Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds

Phloem fibers are important elements of plant architecture and the target product of many fiber crops. A key stage in fiber development is intrusive elongation, the mechanisms of which are largely unknown. Integrated analysis of miRNA and mRNA expression profiles in intrusivelygrowing fibers obtained by laser microdissection from flax (Linum usitatissimum L.) stem revealed all 124 known flax miRNA from 23 gene families and the potential targets of differentially expressed miRNAs. A comparison of the expression between phloem fibers at different developmental stages, and parenchyma and xylem tissues demonstrated that members of miR159, miR166, miR167, miR319, miR396 families were down-regulated in intrusively growing fibers. Some putative target genes of these miRNA families, such as those putatively encoding growth-regulating factors, an argonaute family protein, and a homeobox-leucine zipper family protein were up-regulated in elongating fibers. miR160, miR169, miR390, and miR394 showed increased expression. Changes in the expression levels of miRNAs and their target genes did not match expectations for the majority of predicted target genes. Taken together, poorly understood intrusive fiber elongation, the key process of phloem fiber development, was characterized from a miRNA-target point of view, giving new insights into its regulation.

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Development of a tRNA-Derived Small RNA Prognostic Panel and Their Potential Functions in Osteosarcoma

Frontiers in Oncology ◽

10.3389/fonc.2021.652040 ◽

2021 ◽

Vol 11 ◽

Author(s):

Zhenming Tang ◽

Shuhui Zhang ◽

Zhougui Ling

Keyword(s):

Small Rna ◽

Target Genes ◽

Cox Model ◽

Expression Profiles ◽

Survival Rates ◽

Low Risk ◽

Validation Dataset ◽

Therapeutic Outcomes ◽

Risk Patients ◽

Geo Database

BackgroundTherapeutic outcomes of osteosarcoma treatment have not significantly improved in several decades. Therefore, strong prognostic biomarkers are urgently needed.MethodsWe first extracted the tRNA-derived small RNA (tsRNA) expression profiles of osteosarcoma from the GEO database. Then, we performed a unique module analysis and use the LASSO-Cox model to select survival-associated tsRNAs. Model effectiveness was further verified using an independent validation dataset. Target genes with selected tsRNAs were predicted using RNAhybrid.ResultsA LASSO-Cox model was established to select six prognostic tsRNA biomarkers: tRF-33-6SXMSL73VL4YDN, tRF-32-6SXMSL73VL4YK, tRF-32-M1M3WD8S746D2, tRF-35-RPM830MMUKLY5Z, tRF-33-K768WP9N1EWJDW, and tRF-32-MIF91SS2P46I3. We developed a prognostic panel for osteosarcoma patients concerning their overall survival by high-low risk. Patients with a low-risk profile had improved survival rates in training and validation dataset.ConclusionsThe suggested prognostic panel can be utilized as a reliable biomarker to predict osteosarcoma patient survival rates.

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miRNA activity inferred from single cell mRNA expression

Scientific Reports ◽

10.1038/s41598-021-88480-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Morten Muhlig Nielsen ◽

Jakob Skou Pedersen

Keyword(s):

Mrna Expression ◽

Single Cell ◽

Target Genes ◽

Expression Profiles ◽

Single Cells ◽

Enrichment Analysis ◽

Sequence Motifs ◽

Data Set ◽

Motif Enrichment ◽

Activity Measures

AbstractHigh throughput single-cell RNA sequencing (scRNAseq) can provide mRNA expression profiles for thousands of cells. However, miRNAs cannot currently be studied at the same scale. By exploiting that miRNAs bind well-defined sequence motifs and typically down-regulate target genes, we show that motif enrichment analysis can be used to derive miRNA activity estimates from scRNAseq data. Motif enrichment analyses have traditionally been used to derive binding motifs for regulatory factors, such as miRNAs or transcription factors, that have an effect on gene expression. Here we reverse its use. By starting from the miRNA seed site, we derive a measure of activity for miRNAs in single cells. We first establish the approach on a comprehensive set of bulk TCGA cancer samples (n = 9679), with paired mRNA and miRNA expression profiles, where many miRNAs show a strong correlation with measured expression. By downsampling we show that the method can be used to estimate miRNA activity in sparse data comparable to scRNAseq experiments. We then analyze a human and a mouse scRNAseq data set, and show that for several miRNA candidates, including liver specific miR-122 and muscle specific miR-1 and miR-133a, we obtain activity measures supported by the literature. The methods are implemented and made available in the miReact software. Our results demonstrate that miRNA activities can be estimated at the single cell level. This allows insights into the dynamics of miRNA activity across a range of fields where scRNAseq is applied.

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Integrative Analysis of miRNA and mRNA Expression Profiles in Calcium Oxalate Nephrolithiasis Rat Model

BioMed Research International ◽

10.1155/2017/8306736 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 3

Author(s):

Chuangxin Lan ◽

Dong Chen ◽

Xiongfa Liang ◽

Jian Huang ◽

Tao Zeng ◽

...

Keyword(s):

Calcium Oxalate ◽

Mrna Expression ◽

Target Genes ◽

Expression Profiles ◽

Critical Role ◽

Group Versus ◽

Receptor Interaction ◽

Control Group ◽

Calcium Oxalate Stone ◽

Qrt Pcr

The microRNA (miRNA) expression profiles and their biological functions in calcium oxalate nephrolithiasis remain unclear. In this study, we investigate the miRNA and mRNA expression profiles of kidney tissues in calcium oxalate stone rats. 16 Sprague Dawley rats were divided into control group and stone-forming group. 24-hour urine samples and kidney tissues were collected for biochemical and histological determination after 4 weeks. MiRNA and mRNA microarray were applied to evaluate the miRNA and mRNA expression profiles. To validate the microarray results, the quantitative real-time PCR (qRT-PCR) was performed. A total of 38 miRNAs and 2728 mRNAs were significantly and differentially expressed in kidney tissues of stone-forming group versus control group. Gene Ontology (GO) analysis revealed that most of the target genes were enriched in terms of oxidation reduction, ion transport, inflammatory response, and response to wounding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of these targets highlights their critical role in cytokine-cytokine receptor interaction, gap junction, and chemokine signaling pathway. Furthermore, the reliability of the microarray-based results was confirmed by using qRT-PCR determination. The miRNA and mRNA expressions in calcium oxalate stone rat kidneys might provide a basis for further research on urolithiasis mechanism.

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Joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in gastric cancer

Cancer Cell International ◽

10.1186/s12935-020-01554-8 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Zhi Lv ◽

Liping Sun ◽

Qian Xu ◽

Chengzhong Xing ◽

Yuan Yuan

Keyword(s):

Gastric Cancer ◽

Mrna Expression ◽

Expression Analysis ◽

Target Genes ◽

Expression Profiles ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Joint Analysis ◽

Gene Enrichment Analysis ◽

Gene Enrichment

Abstract Background N6-methyladenosine (m6A) modification might be closely associated with the genesis and development of gastric cancer (GC). Currently, the evidence established by high-throughput assay for GC-related m6A patterns based on long non-coding RNAs (lncRNAs) remains limited. Here, a joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in GC was performed to explore the regulatory roles of m6A modification in lncRNAs. Methods Three subjects with primary GC were enrolled in our study and paired sample was randomly selected from GC tissue and adjacent normal tissue for each case. Methylated RNA Immunoprecipitation NextGeneration Sequencing (MeRIP-Seq) and Microarray Gene Expression Profiling was subsequently performed. Then co-expression analysis and gene enrichment analysis were successively conducted. Results After data analysis, we identified 191 differentially m6A-methylated lncRNAs, 240 differentially expressed lncRNAs and 229 differentially expressed mRNAs in GC. Furthermore, four differentially m6A-methylated and expressed lncRNAs (dme-lncRNAs) were discovered including RASAL2-AS1, LINC00910, SNHG7 and LINC01105. Their potential target genes were explored by co-expression analysis. And gene enrichment analysis suggested that they might influence the cellular processes and biological behaviors involved in mitosis and cell cycle. The potential impacts of these targets on GC cells were further validated by CCLE database and literature review. Conclusions Four novel dme-lncRNAs were identified in GC, which might exert regulatory roles on GC cell proliferation. The present study would provide clues for the lncRNA m6A methylation-based research on GC epigenetic etiology and pathogenesis.

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Expression characteristics of pineal miRNAs at ovine different reproductive stages and the identification of miRNAs targeting the AANAT gene

BMC Genomics ◽

10.1186/s12864-021-07536-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Ran Di ◽

Qiu-Yue Liu ◽

Shu-Hui Song ◽

Dong-Mei Tian ◽

Jian-Ning He ◽

...

Keyword(s):

Pineal Gland ◽

Mrna Expression ◽

Breeding Season ◽

Target Genes ◽

Expression Profiles ◽

Mirna Gene ◽

Luciferase Reporter ◽

Seasonal Reproduction ◽

Expression Characteristics

Abstract Background Many recent studies have shown that miRNAs play important roles in the regulation of animal reproduction, including seasonal reproduction. The pineal gland is a crucial hub in the regulation of seasonal reproduction. However, little is known about the expression characteristics of pineal miRNAs in different reproductive seasons (anestrus and breeding season). Therefore, the expression profiles and regulatory roles of ovine pineal miRNAs were investigated during different reproductive stages using Solexa sequencing technology and dual luciferase reporter assays. Results A total of 427 miRNAs were identified in the sheep pineal gland. Significant differences in miRNA expression were demonstrated between anestrus and the breeding season in terms of the frequency distributions of miRNA lengths, number of expressed miRNAs, and specifically and highly expressed miRNAs in each reproductive stage. KEGG analysis of the differentially expressed (DE) miRNAs between anestrus and the breeding season indicated that they are significantly enriched in pathways related to protein synthesis, secretion and uptake. Furthermore, transcriptome analysis revealed that many target genes of DE miRNAs in the ribosome pathway showed relatively low expression in the breeding season. On the other hand, analyses combining miRNA-gene expression data with target relationship validation in vitro implied that miR-89 may participate in the negative regulation of aralkylamine N-acetyltransferase (AANAT) mRNA expression by targeting its 3’UTR at a unique binding site. Conclusions Our results provide new insights into the expression characteristics of sheep pineal miRNAs at different reproductive stages and into the negative regulatory effects of pineal miRNAs on AANAT mRNA expression.

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Identification of a Distinct miRNA Regulatory Network in the Tumor Microenvironment of Transformed Mycosis Fungoides

Cancers ◽

10.3390/cancers13225854 ◽

2021 ◽

Vol 13 (22) ◽

pp. 5854

Author(s):

Cosimo Di Raimondo ◽

Zhen Han ◽

Chingyu Su ◽

Xiwei Wu ◽

Hanjun Qin ◽

...

Keyword(s):

Tumor Microenvironment ◽

Mrna Expression ◽

Mycosis Fungoides ◽

Molecular Mechanisms ◽

Target Genes ◽

Cell Transformation ◽

Expression Profiles ◽

Poor Response ◽

Rna Seq ◽

Dismal Prognosis

Large cell transformation of mycosis fungoides (LCT-MF) occurs in 20–50% of advanced MF and is generally associated with poor response and dismal prognosis. Although different mechanisms have been proposed to explain the pathogenesis, little is known about the role of microRNAs (miRs) in transcriptional regulation of LCT-MF. Here, we investigated the miR and mRNA expression profile in lesional skin samples of patients with LCT-MF and non-LCT MF using RNA-seq analysis. We found miR-146a and miR-21 to be significantly upregulated, and miR-708 the most significantly downregulated miR in LCT-MF. Integration of miR and mRNA expression profiles revealed the miR-regulated networks in LCT-MF. Ingenuity pathway analysis (IPA) demonstrated the involvement of genes for ICOS-ICOSL, PD1-PDL1, NF-κB, E2F transcription, and molecular mechanisms of cancer signaling pathways. Quantitative real time (qRT)-PCR results of target genes were consistent with the RNA-seq data. We further identified the immunosuppressive tumor microenvironment (TME) in LCT-MF. Moreover, our data indicated that miR-146a, -21 and -708 are associated with the immunosuppressive TME in LCT-MF. Collectively, our results suggest that the key LCT-MF associated miRs and their regulated networks may provide insights into its pathogenesis and identify promising targets for novel therapeutic strategies.

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Bioinformatics analysis of miRNA and mRNA expression profiles to reveal the key miRNAs and genes in osteoarthritis

Journal of Orthopaedic Surgery and Research ◽

10.1186/s13018-021-02201-2 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Pei-yan Huang ◽

Jun-guo Wu ◽

Jun Gu ◽

Tie-qi Zhang ◽

Ling-feng Li ◽

...

Keyword(s):

Mrna Expression ◽

Expression Profile ◽

Target Genes ◽

Glycogen Synthase ◽

Expression Profiles ◽

Mirna Gene ◽

Functional Enrichment ◽

Joint Disease ◽

Expression Levels ◽

Qrt Pcr

Abstract Background Osteoarthritis (OA) is a chronic degenerative joint disease and the most frequent type of arthritis. This study aimed to identify the key miRNAs and genes associated with OA progression. Methods The GSE105027 (microRNA [miRNA/miR] expression profile; 12 OA samples and 12 normal samples) and GSE48556 (messenger RNA [mRNA] expression profile; 106 OA samples and 33 normal samples) datasets were selected from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and miRNAs (DEMs) were analyzed using the limma and ROCR packages in R, respectively. The target genes that negatively correlated with the DEMs were predicted, followed by functional enrichment analysis and construction of the miRNA-gene and miRNA-transcription factor (TF)-gene regulatory networks. Additionally, key miRNAs and genes were screened, and their expression levels were verified by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results A total of 1696 DEGs (739 upregulated and 957 downregulated) and 108 DEMs (56 upregulated and 52 downregulated) were identified in the OA samples. Furthermore, 56 target genes that negatively correlated with the DEMs were predicted and found to be enriched in three functional terms (e.g., positive regulation of intracellular protein transport) and three pathways (e.g., human cytomegalovirus infection). In addition, three key miRNAs (miR-98-5p, miR-7-5p, and miR-182-5p) and six key genes (murine double minute 2, MDM2; glycogen synthase kinase 3-beta, GSK3B; transmembrane P24-trafficking protein 10, TMED10; DDB1 and CUL4-associated factor 12, DCAF12; caspase 3, CASP3; and ring finger protein 44, RNF44) were screened, among which the miR-7-5p → TMED10/DCAF12, miR-98-5p → CASP3/RNF44, and miR-182-5p → GSK3B pairs were observed in the regulatory network. Moreover, the expression levels of TMED10, miR-7-5p, CASP3, miR-98-5p, GSK3B, and miR-182-5p showed a negative correlation with qRT-PCR verification. Conclusion MiR-98-5p, miR-7-5p, miR-182-5p, MDM2, GSK3B, TMED10, DCAF12, CASP3, and RNF44 may play critical roles in OA progression.

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A combined microRNA and transcriptome analysis illuminates the resistance response of rice against brown planthopper

10.21203/rs.2.17550/v2 ◽

2020 ◽

Author(s):

Jiaoyan Tan ◽

Yan Wu ◽

Jianping Guo ◽

Huimin Li ◽

Lili Zhu ◽

...

Keyword(s):

Mrna Expression ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Brown Planthopper ◽

Differentially Expressed ◽

Integrated Analysis ◽

Resistance Response

Abstract Background : The brown planthopper (BPH, Nilaparvata lugens Stål) is a kind of phloem-feeding pest that adversely affects rice yield. Recently, the BPH-resistance gene, BPH6 , was cloned and applied in rice breeding to effectively control BPH. However, the molecular mechanisms underlying BPH6 are poorly understood. Results: Here, an integrated miRNA and mRNA expression profiling analysis was performed on BPH6 -transgenic (BPH6G) and Nipponbare (wild type, WT) plants after BPH infestation, and a total of 217 differentially expressed miRNAs (DEMs) and 7,874 differentially expressed mRNAs (DEGs) were identified. 29 miRNAs, including members of miR160, miR166 and miR169 family were opposite expressed during early or late feeding stages between the two varieties, whilst 9 miRNAs were specifically expressed in BPH6G plants, suggesting involvement of these miRNAs in BPH6 -mediated resistance to BPH. In the transcriptome analysis, 949 DEGs were opposite expressed during early or late feeding stages of the two genotypes, which were enriched in metabolic processes, cellular development, cell wall organization, cellular component movement and hormone transport, and certain primary and secondary metabolite synthesis. 24 genes were further selected as candidates for BPH resistance. Integrated analysis of the DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were candidate miRNA-mRNA pairs for BPH resistance, 18 pairs were verified by qRT-PCR, and two pairs were confirmed by in vivo analysis. Conclusions: For the first time, we reported integrated small RNA and transcriptome sequencing to illustrate resistance mechanisms against BPH in rice. Our results provide a valuable resource to ascertain changes in BPH-induced miRNA and mRNA expression profiles and enable to comprehend plant-insect interactions and find a way for efficient insect control.

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Identification and Comparative Profiling of microRNAs at Different Diapause Stages of Galeruca Daurica Adults

10.21203/rs.3.rs-70765/v1 ◽

2020 ◽

Author(s):

Tian-Feng Duan ◽

Ling Li ◽

Yao Tan ◽

Yan-Yan Li ◽

Bao-Ping Pang

Keyword(s):

Small Rna ◽

Target Genes ◽

Expression Profiles ◽

Mapk Signaling ◽

Transcriptional Level ◽

Regulate Gene Expression ◽

Small Noncoding Rnas ◽

Physiological Processes ◽

Summer Diapause ◽

G Protein Coupled

Abstract Background: MicroRNAs (miRNAs) are a class of small noncoding RNAs of approximately 22 nt in length, which regulate gene expression at the post-transcriptional level. Although the regulatory roles of miRNAs in various physiological processes throughout insect development have been investigated, it is almost unknown about the roles of miRNAs involved in the regulation of diapause in insects.Results: We constructed 12 small RNA libraries from Galeruca daurica adults at different diapause stages: pre-diapause (PD), diapause (D), post-diapause 1 (TD1), and post-diapause 2 (TD2). Using Illumina sequencing, a total of 95.06 million valid reads was obtained, and 230 miRNAs, including 143 conserved and 87 novel miRNAs, were identified from G. daurica. The expression profiles of these miRNAs were assessed across different diapause stages and miRNAs that were highly expressed at different diapause stages were identified. Comparative analysis of read counts indicated that both conserved and novel miRNAs were differently expressed among the four different diapause stages, and the differential expression was validated via qRT-PCR. The 25, 11, 15, 14, 26, and one miRNAs were differentially expressed in D/PD, D/TD1, D/TD2, TD1/PD, TD2/PD, and TD2/TD1, respectively. The KEGG and GO analysis of the predicted target genes suggested the essential roles of miRNAs in the regulation of summer diapause in G. daurica, especially via the juvenile hormone, ribosome, MAPK signaling, mTOR signaling, Ca2+ signaling, and G-protein coupled receptor signaling pathways.Conclusion: Our research results indicate that miRNAs may be involved in the regulation of summer diapause in G. daurica, and these results also provide an important new small RNA genomics resource for further studies on insect diapause.

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