javed ◽

...

Keyword(s):

Rna Sequencing ◽

Root Development ◽

Small Rna ◽

Mirna Expression ◽

Lateral Root ◽

Differentially Expressed ◽

Root Tip ◽

Small Rna Sequencing ◽

Sequencing Analysis ◽

Root Restriction

Root restriction cultivation (RRC) can influence plant root architecture, but its root phenotypic changes and molecular mechanisms are still unknown. In this study, phenotype observations of grapevine root under RRC and control cultivation (nRC) at 12 time points were conducted, and the root phenotype showed an increase of adventitious and lateral root numbers and root tip degeneration after RRC cultivation from 70 days after planting (DAP). The 70 and 125 DAP sampling of two different cultivations, named nR70, RR70, nR125, and RR125, were selected for small RNA sequencing. A total of 153 known miRNAs and 119 predicted novel miRNAs were obtained. Furthermore, BLAST was used to predict the novel miRNAs with miRBase databases using the default parameters; 96 of the 119 predicted novel miRNAs were similar to other species, and the remaining 23 grapevine-specific novel miRNAs were obtained. There were 26, 33, 26, and 32 miRNAs that were differentially expressed in different comparison groups (RR70 vs. nR70, RR125 vs. nR125, nR125 vs. nR70 and RR125 vs. RR70). Target genes prediction of differentially expressed miRNAs was annotated on a variety of biological processes, and 24 participated in root development. Moreover, multiple miRNAs were found to jointly regulate lateral root development under root restriction conditions. The miRNA expression pattern comparison between RRC and nRC may provide a framework for the future analysis of miRNAs associated with root development in grapevine.

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