scholarly journals Integration of Transcriptomes, Small RNAs, and Degradome Sequencing to Identify Putative miRNAs and their Targets Related to Eu-Rubber Biosynthesis in Eucommia ulmoides

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 623
Author(s):  
Jing Ye ◽  
Wenjing Han ◽  
Ruisheng Fan ◽  
Minhao Liu ◽  
Long Li ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Vital Role ◽  
Eucommia Ulmoides ◽  
Messenger Rnas ◽  
Rubber Biosynthesis ◽  
Degradome Sequencing ◽  
The Eu

Eucommia ulmoides has attracted much attention as a valuable natural rubber (Eu-rubber) production tree. As a strategic material, Eu-rubber plays a vital role in general and defence industries. However, the study of Eu-rubber biosynthesis at a molecular level is scarce, and the regulatory network between microRNAs (miRNAs) and messenger RNAs (mRNAs) in Eu-rubber biosynthesis has not been assessed. In this study, we comprehensively analyzed the transcriptomes, small RNAs (sRNAs) and degradome to reveal the regulatory network of Eu-rubber biosynthesis in E. ulmoides. A total of 82,065 unigenes and 221 miRNAs were identified using high-throughput sequencing; 20,815 targets were predicted using psRNATarget software. Of these targets, 779 miRNA-target pairs were identified via degradome sequencing. Thirty-one miRNAs were differentially expressed; 22 targets of 34 miRNAs were annotated in the terpenoid backbone biosynthesis pathway (ko00900) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG). These miRNAs were putatively related to Eu-rubber biosynthesis. A regulatory network was constructed according to the expression profiles of miRNAs and their targets. These results provide a comprehensive analysis of transcriptomics, sRNAs and degradome to reveal the Eu-rubber accumulation, and provide new insights into genetic engineering techniques which may improve the content of Eu-rubber in E. ulmoides.

Dysregulation of tRNA-derived small RNAs and their potential roles in lupus nephritis

Lupus ◽  
2021 ◽  
pp. 096120332110614
Author(s):  
Yan Liang ◽  
Ji Zhang ◽  
Wenxian Qiu ◽  
Bo Chen ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Signaling Pathway ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Pcr Analysis ◽  
Clinical Indicators ◽  
Qrt Pcr

Objective Lupus nephritis (LN) is a major end-organ complication of systemic lupus erythematosus (SLE), and the molecular mechanism of LN is not completely clear. Accumulating pieces of evidence indicate the potential vital role of tRNA-derived small RNAs (tsRNAs) in human diseases. Current study aimed to investigate the potential roles of tsRNAs in LN. Methods We herein employed high‐throughput sequencing to screen the expression profiles of tsRNAs in renal tissues of the LN and control groups. To validate the sequencing data, we performed quantitative real-time PCR (qRT-PCR) analysis. Correlational analysis of verified tsRNAs expression and clinical indicators was conducted using linear regression. The potential target genes were also predicted. The biological functions of tsRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results Our findings revealed that the expression profiles of tsRNAs were significantly altered in the kidney tissues from LN patients compared with control. Overall, 160 tsRNAs were significantly dysregulated in the LN group, of which 79 were upregulated, whereas 81 were downregulated. Subsequent qRT-PCR results confirmed the different expression of candidate tsRNAs. Correlation analysis results found that expression of verified tsRNAs were correlated to clinical indicators. The target prediction results revealed that verified tsRNAs might act on 712 target genes. Further bioinformatics analysis uncovered tsRNAs might participate in the pathogenesis of LN through several associated pathways, including cell adhesion molecules, MAPK signaling pathway, PI3K-Akt signaling pathway and B cell receptor signaling pathway. Conclusion This study provides a novel insight for studying the mechanism of LN.

scholarly journals Good Manufacturing Practice: The Role of Local Manufacturers and Competent Authorities

2010 ◽  
Vol 61 (4) ◽  
pp. 425-436 ◽  
Author(s):  
Siniša Tomić ◽  
Anita Sučić ◽  
Adrijana Martinac
Keyword(s):  
Regulatory Network ◽  
Good Manufacturing Practice ◽  
Pharmaceutical Product ◽  
Vital Role ◽  
Medicinal Products ◽  
Eu Member States ◽  
Eu Membership ◽  
European Regulatory ◽  
The Eu

Good Manufacturing Practice: The Role of Local Manufacturers and Competent AuthoritiesIn every country, a manufacturer of medicinal products for either human or veterinary use is required to operate in compliance with local legislation. In all EU Member States, legislation is approximated to the effect that they are committed to abide by the same standards. The candidate countries transpose the acquis into their national legislation, including the good manufacturing practice (GMP). Consequently, the local manufacturer is required to strictly comply with GMP and the manufacturing licence, including for medicinal products exclusively intended for export. A vital role is also played by national regulatory authorities, in Croatia by the Agency for Medicinal Products and Medical Devices which issues the manufacturing licence, GMP certificate, and the Certificate of a Pharmaceutical Product (CPP) and conducts laboratory control of products. GMP inspection is carried out by the Pharmaceutical Inspectorate with the Ministry of Health and Social Welfare. Both authorities are responsible only for human medicines. There are legislative issues not yet harmonised with the acquis, but as a country aspiring for the EU membership, Croatia is expected to demonstrate that its industry and competent authorities are able to conform to current requirements and thus fully adhere to the integrated European regulatory network. Hence the importance of strengthening the institutional capacity of the competent authorities, as insufficient resources may have a direct bearing on patients by limiting their access to affordable treatment.

scholarly journals fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Roshan Regmi ◽  
Toby E. Newman ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire
Keyword(s):  
Disease Resistance ◽  
Small Rnas ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Differentially Expressed ◽  
Disease Resistance Gene ◽  
Ethylene Response Factor ◽  
Post Inoculation ◽  
Necrotrophic Pathogen ◽  
Degradome Sequencing

Abstract Background Small RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed B. napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem. Results We identified different classes of sRNAs from B. napus using high throughput sequencing of replicated mock and infected samples at 24 h post-inoculation (HPI). Overall, 3999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. These 730 up-regulated sRNAs targeted 64 genes, including disease resistance proteins and transcriptional regulators. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 2124 cleaved mRNA products from these miRNAs from combined mock and infected samples. Among these, 50 genes were specific to infection. Altogether, 20 conserved miRNAs were differentially expressed and 8 transcripts were cleaved by the differentially expressed miRNAs miR159, miR5139, and miR390, suggesting they may have a role in the S. sclerotiorum response. A miR1885-triggered disease resistance gene-derived secondary sRNA locus was also identified and verified with degradome sequencing. We also found further evidence for silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5′-RACE and RT-qPCR. Conclusions The findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.

scholarly journals Different classes of small RNAs are essential for head regeneration in the planarian Dugesia japonica

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhonghong Cao ◽  
David Rosenkranz ◽  
Suge Wu ◽  
Hongjin Liu ◽  
Qiuxiang Pang ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Evolutionary Conservation ◽  
Body Parts ◽  
Promising Candidate ◽  
Dugesia Japonica ◽  
Head Regeneration

Abstract Background Planarians reliably regenerate all body parts after injury, including a fully functional head and central nervous system. But until now, the expression dynamics and functional role of miRNAs and other small RNAs during the process of head regeneration are not well understood. Furthermore, little is known about the evolutionary conservation of the relevant small RNAs pathways, rendering it difficult to assess whether insights from planarians will apply to other taxa. Results In this study, we applied high throughput sequencing to identify miRNAs, tRNA fragments and piRNAs that are dynamically expressed during head regeneration in Dugesia japonica. We further show that knockdown of selected small RNAs, including three novel Dugesia-specific miRNAs, during head regeneration induces severe defects including abnormally small-sized eyes, cyclopia and complete absence of eyes. Conclusions Our findings suggest that a complex pool of small RNAs takes part in the process of head regeneration in Dugesia japonica and provide novel insights into global small RNA expression profiles and expression changes in response to head amputation. Our study reveals the evolutionary conserved role of miR-124 and brings further promising candidate small RNAs into play that might unveil new avenues for inducing restorative programs in non-regenerative organisms via small RNA mimics based therapies.

scholarly journals Combined degradome and replicated small RNA sequencing identifies Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

2020 ◽  
Author(s):  
Roshan Regmi ◽  
Toby E. Newman ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire
Keyword(s):  
Brassica Napus ◽  
Small Rnas ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Small Rna Sequencing ◽  
Disease Resistance Gene ◽  
Ethylene Response Factor ◽  
Post Inoculation ◽  
Necrotrophic Pathogen ◽  
Degradome Sequencing

AbstractBackgroundSmall RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed Brassica napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem.ResultsWe identified different classes of sRNAs from B. napus by high throughput sequencing of replicated mock and infected samples at 24 hours post-inoculation (HPI). Overall, 3,999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. Degradome sequencing identified numerous likely sRNA targets that were enriched for immunity-related GO terms, including those related to jasmonic acid signalling, during infection. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 434 unique cleaved mRNA products from these miRNAs, of which 50 were unique to the infected library. A novel miR1885-triggered disease resistance gene-derived secondary sRNA locus was identified and verified with degradome sequencing. We also experimentally validated silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5’-RACE.ConclusionsThe findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.

scholarly journals Identification of a Potentially Functional microRNA–mRNA Regulatory Network in Lung Adenocarcinoma Using a Bioinformatics Analysis

2021 ◽  
Vol 9 ◽  
Author(s):  
Xiao-Jun Wang ◽  
Jing Gao ◽  
Zhuo Wang ◽  
Qin Yu
Keyword(s):  
Lung Adenocarcinoma ◽  
Regulatory Network ◽  
Vital Role ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Messenger Rnas ◽  
Ppi Network ◽  
Tissue Samples ◽  
Go Analysis ◽  
Kegg Pathways

BackgroundLung adenocarcinoma (LUAD) is a common lung cancer with a high mortality, for which microRNAs (miRNAs) play a vital role in its regulation. Multiple messenger RNAs (mRNAs) may be regulated by miRNAs, involved in LUAD tumorigenesis and progression. However, the miRNA–mRNA regulatory network involved in LUAD has not been fully elucidated.MethodsDifferentially expressed miRNAs and mRNA were derived from the Cancer Genome Atlas (TCGA) dataset in tissue samples and from our microarray data in plasma (GSE151963). Then, common differentially expressed (Co-DE) miRNAs were obtained through intersected analyses between the above two datasets. An overlap was applied to confirm the Co-DEmRNAs identified both in targeted mRNAs and DEmRNAs in TCGA. A miRNA–mRNA regulatory network was constructed using Cytoscape. The top five miRNA were identified as hub miRNA by degrees in the network. The functions and signaling pathways associated with the hub miRNA-targeted genes were revealed through Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The key mRNAs in the protein–protein interaction (PPI) network were identified using the STRING database and CytoHubba. Survival analyses were performed using Gene Expression Profiling Interactive Analysis (GEPIA).ResultsThe miRNA–mRNA regulatory network consists of 19 Co-DEmiRNAs and 760 Co-DEmRNAs. The five miRNAs (miR-539-5p, miR-656-3p, miR-2110, let-7b-5p, and miR-92b-3p) in the network were identified as hub miRNAs by degrees (>100). The 677 Co-DEmRNAs were targeted mRNAs from the five hub miRNAs, showing the roles in the functional analyses of the GO analysis and KEGG pathways (inclusion criteria: 836 and 48, respectively). The PPI network and Cytoscape analyses revealed that the top ten key mRNAs were NOTCH1, MMP2, IGF1, KDR, SPP1, FLT1, HGF, TEK, ANGPT1, and PDGFB. SPP1 and HGF emerged as hub genes through survival analysis. A high SPP1 expression indicated a poor survival, whereas HGF positively associated with survival outcomes in LUAD.ConclusionThis study investigated a miRNA–mRNA regulatory network associated with LUAD, exploring the hub miRNAs and potential functions of mRNA in the network. These findings contribute to identify new prognostic markers and therapeutic targets for LUAD patients in clinical settings.

Abstract 298: Identification of LncRNA-miRNA-mRNA Network in Myocardium After Successful Resuscitation in a Rat Model of Prolonged Cardiac Arrest

Circulation ◽  
2018 ◽  
Vol 138 (Suppl_2) ◽  
Author(s):  
Jingying Hou ◽  
Zhengfei Yang ◽  
Wanchun Tang
Keyword(s):  
Cardiac Arrest ◽  
Rat Model ◽  
Regulatory Network ◽  
High Throughput Sequencing ◽  
Ischemia Reperfusion Injury ◽  
Myocardial Dysfunction ◽  
Expression Profiles ◽  
Ischemia Reperfusion ◽  
Sprague Dawley ◽  
Successful Resuscitation

Introduction: Previous studies have indicated that lncRNA participates in regional myocardial ischemia-reperfusion injury (IRI). However, the lncRNA-miRNA-mRNA crosstalk in the global myocardial IRI, which is implicated in the pathophysiology of post-resuscitation myocardial dysfunction (PRMD), has still not been explored. Hypothesis: To identify lncRNA-miRNA-mRNA regulatory network in myocardium after successful resuscitation in a rat model of prolonged cardiac arrest. Methods: Six male Sprague Dawley rats were randomized into sham control and ventricular fibrillation (VF)-CPR groups, with three rats in each group. VF was induced and untreated for 8 minutes. Defibrillation was attempted after 8 minutes of CPR. Heart tissue was obtained at 6 hours after resuscitation and lncRNA, miRNA and mRNA expression profiles were examined by using high-throughput sequencing. LncRNA-miRNA-mRNA interaction network was predicted and constructed. Results: Numbers of differentially expressed (DE) lncRNA, miRNA and mRNA were detected (Fig 1A). LncRNAs co-located or co-expressed target mRNAs and DE mRNAs were revealed (Fig 1B). The intersection of DE mRNAs with targeted mRNA of DE miRNAs was made (Fig 1C). A total of 129 feed forward loops were predicted as lncRNA-associated ceRNA networks,with 126 lncRNA (up)-miRNA (down)-mRNA (up) and 3 lncRNA (down)-miRNA (up)-mRNA (down) (Fig 2). Conclusions: LncRNA-miRNA-mRNAs network was predicted and constructed in myocardium after successful resuscitation in a rat model of prolonged cardiac arrest. Further exploration into the specific functional roles of the ceRNA regulatory network will be conducive for the treatment of PRMD.

scholarly journals Integration of small RNA, degradome and proteome sequencing in Oryza sativa reveals a delayed senescence network in tetraploid rice seed

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242260
Author(s):  
Baosheng Huang ◽  
Lu Gan ◽  
Dongjie Chen ◽  
Yachun Zhang ◽  
Yujie Zhang ◽  
...  
Keyword(s):  
Antioxidant Enzymes ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
Rice Seed ◽  
Sequencing Analysis ◽  
Delayed Senescence ◽  
Degradome Sequencing ◽  
Rice Seeds ◽  
Diploid Rice

Seed of rice is an important strategic resource for ensuring the security of China's staple food. Seed deterioration as a result of senescence is a major problem during seed storage, which can cause major economic losses. Screening among accessions in rice germplasm resources for traits such as slow senescence and increased seed longevity during storage is, therefore, of great significance. However, studies on delayed senescence in rice have been based mostly on diploid rice seed to date. Despite better tolerance have been verified by the artificial aging treatment for polyploid rice seed, the delayed senescence properties and delayed senescence related regulatory mechanisms of polyploid rice seed are rarely reported, due to the lack of polyploid rice materials with high seed set. High-throughput sequencing was applied to systematically investigate variations in small RNAs, the degradome, and the proteome between tetraploid and diploid rice seeds. Degradome sequencing analysis of microRNAs showed that expression of miR-164d, which regulates genes encoding antioxidant enzymes, was changed significantly, resulting in decreased miRNA-mediated cleavage of target genes in tetraploid rice. Comparisons of the expression levels of small RNAs (sRNAs) in the tetraploid and diploid libraries revealed that 12 sRNAs changed significantly, consistent with the findings from degradome sequencing. Furthermore, proteomics also showed that antioxidant enzymes were up-regulated in tetraploid rice seeds, relative to diploids.

Identification of circRNA-miRNA-mRNA Regulatory Network in Bladder Cancer by Integrated Analysis

2021 ◽  
pp. 1-11
Author(s):  
Peng Chen ◽  
Juan Chen ◽  
Long He ◽  
Cheng Du ◽  
Xialu Wang
Keyword(s):  
Bladder Cancer ◽  
Regulatory Network ◽  
Functional Annotation ◽  
Expression Profiles ◽  
Vital Role ◽  
Circular Rnas ◽  
Integrated Analysis ◽  
Recurrence Rates ◽  
Qrt Pcr ◽  
P53 Signaling

<b><i>Introduction:</i></b> Bladder cancer (BC) is a common malignant tumor in the urinary system with high mortality and recurrence rates. This study sought to identify crucial circular RNAs (circRNAs) associated with BC. <b><i>Methods:</i></b> The mRNA, miRNA, and circRNA expression profiles of BC were downloaded from GEO database. The differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), and circRNAs (DEcircRNAs) were identified using bioinformatics method. Combining circRNA-miRNA pairs with miRNA-mRNA pairs, the competing endogenous RNA (ceRNA; DEcircRNA-DEmi­RNA-DEmRNA) regulatory network was constructed. Functional annotation of host gene of DEcircRNAs and DEmRNAs in ceRNA regulatory network were performed. qRT-PCR validation was performed. <b><i>Results:</i></b> A total of 4,003 DEmRNAs, 25 DEmiRNAs, and 119 DEcircRNAs were obtained. The ceRNA network contained 18 circRNA-miRNA pairs and 699 mi­RNA-mRNA pairs, including 17 circRNAs, 4 miRNAs, and 624 mRNAs. Functional annotation of DEmRNAs in ceRNA regulatory network revealed that these DEmRNAs were significantly enriched in glycerolipid metabolism, p53 signaling pathway, and oocyte meiosis. Except for hsa_circ_0028173, expression of the others in the qRT-PCR results was consistent with that in our integrated analysis, generally. <b><i>Conclusion:</i></b> We speculate that hsa_circ_0008035/hsa-miR-107/MSRB3 and hsa_circ_0028173/hsa-miR-338-3p/TPX2/GATA3 interaction pairs may play a vital role in BC.

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