scholarly journals The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis

2022 ◽  
Vol 119 (3) ◽  
pp. e2103527119
Author(s):  
Johanna Wong-Bajracharya ◽  
Vasanth R. Singan ◽  
Remo Monti ◽  
Krista L. Plett ◽  
Vivian Ng ◽  
...  
Keyword(s):  
Developmental Process ◽  
Experimental Testing ◽  
Eucalyptus Grandis ◽  
Target Prediction ◽  
Ectomycorrhizal Fungus ◽  
Model Systems ◽  
Sequencing Data ◽  
Symbiotic Interaction ◽  
Host Signaling ◽  
Fungal Interactions

Small RNAs (sRNAs) are known to regulate pathogenic plant–microbe interactions. Emerging evidence from the study of these model systems suggests that microRNAs (miRNAs) can be translocated between microbes and plants to facilitate symbiosis. The roles of sRNAs in mutualistic mycorrhizal fungal interactions, however, are largely unknown. In this study, we characterized miRNAs encoded by the ectomycorrhizal fungus Pisolithus microcarpus and investigated their expression during mutualistic interaction with Eucalyptus grandis. Using sRNA sequencing data and in situ miRNA detection, a novel fungal miRNA, Pmic_miR-8, was found to be transported into E. grandis roots after interaction with P. microcarpus. Further characterization experiments demonstrate that inhibition of Pmic_miR-8 negatively impacts the maintenance of mycorrhizal roots in E. grandis, while supplementation of Pmic_miR-8 led to deeper integration of the fungus into plant tissues. Target prediction and experimental testing suggest that Pmic_miR-8 may target the host NB-ARC domain containing transcripts, suggesting a potential role for this miRNA in subverting host signaling to stabilize the symbiotic interaction. Altogether, we provide evidence of previously undescribed cross-kingdom sRNA transfer from ectomycorrhizal fungi to plant roots, shedding light onto the involvement of miRNAs during the developmental process of mutualistic symbioses.

scholarly journals Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data

2021 ◽  
Vol 99 (2) ◽  
Author(s):  
Yuhua Fu ◽  
Pengyu Fan ◽  
Lu Wang ◽  
Ziqiang Shu ◽  
Shilin Zhu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Target Prediction ◽  
Large Data ◽  
Sequencing Data ◽  
Regulate Gene Expression ◽  
High Throughput Sequencing Data ◽  
Annotation Information ◽  
Public Data ◽  
Broad Variety

Abstract Despite the broad variety of available microRNA (miRNA) research tools and methods, their application to the identification, annotation, and target prediction of miRNAs in nonmodel organisms is still limited. In this study, we collected nearly all public sRNA-seq data to improve the annotation for known miRNAs and identify novel miRNAs that have not been annotated in pigs (Sus scrofa). We newly annotated 210 mature sequences in known miRNAs and found that 43 of the known miRNA precursors were problematic due to redundant/missing annotations or incorrect sequences. We also predicted 811 novel miRNAs with high confidence, which was twice the current number of known miRNAs for pigs in miRBase. In addition, we proposed a correlation-based strategy to predict target genes for miRNAs by using a large amount of sRNA-seq and RNA-seq data. We found that the correlation-based strategy provided additional evidence of expression compared with traditional target prediction methods. The correlation-based strategy also identified the regulatory pairs that were controlled by nonbinding sites with a particular pattern, which provided abundant complementarity for studying the mechanism of miRNAs that regulate gene expression. In summary, our study improved the annotation of known miRNAs, identified a large number of novel miRNAs, and predicted target genes for all pig miRNAs by using massive public data. This large data-based strategy is also applicable for other nonmodel organisms with incomplete annotation information.

scholarly journals 1450-1545 Young Investigator Awards & Presentations Basic/Translational Exploring cellular subpopulations in glioblastoma and matched organoids using single-cell RNA-seq 52

2018 ◽  
Vol 45 (S3) ◽  
pp. S13-S14
Author(s):  
VG LeBlanc ◽  
D Trinh ◽  
M Hughes ◽  
I Luthra ◽  
D Livingstone ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Tissue Sample ◽  
Expression Patterns ◽  
Model Systems ◽  
Sequencing Data ◽  
Tissue Samples ◽  
Original Tumour ◽  
Current Therapies ◽  
Intratumoural Heterogeneity

Glioblastomas (GBMs) account for nearly half of all primary malignant brain tumours, and current therapies are often only marginally effective. Our understanding of the underlying biology of these tumours and the development of new therapies have been complicated in part by widespread inter- and intratumoural heterogeneity. To characterize this heterogeneity, we performed regional subsampling of primary glioblastomas and derived organoids from these tissue samples. We then performed single-cell RNA-sequencing (scRNA-seq) on these primary regional subsamples and 1-3 matched organoids per sample. We have profiled samples from six tumour sets to date and have obtained sequencing data for 21,234 primary tissue cells and 14,742 organoid cells. While the most apparent differences in gene expression appear to be between individual tumours, we were also able to identify similar cellular subpopulations across tissue samples and across organoids. Importantly, organoids derived from the same tissue sample appeared to be composed of similar cellular subpopulations and were highly comparable to each other, indicating that replicate organoids faithfully represent the original tumour tissue. Overall, our scRNA-seq approach will help evaluate the utility of tumour-derived organoids as model systems for GBM and will aid in identifying cellular subpopulations defined by gene expression patterns, both in primary GBM regional subsamples and their associated organoids. These analyses will allow for the characterization of clonal or subclonal populations that are likely to respond to different therapeutic approaches and may also uncover novel therapeutic targets previously unrevealed through bulk analyses.

scholarly journals Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution

2019 ◽  
Author(s):  
M-M Aynaud ◽  
O Mirabeau ◽  
N Gruel ◽  
S Grossetête ◽  
V Boeva ◽  
...  
Keyword(s):  
Single Cell ◽  
Ewing Sarcoma ◽  
Cell Transformation ◽  
Cell Types ◽  
Intratumoral Heterogeneity ◽  
Model Systems ◽  
Open Chromatin ◽  
Sequencing Data ◽  
Time Resolved ◽  
Super Enhancer

SummaryEWSR1-FLI1, the chimeric oncogene specific for Ewing sarcoma (EwS), induces a cascade of signaling events leading to cell transformation. However, it remains elusive how genetically homogeneous EwS cells can drive heterogeneity of transcriptional programs. Here, we combined independent component analysis of single cell RNA-sequencing data from diverse cell types and model systems with time-resolved mapping of EWSR1-FLI1 binding sites and of open chromatin regions to characterize dynamic cellular processes associated with EWSR1-FLI1 activity. We thus defined an exquisitely specific and direct, super-enhancer-driven EWSR1-FLI1 program. In EwS tumors, cell proliferation was associated with a well-defined range of EWSR1-FLI1 activity; moreover, cells with a high EWSR1-FLI1 activity presented a strong oxidative phosphorylation metabolism. In contrast, a subpopulation of cells from below and above optimal EWSR1-FLI1 activity was characterized by increased hypoxia. Overall, our study reveals sources of intratumoral heterogeneity within Ewing tumors.

scholarly journals Expression Profiles of tRNA-Derived Small RNAs and Their Potential Roles in Primary Nasopharyngeal Carcinoma

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhaoyi Lu ◽  
Kai Su ◽  
Xiaomin Wang ◽  
Mingjie Zhang ◽  
Shiyin Ma ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Small Rnas ◽  
Target Genes ◽  
Expression Profiles ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Diagnostic Efficiency ◽  
Sequencing Data ◽  
Qrt Pcr

Introduction: tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs, are divided into two categories: tRNA-related fragments (tRFs) and tRNA halves (tiRNAs). Abnormal expression of tsRNAs has been found in diverse cancers, which indicates that further understanding of the function of tsRNAs will help identify new biomarkers and potential therapeutic targets. Until now, the underlying roles of tsRNAs in primary nasopharyngeal carcinoma (NPC) are still unknown.Methods: tRF and tiRNA sequencing was performed on four pairs of NPC tissues and healthy controls. Thirty pairs of NPC samples were used for quantitative real-time polymerase chain reaction (qRT-PCR) verification, and the ROC analysis was used to evaluate the diagnostic efficiency initially. Target prediction and bioinformatics analysis of validated tRFs and tiRNAs were conducted to explore the mechanisms of tsRNAs in NPC’s pathogenesis.Results: A total of 158 differentially expressed tRFs and tiRNAs were identified, of which 88 are upregulated and 70 are downregulated in NPC. Three validated tRFs in the results of qRT-PCR were consistent with the sequencing data: two upregulations (tRF-1:28-Val-CAC-2 and tRF-1:24-Ser-CGA-1-M3) and one downregulation (tRF-55:76-Arg-ACG-1-M2). The GO and KEGG pathway enrichment analysis showed that the potential target genes of validated tRFs are widely enriched in cancer pathways. The related modules may play an essential role in the pathogenesis of NPC.Conclusions: The tsRNAs may become a novel class of biological diagnostic indicators and possible targets for NPC.

Comprehensive Analysis of Aberrantly Expressed CircRNAs in the Ossification of the Posterior Longitudinal Ligament

2021 ◽  
Author(s):  
Qi-Chang Gao ◽  
Zhi-Zhuang Zhang ◽  
Tuo Shao ◽  
Wei-Long Tang ◽  
Yu-Hang Hu ◽  
...  
Keyword(s):  
Biological Process ◽  
Expression Profiles ◽  
Treatment Options ◽  
Osteoclast Differentiation ◽  
Target Prediction ◽  
Posterior Longitudinal Ligament ◽  
Neurological Deficits ◽  
P Value ◽  
Sequencing Data ◽  
Kegg Pathways

Abstract Introduction With causing severe neurological deficits, ossification of the posterior longitudinal ligament (OPLL) has attracted attention in mounting numbers. Increasing evidence shows that circRNAs act as a vital regulatory role in the biological process of human disease development. However, the potential mechanism of circRNAs in OPLL was not fully revealed.MethodsIn this study, 3 OPLL patients and 3 controls were selected for Microarray analysis, and the expression profiles of circRNAs were established. TargetScan and Miranda's miRNA target prediction software were used to predict the circRNA-microRNA interaction. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to identify the biological process and key pathways. we used the STRING database to analyze and construct a Protein-Protein Interaction (PPI) network. Several circRNAs were randomly selected for quantitative real-time PCR (qRT-PCR) validation. ResultsMicroarray data profiling indicated that 489 circRNAs (234 up and 255 down) were highly differentially expressed with setting screening criteria (FC ≥ 2.0 and p-value ≤ 0.05). GO enrichment and KEGG pathways analysis revealed some processes and pathways that might influence the progress of OPLL such as osteoclast differentiation, vasopressin-regulated water reabsorption, Wnt, MAPK, VEGF signaling pathway. We have obtained some significant genes such as AKT3, ACVR1, RBPJ, NFATC1, PTK2, SLC8A1. Extended sample verification results were consistent with sequencing data.Conclusions It is the first study for portraying circRNAs expression profiles of OPLL. This provides new ideas for the prevention and alleviation of OPLL. The specific functions and mechanisms of circRNAs in OPLL should be further verified to provide more clinical treatment options for OPLL patients.

scholarly journals Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides inSinorhizobium meliloti

2017 ◽  
Vol 200 (3) ◽  
Author(s):  
Melanie J. Barnett ◽  
Sharon R. Long
Keyword(s):  
Cell Surface ◽  
Biofilm Formation ◽  
Sinorhizobium Meliloti ◽  
Developmental Process ◽  
Root Nodules ◽  
Critical Role ◽  
Nitrogen Fixing ◽  
Symbiotic Interaction ◽  
Content Type ◽  
Mutant Phenotypes

ABSTRACTSinorhizobium melilotiis a soil-dwelling alphaproteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important both for adapting to stresses in the soil and for the development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides I (EPS-I; succinoglycan) and II (EPS-II; galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots. Previous genetic screens discovered mutants with impaired EPS production, allowing the delineation of EPS biosynthetic pathways. Here we report on a genetic screen to isolate mutants with mucoid colonial morphologies that suggest EPS overproduction. Screening with Tn5-110, which allows the recovery of both null and upregulation mutants, yielded 47 mucoid mutants, most of which overproduce EPS-I; among the 30 unique genes and intergenic regions identified, 14 have not been associated with EPS production previously. We identified a new protein-coding gene,emmD, which may be involved in the regulation of EPS-I production as part of the EmmABC three-component regulatory circuit. We also identified a mutant defective in EPS-I production, motility, and symbiosis, where Tn5-110 was not responsible for the mutant phenotypes; these phenotypes result from a missense mutation inrpoAcorresponding to the domain of the RNA polymerase alpha subunit known to interact with transcription regulators.IMPORTANCEThe alphaproteobacteriumSinorhizobium meliloticonverts dinitrogen to ammonium while inhabiting specialized plant organs termed root nodules. The transformation ofS. melilotifrom a free-living soil bacterium to a nitrogen-fixing plant symbiont is a complex developmental process requiring close interaction between the two partners. As the interface between the bacterium and its environment, theS. meliloticell surface plays a critical role in adaptation to varied soil environments and in interaction with plant hosts. We isolated and characterizedS. melilotimutants with increased production of exopolysaccharides, key cell surface components. Our diverse set of mutants suggests roles for exopolysaccharide production in growth, metabolism, cell division, envelope homeostasis, biofilm formation, stress response, motility, and symbiosis.

scholarly journals Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 441 ◽  
Author(s):  
Ho ◽  
Geisler
Keyword(s):  
Transcription Factors ◽  
Dna Sequences ◽  
Developmental Stages ◽  
Experimental Testing ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Model Systems ◽  
Whole Genome Sequence ◽  
Cis Acting ◽  
Biotic Stresses

The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data. In this study, we tested the applicability of two algorithms developed for other model systems for the identification of biologically significant CREs of co-expressed genes from rice. CREs were identified from the DNA sequences located upstream from the transcription start sites, untranslated regions (UTRs), and introns, and downstream from the translational stop codons of co-expressed genes. The biologically significance of each CRE was determined by correlating their absence and presence in each gene with that gene’s expression profile using a meta-database constructed from 50 rice microarray data sets. The reliability of these methods in the predictions of CREs and their corresponding TFs was supported by previous wet lab experimental data and a literature review. New CREs corresponding to abiotic stresses, biotic stresses, specific tissues, and developmental stages were identified from rice, revealing new pieces of information for future experimental testing. The effectiveness of some—but not all—CREs was found to be affected by copy number, position, and orientation. The corresponding TFs that were most likely correlated with each CRE were also identified. These findings not only contribute to the prioritization of candidates for further analysis, the information also contributes to the understanding of the gene regulatory network.

scholarly journals PAREameters: a tool for computational inference of plant miRNA–mRNA targeting rules using small RNA and degradome sequencing data

2020 ◽  
Vol 48 (5) ◽  
pp. 2258-2270 ◽  
Author(s):  
Joshua Thody ◽  
Vincent Moulton ◽  
Irina Mohorianu
Keyword(s):  
Small Rna ◽  
Mirna Target ◽  
Target Prediction ◽  
Model Organisms ◽  
Messenger Rnas ◽  
Mirna Target Prediction ◽  
Sequencing Data ◽  
Translation Rate ◽  
Degradome Sequencing ◽  
Using Data

Abstract MicroRNAs (miRNAs) are short, non-coding RNAs that modulate the translation-rate of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex to sequence-specific targets. In plants, this typically results in cleavage and subsequent degradation of the mRNA. Degradome sequencing is a high-throughput technique developed to capture cleaved mRNA fragments and thus can be used to support miRNA target prediction. The current criteria used for miRNA target prediction were inferred on a limited number of experimentally validated A. thaliana interactions and were adapted to fit these specific interactions; thus, these fixed criteria may not be optimal across all datasets (organisms, tissues or treatments). We present a new tool, PAREameters, for inferring targeting criteria from small RNA and degradome sequencing datasets. We evaluate its performance using a more extensive set of experimentally validated interactions in multiple A. thaliana datasets. We also perform comprehensive analyses to highlight and quantify the differences between subsets of miRNA–mRNA interactions in model and non-model organisms. Our results show increased sensitivity in A. thaliana when using the PAREameters inferred criteria and that using data-driven criteria enables the identification of additional interactions that further our understanding of the RNA silencing pathway in both model and non-model organisms.

scholarly journals A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism in Epichloë spp.

2015 ◽  
Vol 28 (3) ◽  
pp. 218-231 ◽  
Author(s):  
Carla J. Eaton ◽  
Pierre-Yves Dupont ◽  
Peter Solomon ◽  
William Clayton ◽  
Barry Scott ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Core Gene ◽  
Phytopathogenic Fungi ◽  
Primary Metabolism ◽  
Symbiotic Interaction ◽  
Genes Encoding ◽  
Degradative Enzymes ◽  
Fungal Interactions ◽  
Molecular Patterns

Beneficial plant–fungal interactions play an important role in the ability of plants to survive changing environmental conditions. In contrast, phytopathogenic fungi fall at the opposite end of the symbiotic spectrum, causing reduced host growth or even death. In order to exploit beneficial interactions and prevent pathogenic ones, it is essential to understand the molecular differences underlying these alternative states. The association between the endophyte Epichloë festucae and Lolium perenne (perennial ryegrass) is an excellent system for studying these molecular patterns due to the existence of several fungal mutants that have an antagonistic rather than a mutualistic interaction with the host plant. By comparing gene expression in a wild-type beneficial association with three mutant antagonistic associations disrupted in key signaling genes, we identified a core set of 182 genes that show common differential expression patterns between these two states. These gene expression changes are indicative of a nutrient-starvation response, as supported by the upregulation of genes encoding degradative enzymes, transporters, and primary metabolism, and downregulation of genes encoding putative small-secreted proteins and secondary metabolism. These results suggest that disruption of a mutualistic symbiotic interaction may lead to an elevated uptake and degradation of host-derived nutrients and cell-wall components, reminiscent of phytopathogenic interactions.

scholarly journals hnRNPK-regulated LINC00263 promotes malignant phenotypes through miR-147a/CAPN2

2021 ◽  
Vol 12 (4) ◽  
Author(s):  
Woo Joo Lee ◽  
Chang Hoon Shin ◽  
Haein Ji ◽  
Seong Dong Jeong ◽  
Mi-So Park ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cancer Progression ◽  
Rna Binding ◽  
Critical Role ◽  
Target Prediction ◽  
Direct Interaction ◽  
Metastatic Potential ◽  
Luciferase Reporter ◽  
Small Rna Sequencing ◽  
Sequencing Data

AbstractMalignant characteristics of cancers, represented by rapid cell proliferation and high metastatic potential, are a major cause of high cancer-related mortality. As a multifunctional RNA-binding protein, heterogeneous nuclear ribonucleoprotein K (hnRNPK) is closely associated with cancer progression in various types of cancers. In this study, we sought to identify hnRNPK-regulated long intergenic non-coding RNAs (lincRNAs) that play a critical role in the regulation of cancer malignancy. We found that hnRNPK controlled malignant phenotypes including invasiveness, proliferation, and clonogenicity. RNA sequencing and functional studies revealed that LINC00263, a novel target of hnRNPK, is involved in the oncogenic functions of hnRNPK. Knockdown of LINC00263 mitigated the malignant capabilities. Conversely, increased malignant phenotypes were observed in LINC00263-overexpressing cells. Since LINC00263 was mainly localized in the cytosol and highly enriched in Argonaute 2-immunoprecipitation (Ago2-IP), we hypothesized that LINC00263 acts as a competitive endogenous RNA (ceRNA), and thus sought to identify LINC00263-associated microRNAs. Using small RNA sequencing followed by antisense oligonucleotide pull-down, miR-147a was selected for further study. We found that miR-147a negatively regulates LINC00263 via direct interaction, thus suppressing malignant capabilities. Moreover, knockdown of hnRNPK and LINC00263 upregulated miR-147a, indicating that LINC00263 serves as a ceRNA for miR-147a. By analyzing RNA sequencing data and miRNA target prediction, calpain 2 (CAPN2) was identified as a putative target of miR-147a. Ago2-IP and luciferase reporter assay revealed that miR-147a suppressed CAPN2 expression by directly binding to the 3′UTR of CAPN2 mRNA. In addition, we found that the weakened malignant capabilities following knockdown of hnRNPK or LINC00263 were restored by miR-147a inhibition or CAPN2 overexpression. Furthermore, our findings were validated in various other types of cancer cells including lung cancer, colorectal cancer, neuroblastoma, and melanoma. Collectively, we demonstrate that hnRNPK-regulated LINC00263 plays an important role in cancer malignancy by acting as a miR-147a decoy and thus upregulating CAPN2.

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