scholarly journals Transcriptome and miRNAome reveal components regulating primary thickening of bamboo shoots

2021 ◽  
Author(s):  
Ying Li ◽  
Deqiang Zhang ◽  
Yongfeng Lou ◽  
Xinmin An ◽  
Zhimin Gao
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Mirna Gene ◽  
Wood Property ◽  
Moso Bamboo ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Thick Wall ◽  
Small Rna Sequencing ◽  
Bamboo Shoots

Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. The present study identified a total of 58,652 genes and 521 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild type (WT) Moso bamboo (Phyllostachys edulis) and a thick wall (TW) variant (P. edulis cv. Pachyloen) at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 11,636 (54.05%) differentially expressed genes (DEGs) and 515 (98.85%) differentially expressed miRNAs (DEmiRs) were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations each between two successive stages (WTS2/TWS2_vs_WTS1/TWS1, WTS3/TWS3_vs_WTS2/TWS2, WTS4/TWS4_vs_WTS3/TWS3 and WTS5/TWS5_vs_WTS4/TWS4), and the WTTW group was composed of five between two relative stages (TWS1-5_vs_WTS1-5). Additionally, among the phytohormones, zeatin (ZT) showed more remarkable changes in concentrations than indole-3-acetic acid (IAA), gibberellic acid (GA3), and abscisic acid (ABA) throughout the five stages in the WT and the TW groups. Moreover, 118 sites were identified for 590 miRNA-mRNA pairs via degradome sequencing. The dual-luciferase reporter assay confirmed that 14 miRNAs bound to 12 targets. Fluorescence in situ hybridization (FISH) localized miR166 and miR160 in the shoot apical meristem (SAM) and the procambium of Moso bamboo shoots at the S1 stage. Thus, primary thickening is a complex process regulated by miRNA-gene-phytohormone networks, and the miRNAome and transcriptome dynamics regulate phenotypic plasticity. These findings provide insights into the molecular mechanisms underlying wood formation and properties and propose targets for bamboo breeding.

scholarly journals Multi-omics Analysis Reveals Whether and how Naphthylacetic Acid Affects the Quality of Rehmannia Glutinosa

2020 ◽  
Author(s):  
Jianjun LI ◽  
Luying SHAO ◽  
Jialin ZHU ◽  
Jingxiao MA ◽  
Yanqing ZHOU ◽  
...  
Keyword(s):  
Small Rna ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rehmannia Glutinosa ◽  
Degradome Sequencing ◽  
Differentially Expressed Mirnas ◽  
Naphthylacetic Acid

Abstract Background: Rehmannia glutinosa (R.glutinosa) is an important medicinal plant. The tuberous root of R.glutinosa is often used as herbal medicine. Naphthylacetic acid (NAA) as expansin can improve its yield, but knowledge about gene regulation and metabolome in its root is limited.Results: Full-length transcriptome, next generation transcriptome(NGS), small RNA and degradome sequencing and metabolomics were used to elucidate whether and how NAA affected its quality.30 differential expression metabolites (DEMs) (11 upregulated, 19downregulated) were identified, but catalpol and Rehmannioside D as quality standards were unchanged in its tuberous roots under control and NAA conditions (CKs and NTs); Their NGS identified 1,113 differentially expressed transcripts (DETs) (596 upregulated, 517downregulated) verified by RT-qPCR; Small RNA sequencing identified 78miRNAs (11known, 67 novel), of which 3 were differentially expressed miRNAs (1upregulated, 2downregulated). Among them, 274 differentially expressed miRNAs target transcripts (DEMTs) were predicted found and then validated by degradome sequencing; DETs and DEMTs were mainly related to metabolism. 4 miRNA-mRNA interaction pairs that regulates 4 metabolites (2 negatively correlated, 2 positively correlated) were identified; DETs, DEMs, differentially expressed miRNAs and DEMTs involved in phenylpropanoid biosynthesis regulated metabolites.Conclusions: The identification of DETs, DEMs, differentially expressed miRNAs and DEMTs could help to elucidate the regulatory networks and molecular mechanisms important for NAA-improving root quality of R.glutinosa.

scholarly journals Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress

2021 ◽  
Vol 11 ◽  
Author(s):  
Xing Huang ◽  
Yongsheng Liang ◽  
Baoqing Zhang ◽  
Xiupeng Song ◽  
Yangrui Li ◽  
...  
Keyword(s):  
Cold Stress ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Transcriptional Regulatory Network ◽  
Mirna Gene ◽  
Signal Transduction Pathway ◽  
Early Response ◽  
Differentially Expressed ◽  
Transcriptional Analysis ◽  
Late Embryogenesis Abundant Protein

Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress.

scholarly journals Multi–Omics Analysis of Key microRNA–mRNA Metabolic Regulatory Networks in Skeletal Muscle of Obese Rabbits

2021 ◽  
Vol 22 (8) ◽  
pp. 4204
Author(s):  
Yanhong Li ◽  
Jie Wang ◽  
Mauricio A. Elzo ◽  
Mingchuan Gan ◽  
Tao Tang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Metabolic Diseases ◽  
Muscle Metabolism ◽  
Rabbit Skeletal Muscle ◽  
Differentially Expressed ◽  
Control Group ◽  
Small Rna Sequencing ◽  
Non Coding Rna

microRNAs (miRNAs), small non-coding RNA with a length of about 22 nucleotides, are involved in the energy metabolism of skeletal muscle cells. However, their molecular mechanism of metabolism in rabbit skeletal muscle is still unclear. In this study, 16 rabbits, 8 in the control group (CON–G) and 8 in the experimental group (HFD–G), were chosen to construct an obese model induced by a high–fat diet fed from 35 to 70 days of age. Subsequently, 54 differentially expressed miRNAs, 248 differentially expressed mRNAs, and 108 differentially expressed proteins related to the metabolism of skeletal muscle were detected and analyzed with three sequencing techniques (small RNA sequencing, transcriptome sequencing, and tandem mass tab (TMT) protein technology). It was found that 12 miRNAs and 12 core genes (e.g., CRYL1, VDAC3 and APIP) were significantly different in skeletal muscle from rabbits in the two groups. The network analysis showed that seven miRNA-mRNA pairs were involved in metabolism. Importantly, two miRNAs (miR-92a-3p and miR-30a/c/d-5p) regulated three transcription factors (MYBL2, STAT1 and IKZF1) that may be essential for lipid metabolism. These results enhance our understanding of molecular mechanisms associated with rabbit skeletal muscle metabolism and provide a basis for future studies in the metabolic diseases of human obesity.

scholarly journals Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Biomolecules ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 609 ◽  
Author(s):  
Shan ◽  
Yang ◽  
Xu ◽  
Zhu ◽  
Gao
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Secondary Cell Wall ◽  
Expression Patterns ◽  
Wood Property ◽  
Moso Bamboo ◽  
Functional Studies ◽  
Bamboo Shoots ◽  
Potential Association ◽  
Nac Gene Family

NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.

scholarly journals Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

2019 ◽  
Vol 20 (10) ◽  
pp. 2391 ◽  
Author(s):  
Jiayang Xu ◽  
Qiansi Chen ◽  
Pingping Liu ◽  
Wei Jia ◽  
Zheng Chen ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Crop Yields ◽  
Antioxidant Activities ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Alkali Stress ◽  
Rna Seq ◽  
Alkali Tolerance

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

scholarly journals Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Liang ◽  
Kunhua Wei ◽  
Fan Wei ◽  
Shuangshuang Qin ◽  
Chuanhua Deng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Small Rna ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Severe Drought ◽  
A Genome ◽  
Sophora Tonkinensis

Abstract Background Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. Results To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. Conclusion This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

scholarly journals Identification of microRNAs Targeting the Transporter Associated with Antigen Processing TAP1 in Melanoma

2020 ◽  
Vol 9 (9) ◽  
pp. 2690
Author(s):  
Maria-Filothei Lazaridou ◽  
Chiara Massa ◽  
Diana Handke ◽  
Anja Mueller ◽  
Michael Friedrich ◽  
...  
Keyword(s):  
T Cell ◽  
Antigen Processing ◽  
Molecular Mechanisms ◽  
Hla Class I ◽  
Melanoma Cells ◽  
Class I ◽  
Peptide Transporter ◽  
Luciferase Reporter ◽  
Small Rna Sequencing ◽  
Aberrant Expression

The underlying molecular mechanisms of the aberrant expression of components of the HLA class I antigen processing and presentation machinery (APM) in tumors leading to evasion from T cell-mediated immune surveillance could be due to posttranscriptional regulation mediated by microRNAs (miRs). So far, some miRs controlling the expression of different APM components have been identified. Using in silico analysis and an miR enrichment protocol in combination with small RNA sequencing, miR-26b-5p and miR-21-3p were postulated to target the 3′ untranslated region (UTR) of the peptide transporter TAP1, which was confirmed by high free binding energy and dual luciferase reporter assays. Overexpression of miR-26b-5p and miR-21-3p in melanoma cells downregulated the TAP1 protein and reduced expression of HLA class I cell surface antigens, which could be reverted by miR inhibitors. Moreover, miR-26b-5p overexpression induced a decreased T cell recognition. Furthermore, an inverse expression of miR-26b-5p and miR-21-3p with TAP1 was found in primary melanoma lesions, which was linked with the frequency of CD8+ T cell infiltration. Thus, miR-26-5p and miR-21-3p are involved in the HLA class I-mediated immune escape and might be used as biomarkers or therapeutic targets for HLA class Ilow melanoma cells.

Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo

2020 ◽  
Vol 40 (11) ◽  
pp. 1487-1508
Author(s):  
Gui-Yun Tao ◽  
Muthusamy Ramakrishnan ◽  
Kunnummal Kurungara Vinod ◽  
Kim Yrjälä ◽  
Viswanathan Satheesh ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Rapid Growth ◽  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Moso Bamboo ◽  
Differentially Expressed ◽  
Molecular Networks ◽  
Growth Stages ◽  
Cellular Pathways

Abstract Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein–protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.

scholarly journals nSARS-Cov-2, pulmonary edema and thrombosis: possible molecular insights using miRNA-gene circuits in regulatory networks

ExRNA ◽  
2020 ◽  
Vol 2 (1) ◽  
Author(s):  
P. Khurana ◽  
A. Gupta ◽  
R. Sugadev ◽  
Y. K. Sharma ◽  
R. Varshney ◽  
...  
Keyword(s):  
Pulmonary Edema ◽  
Antigen Presentation ◽  
Signaling Pathways ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Mirna Gene ◽  
Protein Stabilization ◽  
Molecular Signature ◽  
Potential Candidate ◽  
Regulatory Circuits

Abstract Background Given the worldwide spread of the novel Severe Acute Respiratory Syndrome Coronavirus 2 (nSARS-CoV-2) infection pandemic situation, research to repurpose drugs, identify novel drug targets, vaccine candidates have created a new race to curb the disease. While the molecular signature of nSARS-CoV-2 is still under investigation, growing literature shows similarity among nSARS-CoV-2, pulmonary edema, and thromboembolic disorders due to common symptomatic features. A network medicine approach is used to to explore the molecular complexity of the disease and to uncover common molecular trajectories of edema and thrombosis with nSARS-CoV-2. Results and conclusion A comprehensive nSARS-CoV-2 responsive miRNA: Transcription Factor (TF): gene co-regulatory network was built using host-responsive miRNAs and it’s associated tripartite, Feed-Forward Loops (FFLs) regulatory circuits were identified. These regulatory circuits regulate signaling pathways like virus endocytosis, viral replication, inflammatory response, pulmonary vascularization, cell cycle control, virus spike protein stabilization, antigen presentation, etc. A unique miRNA-gene regulatory circuit containing a consortium of four hub FFL motifs is proposed to regulate the virus-endocytosis and antigen-presentation signaling pathways. These regulatory circuits also suggest potential correlations/similarity in the molecular mechanisms during nSARS-CoV-2 infection, pulmonary diseases and thromboembolic disorders and thus could pave way for repurposing of drugs. Some important miRNAs and genes have also been proposed as potential candidate markers. A detailed molecular snapshot of TGF signaling as the common pathway, that could play an important role in controlling common pathophysiologies among diseases, is also put forth.

Uncovering of Key Pathways and miRNAs for Intracranial Aneurysm Based on Weighted Gene Co-Expression Network Analysis

2022 ◽  
pp. 1-12
Author(s):  
Zhengfei Ma ◽  
Ping Zhong ◽  
Peidong Yue ◽  
Zhongwu Sun
Keyword(s):  
Network Analysis ◽  
Intracranial Aneurysm ◽  
Differentially Expressed Genes ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Area Under The Curve ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed

<b><i>Background:</i></b> Intracranial aneurysm (IA) is a serious cerebrovascular disease. The identification of key regulatory genes can provide research directions for early diagnosis and treatment of IA. <b><i>Methods:</i></b> Initially, the miRNA and mRNA data were downloaded from the Gene Expression Omnibus database. Subsequently, the limma package in R was used to screen for differentially expressed genes. In order to investigate the function of the differentially expressed genes, a functional enrichment analysis was performed. Moreover, weighted gene co-expression network analysis (WGCNA) was performed to identify the hub module and hub miRNAs. The correlations between miRNAs and mRNAs were assessed by constructing miRNA-mRNA regulatory networks. In addition, in vitro validation was performed. Finally, diagnostic analysis and electronic expression verification were performed on the GSE122897 dataset. <b><i>Results:</i></b> In the present study, 955 differentially expressed mRNAs (DEmRNAs, 480 with increased and 475 with decreased expression) and 46 differentially expressed miRNAs (DEmiRNAs, 36 with increased and 10 with decreased expression) were identified. WGCNA demonstrated that the yellow module was the hub module. Moreover, 16 hub miRNAs were identified. A total of 1,124 negatively regulated miRNA-mRNA relationship pairs were identified. Functional analysis demonstrated that DEmRNAs in the targeted network were enriched in vascular smooth muscle contraction and focal adhesion pathways. In addition, the area under the curve of 16 hub miRNAs was &#x3e;0.8. It is implied that 16 hub miRNAs may be used as potential diagnostic biomarkers of IA. <b><i>Conclusion:</i></b> Hub miRNAs and key signaling pathways were identified by bioinformatics analysis. This evidence lays the foundation for understanding the underlying molecular mechanisms of IA and provided potential therapeutic targets for the treatment of this disease.

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