scholarly journals Identification of differentially expressed microRNAs under imidacloprid exposure in Sitobion avenae Fabricius

2020 ◽  
Author(s):  
Baizhong Zhang ◽  
Shouping Zhang ◽  
Xu Su ◽  
Lanfen Xie ◽  
Wen-Yang Dong ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Control Analysis ◽  
Sequencing Technology ◽  
Short Read Sequencing ◽  
Kegg Pathway Analysis ◽  
Candidate Target ◽  
Non Coding Rnas

Abstract Background: MicroRNAs (miRNAs), which are short single-stranded non-coding RNAs, regulate the expression of target genes, especially those involved in the regulation or metabolism of endogenous or xenobiotic compounds. Results: De novo assemblies of the transcriptome of Sitobion avenae Fabricius under control conditions and under imidacloprid treatment were obtained using Illumina short-read sequencing technology. Fifty-seven miRNAs, of which 36 were known and 21 were novel, were identified. Quantitative analysis of miRNA levels showed that 5 miRNAs were significantly up-regulated, and 11 miRNAs were significantly down-regulated in the nymphs of S. avenae treated with imidacloprid in comparison with those of the control. Analysis of the candidate target genes in S. avenae that could be regulated by these miRNAs were also carried out. The functions of the miRNAs, which could potentially regulate target genes that participate in metabolism, regulatory or detoxification pathways in S. avenae, were clarified based on Gene Ontology and KEGG pathway analysis. The effects of the miRNAs api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. Modulation of the abundances of api-miR-1000, api-miR-316, and api-miR-iab-4 by the addition of the correspondign inhibitors to the artificial diet significantly changed the susceptibility of S. avenae to imidacloprid, which further demonstrated the effect of these miRNAs on the regulation or metabolism of insecticides.Conclusion: The results of this study suggested that miRNAs differentially expressed in response to imidacloprid could play a critical regulatory role in the resistance of S. avenae to imidacloprid.

scholarly journals Identification of differentially expressed microRNAs under imidacloprid exposure in Sitobion avenae Fabricius

2019 ◽  
Author(s):  
Baizhong Zhang ◽  
Xu Su ◽  
Lanfen Xie ◽  
Wen-Yang Dong ◽  
Fan-Bin Kong ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Control Analysis ◽  
Sequencing Technology ◽  
Short Read Sequencing ◽  
Kegg Pathway Analysis ◽  
Candidate Target ◽  
Non Coding Rnas

Abstract Background MicroRNAs (miRNAs), which are short single-stranded non-coding RNAs, regulate the expression of target genes, especially those involved in the regulation or metabolism of endogenous or xenobiotic compounds.Results De novo assemblies of the transcriptome of Sitobion avenae Fabricius under control conditions and under imidacloprid treatment were obtained using Illumina short-read sequencing technology. Fifty-seven miRNAs, of which 36 were known and 21 were novel, were identified. Quantitative analysis of miRNA levels showed that five miRNAs were significantly up-regulated, and 11 miRNAs were significantly down-regulated in the nymphs of S. avenae treated with imidacloprid in comparison with those of the control. Analysis of the candidate target genes in S. avenae that could be regulated by these miRNAs were also carried out. The functions of the miRNAs, which could potentially regulate target genes that participate in metabolism, regulatory or detoxification pathways in S. avenae , were clarified based on Gene Ontology and KEGG pathway analysis. The effects of the miRNAs api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. Modulation of the abundances of api-miR-1000, api-miR-316, and api-miR-iab-4 by the addition of the correspondign inhibitors to the artificial diet significantly changed the susceptibility of S. avenae to imidacloprid, which further demonstrated the effect of these miRNAs on the regulation or metabolism of insecticides.Conclusion The results of this study suggested that miRNAs differentially expressed in response to imidacloprid could play a critical regulatory role in the resistance of S. avenae to imidacloprid.

scholarly journals Differentially expressed microRNAs under imidacloprid exposure and identification in Sitobion avenae

2019 ◽  
Author(s):  
Xi-Ling Chen ◽  
Baizhong Zhang ◽  
Junjie Liu ◽  
Liuyang Lu ◽  
Lanfen Xie ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Kegg Pathway ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Sequencing Technology ◽  
Short Read Sequencing ◽  
Quantitative Expression ◽  
Non Coding Rnas ◽  
Candidate Transcript

Abstract Backgroud: MicroRNAs (miRNAs), which are as short single-stranded non-coding RNAs, coudl regulate the expression of target genes, especially regulation or metabolism of endogenous or xenobiotic compounds. Results: The de novo assembly of the transcriptomes was obtained through Illumina short-read sequencing technology in Sitobion avenae. 57 miRNAs, of which 36 were known and 21 were novel were identified. Quantitative expression levels of miRNA showed that the expression of 5 miRNAs were significant up-regulation, and the expression of 11 miRNAs were significant down-regulation in the nymph of S. avenae treated by imidacloprid in comparison with the control, respectively. The candidate transcript target genes in S. avenae that could be regulated by these miRNAs were also carried out. The functions of the miRNAs, which could potentially regulate the target genes participated in the metabolism, regulatory or detoxification of S. avenae were clarified based on Gene Ontology and KEGG pathway. The effects of the miRNAs identified api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. The abundance of api-miR-1000, api-miR-316, and api-miR-iab-4 modulated by the addition of their own inhibitors to the artificial diet could change significantly the susceptibility of S. avenae to imidacloprid, which further proved that the regulatory affect of these miRNAs on regulation or metabolism of insecticides. Conclusion: It suggested that differentially expressed microRNAs under the stress of imidacloprid could play critical regulatory role in the resistance of S. avenae to imidacloprid.

scholarly journals Differentially expressed microRNAs under imidacloprid exposure and identification in Sitobion avenae

2019 ◽  
Author(s):  
Baizhong Zhang ◽  
Jun-Jie Liu ◽  
Liu-yang Lu ◽  
Lan-Fen Xie ◽  
Xi-Ling Chen ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Regulatory Role ◽  
Sequencing Technology ◽  
Quantitative Expression ◽  
Non Coding Rnas ◽  
Putative Transcript

Abstract BACKGROUD MicroRNAs (miRNAs) are short single-stranded non-coding RNAs that regulate the expression of target genes, especially regulation or metabolism of endogenous or xenobiotic compounds. RESULTS The de novo assembly of the transcriptomes was obtained through Illumina short-read sequencing technology in Sitobion avenae. 57 miRNAs, of which 36 were known and 21 were novel were identified. Quantitative expression levels of miRNA showed that the expression of 5 miRNAs were significant up-regulation, and the expression of 11 miRNAs were significant down-regulation in the nymph of S. avenae treated by imidacloprid compared to the control, respectively. The putative transcript target genes in S. avenae that could be regulated by these miRNAs were also carried out. The potential functions of these miRNAs in the regulation of genes involved in the metabolism, regulatory or detoxification of S. avenae were clarified based on Gene Ontology and KEGG pathway. The effects of these miRNAs identified api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. Modulation of the abundance of api-miR-1000, api-miR-316, and api-miR-iab-4 through the addition of inhibitors of api-miR-1000, api-miR-316, and api-miR-iab-4 to the artificial diet significantly altered the susceptibility of S. avenae to imidacloprid, which further proved that the regulatory role of these miRNAs in regulation or metabolism of insecticides. CONCLUSION It suggested that differentially expressed microRNAs under the stress of imidacloprid could play critical regulatory role in the resistance of S. avenae to imidacloprid.

scholarly journals Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 300
Author(s):  
Leyland Fraser ◽  
Łukasz Paukszto ◽  
Anna Mańkowska ◽  
Paweł Brym ◽  
Przemysław Gilun ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Potential Target ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm’s response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.

scholarly journals Identification of microRNAs and relative target genes in Moringa oleifera leaf and callus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefano Pirrò ◽  
Ivana Matic ◽  
Arianna Guidi ◽  
Letizia Zanella ◽  
Angelo Gismondi ◽  
...  
Keyword(s):  
Stress Response ◽  
Moringa Oleifera ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Pcr Analysis ◽  
Microrna Target ◽  
Sequencing Technology ◽  
Important Addition ◽  
Non Coding Rnas ◽  
Growth Development

Abstract MicroRNAs, a class of small, non-coding RNAs, play important roles in plant growth, development and stress response by negatively regulating gene expression. Moringa oleifera Lam. plant has many medical and nutritional uses; however, little attention has been dedicated to its potential for the bio production of active compounds. In this study, 431 conserved and 392 novel microRNA families were identified and 9 novel small RNA libraries constructed from leaf, and cold stress treated callus, using high-throughput sequencing technology. Based on the M. oleifera genome, the microRNA repertoire of the seed was re-evaluated. qRT-PCR analysis confirmed the expression pattern of 11 conserved microRNAs in all groups. MicroRNA159 was found to be the most abundant conserved microRNA in leaf and callus, while microRNA393 was most abundantly expressed in the seed. The majority of predicted microRNA target genes were transcriptional factors involved in plant reproduction, growth/development and abiotic/biotic stress response. In conclusion, this is the first comprehensive analysis of microRNAs in M. oleifera leaf and callus which represents an important addition to the existing M. oleifera seed microRNA database and allows for possible exploitation of plant microRNAs induced with abiotic stress, as a tool for bio-enrichment with pharmacologically important phytochemicals.

scholarly journals Bioinformatic Analysis of Circular RNA-Associated ceRNA Network Associated with Hepatocellular Carcinoma

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Jiacheng Wu ◽  
Shui Liu ◽  
Yien Xiang ◽  
Xianzhi Qu ◽  
Yingjun Xie ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Pathway Analysis ◽  
Target Genes ◽  
Kegg Pathway ◽  
Interaction Network ◽  
Bioinformatic Analysis ◽  
Differentially Expressed ◽  
Qrt Pcr ◽  
Cerna Network ◽  
Kegg Pathway Analysis

Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and is associated with a high mortality rate and poor treatment efficacy. In an attempt to investigate the mechanisms involved in the pathogenesis of HCC, bioinformatic analysis and validation by qRT-PCR were performed. Three circRNA GEO datasets and one miRNA GEO dataset were selected for this purpose. Upon combined biological prediction, a total of 11 differentially expressed circRNAs, 15 differentially expressed miRNAs, and 560 target genes were screened to construct a circRNA-related ceRNA network. GO analysis and KEGG pathway analysis were performed for the 560 target genes. To further screen key genes, a protein-protein interaction network of the target genes was constructed using STRING, and the genes and modules with higher degree were identified by MCODE and CytoHubba plugins of Cytoscape. Subsequently, a module was screened out and subjected to GO enrichment analysis and KEGG pathway analysis. This module included eight genes, which were further screened using TCGA. Finally, UBE2L3 was selected as a key gene and the hsa_circ_0009910–miR-1261–UBE2L3 regulatory axis was established. The relative expression of the regulatory axis members was confirmed by qRT-PCR in 30 pairs of samples, including HCC tissues and adjacent nontumor tissues. The results suggested that hsa_circ_0009910, which was upregulated in HCC tissues, participates in the pathogenesis of HCC by acting as a sponge of miR-1261 to regulate the expression of UBE2L3. Overall, this study provides support for the possible mechanisms of progression in HCC.

scholarly journals RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1565
Author(s):  
Zhiyun Hao ◽  
Yuzhu Luo ◽  
Jiqing Wang ◽  
Jiang Hu ◽  
Xiu Liu ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Signaling Pathway ◽  
Target Genes ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Wnt Signaling Pathway ◽  
Mammary Epithelial ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA with >200 nucleotides in length. Some lncRNAs have been proven to have clear regulatory functions in many biological processes of mammals. However, there have been no reports on the roles of lncRNAs in ovine mammary gland tissues. In the study, the expression profiles of lncRNAs were studied using RNA-Seq in mammary gland tissues from lactating Small-Tailed Han (STH) ewes and Gansu Alpine Merino (GAM) ewes with different milk yield and ingredients. A total of 1894 lncRNAs were found to be expressed. Compared with the GAM ewes, the expression levels of 31 lncRNAs were significantly up-regulated in the mammary gland tissues of STH ewes, while 37 lncRNAs were remarkably down-regulated. Gene Ontogeny (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the target genes of differentially expressed lncRNAs were enriched in the development and proliferation of mammary epithelial cells, morphogenesis of mammary gland, ErbB signaling pathway, and Wnt signaling pathway. Some miRNA sponges of differentially expressed lncRNAs, reported to be associated with lactation and mammary gland morphogenesis, were found in a lncRNA-miRNA network. This study reveals comprehensive lncRNAs expression profiles in ovine mammary gland tissues, thereby providing a further understanding of the functions of lncRNAs in the lactation and mammary gland development of sheep.

scholarly journals Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

2020 ◽  
Author(s):  
Fuhui Han ◽  
Jing Li ◽  
Ranran Zhao ◽  
Lirong Liu ◽  
Lanlan Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Structural Characteristics ◽  
Intramuscular Fat ◽  
Differentially Expressed ◽  
Lipid Deposition ◽  
Sequencing Data ◽  
Dual Purpose ◽  
Intramuscular Lipid ◽  
Non Coding Rnas

Abstract Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). Results: We identified a total of 26,247 genes and 6,935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR.Conclusions: Our study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.

scholarly journals Transcriptome Analysis to Identify the Potential Role of Long non-coding RNAs in Enteric Glial Cells under Hyperglycemia

2020 ◽  
Author(s):  
Xuping Zhu ◽  
Yanyu Li ◽  
Xue Zhu ◽  
Yanmin Jiang ◽  
Xiaowei Zhu ◽  
...  
Keyword(s):  
Autonomic Neuropathy ◽  
Glial Cells ◽  
Transcriptome Analysis ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Enteric Glial Cells ◽  
Non Coding Rnas

Abstract Background Long non-coding RNAs (lncRNAs) are important mediators in the pathogenesis of diabetic gastrointestinal autonomic neuropathy, which has just been reported to have a relation to enteric glial cells (EGCs). However, the role of lncRNAs in the pathogenesis of diabetic gastrointestinal autonomic neuropathy, especially EGCs-related gastrointestinal dysfunction, has never been reported. Methods RNA sequencing technology (RNA-Seq) was used to screen the differential lncRNAs and mRNAs in EGCs under hyperglycemia (300 mmol L− 1 high glucose). Results Totally 4678 differentially expressed lncRNAs (DE lncRNAs) and 6244 differentially expressed mRNAs (DE mRNAs) were obtained. GO enrichment analysis and KEGG pathway analysis showed significant differences. 2910 and 1549 co-expressed mRNAs were respectively expressed in up-regulated and down-regulated DE lncRNA target genes. Several up- or down-regulated lncRNAs were at the key junction points of the regulatory network. Protein-protein interaction networks showed highly connected clusters were TP53, AKT1, Casp9, Casp8, Casp3, TNF, etc, which are known closely related to apoptosis. FLRT3, Fras1, and other related target genes, which revealed the potential function of lncRNAs, may be important targets for differential lncRNAs to regulate the apoptosis of glial cells induced by hyperglycemia. Conclusion In this study, the involvement of lncRNAs in EGCs under hyperglycemia was analyzed using transcriptome analysis.

scholarly journals Exploring the Roles of Fecundity-related mRNAs and Long Non-coding RNAs in the Adrenal Glands of Small-tailed Han Sheep

2020 ◽  
Author(s):  
Qing Xia ◽  
Qiuling Li ◽  
Shangquan Gan ◽  
Xiaofei Guo ◽  
Xiaosheng Zhang ◽  
...  
Keyword(s):  
Adrenal Gland ◽  
Signaling Pathways ◽  
Transforming Growth Factor Beta ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Transforming Growth Factor ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Gene Expressions ◽  
Non Coding Rnas

Abstract Background Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissues between FecB ++ (WW) and FecB BB (MM) sheep in the follicular and luteal phases and key lncRNAs and genes associated with reproduction were identified. Results In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 30 differentially expressed lncRNAs and 210 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Key lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761 , XLOC_357966 , 105614839 and XLOC_212877 targeting CREB1 , PER3 , SMAD1 and TGFBR2 , respectively, appear to play key regulatory roles. Conclusion These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.

Sign in / Sign up

Export Citation Format

Share Document