Profiling of MicroRNAs in Midguts of Plutella xylostella Provides Novel Insights Into the Bacillus thuringiensis Resistance

The diamondback moth (DBM), Plutella xylostella, one of the most destructive lepidopteran pests worldwide, has developed field resistance to Bacillus thuringiensis (Bt) Cry toxins. Although miRNAs have been reported to be involved in insect resistance to multiple insecticides, our understanding of their roles in mediating Bt resistance is limited. In this study, we constructed small RNA libraries from midguts of the Cry1Ac-resistant (Cry1S1000) strain and the Cry1Ac-susceptible strain (G88) using a high-throughput sequencing analysis. A total of 437 (76 known and 361 novel miRNAs) were identified, among which 178 miRNAs were classified into 91 miRNA families. Transcripts per million analysis revealed 12 differentially expressed miRNAs between the Cry1S1000 and G88 strains. Specifically, nine miRNAs were down-regulated and three up-regulated in the Cry1S1000 strain compared to the G88 strain. Next, we predicted the potential target genes of these differentially expressed miRNAs and carried out GO and KEGG pathway analyses. We found that the cellular process, metabolism process, membrane and the catalytic activity were the most enriched GO terms and the Hippo, MAPK signaling pathway might be involved in Bt resistance of DBM. In addition, the expression patterns of these miRNAs and their target genes were determined by RT-qPCR, showing that partial miRNAs negatively while others positively correlate with their corresponding target genes. Subsequently, novel-miR-240, one of the differentially expressed miRNAs with inverse correlation with its target genes, was confirmed to interact with Px017590 and Px007885 using dual luciferase reporter assays. Our study highlights the characteristics of differentially expressed miRNAs in midguts of the Cry1S1000 and G88 strains, paving the way for further investigation of miRNA roles in mediating Bt resistance.

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Characterization of microRNAs during Embryonic Skeletal Muscle Development in the Shan Ma Duck

Animals ◽

10.3390/ani10081417 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1417

Author(s):

Chuan Li ◽

Ting Xiong ◽

Mingfang Zhou ◽

Lei Wan ◽

Suwang Xi ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Target Genes ◽

Mapk Signaling ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Luciferase Reporter ◽

Meat Production ◽

Skeletal Muscle Development ◽

Differentially Expressed Mirnas

Poultry skeletal muscle provides high quality protein for humans. Study of the genetic mechanisms during duck skeletal muscle development contribute to future duck breeding and meat production. In the current study, three breast muscle samples from Shan Ma ducks at embryonic day 13 (E13) and E19 were collected, respectively. We detected microRNA (miRNA) expression using high throughput sequencing following bioinformatic analysis. qRT-PCR validated the reliability of sequencing results. We also identified target prediction results using the luciferase reporter assay. A total of 812 known miRNAs and 279 novel miRNAs were detected in six samples; as a result, 61 up-regulated and 48 down-regulated differentially expressed miRNAs were identified between E13 and E19 (|log2 fold change| ≥ 1 and p ≤ 0.05). Enrichment analysis showed that target genes of the differentially expressed miRNAs were enriched on many muscle development-related gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathways. An interaction network was constructed using the target genes of the differentially expressed miRNAs. These results complement the current duck miRNA database and offer several miRNA candidates for future studies of skeletal muscle development in the duck.

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MicroRNA sequence analysis identifies microRNAs associated with peri-implantitis in dogs

Bioscience Reports ◽

10.1042/bsr20170768 ◽

2017 ◽

Vol 37 (5) ◽

Cited By ~ 10

Author(s):

Xiaolin Wu ◽

Xipeng Chen ◽

Wenxiang Mi ◽

Tingting Wu ◽

Qinhua Gu ◽

...

Keyword(s):

Sequence Analysis ◽

Target Genes ◽

Alveolar Bone ◽

Biological Effects ◽

Bone Destruction ◽

Mapk Signaling ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Mirna Sequence ◽

Differentially Expressed Mirnas

Peri-implantitis, which is characterized by dense inflammatory infiltrates and increased osteoclast activity, can lead to alveolar bone destruction and implantation failure. miRNAs participate in the regulation of various inflammatory diseases, such as periodontitis and osteoporosis. Therefore, the present study aimed to investigate the differential expression of miRNAs in canine peri-implantitis and to explore the functions of their target genes. An miRNA sequence analysis was used to identify differentially expressed miRNAs in peri-implantitis. Under the criteria of a fold-change >1.5 and P<0.01, 8 up-regulated and 30 down-regulated miRNAs were selected for predictions of target genes and their biological functions. Based on the results of Gene Ontology (GO) and KEGG pathway analyses, these miRNAs may fine-tune the inflammatory process in peri-implantitis through an intricate mechanism. The results of quantitative real-time PCR (qRT-PCR) revealed that let-7g, miR-27a, and miR-145 may play important roles in peri-implantitis and are worth further investigation. The results of the present study provide insights into the potential biological effects of the differentially expressed miRNAs, and specific enrichment of target genes involved in the mitogen-activated protein kinase (MAPK) signaling pathway was observed. These findings highlight the intricate and specific roles of miRNAs in inflammation and osteoclastogenesis, both of which are key aspects of peri-implantitis, and thus may contribute to future investigations of the etiology, underlying mechanism, and treatment of peri-implantitis.

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Identification of Differentially Expressed MicroRNAs and Their Potential Target Genes in Adipose Tissue from Pigs with Highly Divergent Backfat Thickness

Animals ◽

10.3390/ani10040624 ◽

2020 ◽

Vol 10 (4) ◽

pp. 624

Author(s):

Kai Xing ◽

Xitong Zhao ◽

Yibing Liu ◽

Fengxia Zhang ◽

Zhen Tan ◽

...

Keyword(s):

Target Genes ◽

Expression Patterns ◽

Fat Deposition ◽

Functional Enrichment ◽

Differentially Expressed ◽

Backfat Thickness ◽

P Value ◽

Sibling Pairs ◽

Differentially Expressed Mirnas

Fatty traits are very important in pig production. However, the role of microRNAs (miRNAs) in fat deposition is not clearly understood. In this study, we compared adipose miRNAs from three full-sibling pairs of female Landrace pigs, with high and low backfat thickness, to investigate the associated regulatory network. We obtained an average of 17.29 million raw reads from six libraries, 62.27% of which mapped to the pig reference genome. A total of 318 pig miRNAs were detected among the samples. Among them, 18 miRNAs were differentially expressed (p-value < 0.05, |log2fold change| ≥ 1) between the high and low backfat groups; 6 were up-regulated and 12 were down-regulated. Functional enrichment of the predicted target genes of the differentially expressed miRNAs, indicated that these miRNAs were involved mainly in lipid and carbohydrate metabolism, and glycan biosynthesis and metabolism. Comprehensive analysis of the mRNA and miRNA transcriptomes revealed possible regulatory relationships for fat deposition. Negatively correlated mRNA–miRNA pairs included miR-137–PPARGC1A, miR-141–FASN, and miR-122-5p–PKM, indicating these interactions may be key regulators of fat deposition. Our findings provide important insights into miRNA expression patterns in the backfat tissue of pig and new insights into the regulatory mechanisms of fat deposition in pig.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

10.21203/rs.2.15327/v1 ◽

2019 ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan Zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 ( PLCβ1) gene was verified to be a target of ssc-mir-423-5p . Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

BMC Genomics ◽

10.1186/s12864-020-07096-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan Zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p. Conclusions This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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Next-generation sequencing analysis reveals segmental patterns of microRNA expression in yak epididymis

Reproduction Fertility and Development ◽

10.1071/rd20113 ◽

2020 ◽

Vol 32 (12) ◽

pp. 1067

Author(s):

Wangsheng Zhao ◽

Eugene Quansah ◽

Meng Yuan ◽

Pengcheng Li ◽

Chuanping Yi ◽

...

Keyword(s):

Gene Expression ◽

Mirna Expression ◽

Expression Patterns ◽

Differentially Expressed ◽

Sequencing Analysis ◽

Differentially Expressed Mirnas ◽

Next Generation Sequencing Analysis ◽

Cauda Epididymidis ◽

Caput Epididymidis

MicroRNAs (miRNAs) have emerged as potent regulators of gene expression and are widely expressed in biological systems. In reproduction, they have been shown to have a significant role in the acquisition and maintenance of male fertility, whereby deletion of Dicer in mouse germ cells leads to infertility. Evidence indicates that this role of miRNAs extends from the testis into the epididymis, controlling gene expression and contributing to regional variations in gene expression. In this study, RNA sequencing technology was used to investigate miRNA expression patterns in the yak epididymis. Region-specific miRNA expression was found in the yak epididymis. In all, 683 differentially expressed known miRNAs were obtained; 190, 186 and 307 differentially expressed miRNAs were identified for caput versus corpus, corpus versus cauda and caput versus cauda region pairs respectively. Kyoto Encyclopedia of Genes and Genomes results showed endocytosis as the most enriched pathway across region pairs, followed by protein processing in the endoplasmic reticulum, phagosome, spliceosome and biosynthesis of amino acids in region pair-specific hierarchical order. Gene ontology results showed varied enrichment in terms including cell, biogenesis, localisation, binding and locomotion across region pairs. In addition, significantly higher miR-34c expression was seen in the yak caput epididymidis relative to the corpus and cauda epididymidis.

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Genome-wide profiling of miRNA expression patterns in tubal endometriosis

Reproduction ◽

10.1530/rep-18-0631 ◽

2019 ◽

Vol 157 (6) ◽

pp. 525-534 ◽

Cited By ~ 4

Author(s):

Hang Qi ◽

Guiling Liang ◽

Jin Yu ◽

Xiaofeng Wang ◽

Yan Liang ◽

...

Keyword(s):

Pathway Analysis ◽

Mirna Expression ◽

Gene Networks ◽

Target Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Mirna Gene ◽

Differentially Expressed ◽

Signal Pathways ◽

Differentially Expressed Mirnas

MicroRNA (miRNA) expression proﬁles in tubal endometriosis (EM) are still poorly understood. In this study, we analyzed the differential expression of miRNAs and the related gene networks and signaling pathways in tubal EM. Four tubal epithelium samples from tubal EM patients and five normal tubal epithelium samples from uterine leiomyoma patients were collected for miRNA microarray. Bioinformatics analyses, including Ingenuity Pathway Analysis (IPA), Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were performed. Quantitative real-time polymerase chain reaction (qRT-PCR) validation of five miRNAs was performed in six tubal epithelium samples from tubal EM and six from control. A total of 17 significantly differentially expressed miRNAs and 4343 potential miRNA-target genes involved in tubal EM were identified (fold change >1.5 and FDR-adjustedPvalue <0.05). IPA indicated connections between miRNAs, target genes and other gynecological diseases like endometrial carcinoma. GO and KEGG analysis revealed that most of the identified genes were involved in the mTOR signaling pathway, SNARE interactions in vesicular transport and endocytosis. We constructed an miRNA-gene-disease network using target gene prediction. Functional analysis showed that the mTOR pathway was connected closely to tubal EM. Our results demonstrate for the first time the differentially expressed miRNAs and the related signal pathways involved in the pathogenesis of tubal EM which contribute to elucidating the pathogenic mechanism of tubal EM-related infertility.

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Screening and validation of differentially expressed microRNAs and target genes in hypertensive mice induced by cytomegalovirus infection

Bioscience Reports ◽

10.1042/bsr20202387 ◽

2020 ◽

Vol 40 (12) ◽

Cited By ~ 1

Author(s):

YunZhong Shi ◽

DongMei Xi ◽

XiaoNi Zhang ◽

Zhen Huang ◽

Na Tang ◽

...

Keyword(s):

Target Genes ◽

Reporter Gene Assay ◽

Differentially Expressed ◽

Luciferase Reporter ◽

Luciferase Reporter Gene ◽

Mcmv Infection ◽

Luciferase Reporter Gene Assay ◽

Qrt Pcr ◽

Gene Assay ◽

Differentially Expressed Mirnas

Abstract Introduction: Multiple studies have suggested an association between cytomegalovirus (CMV) infection and essential hypertension (EH). MicroRNAs (miRNAs) play a critical role in the development of EH by regulating the expression of specific target genes. However, little is known about the role of miRNAs in CMV-induced EH. In the present study, we compared the miRNA expression profiles of samples from normal and murine cytomegalovirus (MCMV)-infected C57BL/6 mice using high-throughput sequencing analysis. Methods: We collected the thoracic aorta, heart tissues, and peripheral blood from 20 normal mice and 20 MCMV-infected mice. We identified differentially expressed miRNAs in the peripheral blood samples and predicted their target genes using bioinformatics tools. We then experimentally validated them using quantitative reverse transcription polymerase chain reaction (qRT-PCR) and the target genes with double luciferase reporter gene assay. Results: We found 118 differentially expressed miRNAs, among which 9 miRNAs were identified as potential MCMV infection-induced hypertension regulators. We then validated the expression of two candidate miRNAs, mmu-miR-1929-3p and mcmv-miR-m01-4-5p, using qRT-PCR. Furthermore, the dual-luciferase reporter gene assay revealed that the 3′-untranslated region (UTR) of endothelin A receptor (Ednra) messenger RNA (mRNA) contained a binding site for mmu-miR-1929-3p. Collectively, our data suggest that MCMV infection can raise the blood pressure and reduce mmu-miR-1929-3p expression in C57BL/6 mice. Moreover, we found that mmu-miR-1929-3p targets the 3′-UTR of the Ednra mRNA. Conclusion: This novel regulatory axis could aid the development of new approaches for the clinical prevention and control of EH.

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Identification of a Key Competing Endogenous RNA Axis, “COL5A1/miR-137-3p/FSTL1”, Associated With Gastric Cancer Progression by Integrated Bioinformatics Analyses and Experimental Verification

10.21203/rs.3.rs-824329/v1 ◽

2021 ◽

Author(s):

Ming Yang ◽

Zhixing Lu ◽

Liang Li ◽

Min Ma ◽

Fei Long ◽

...

Keyword(s):

Gastric Cancer ◽

Cancer Progression ◽

Target Gene ◽

Target Genes ◽

Differentially Expressed ◽

Luciferase Reporter ◽

Migration And Invasion ◽

Bioinformatics Analyses ◽

Immune Infiltration ◽

Differentially Expressed Mirnas

Abstract Background MicroRNAs (miRNAs) and their target genes have been shown to play an important role in gastric cancer (GC), but this role has not been fully clarified. Therefore, our goal was to find the key miRNA-mRNA regulatory network in GC by combining a variety of bioinformatics and experimental analyses. Methods Differentially expressed miRNAs (DEMs) and genes (DEGs) were screened from TCGA and GEO, respectively. Survival-related differentially expressed miRNAs (SRDEMs) were determined by Cox proportional hazards regression and lasso regression analyses. Differentially expressed target genes (DETGs) of SRDEMs were predicted by TargetScan and miRDB and overlapped with DEGs. We constructed a protein–protein interaction (PPI) network of DETGs and conducted weighted gene coexpression network analysis (WGCNA) to screen the hub genes. Then, qRT–PCR and western blotting were performed to detect the expression level, and a dual-luciferase reporter assay was conducted to verify the binding of miRNA and mRNAs. CCK-8, EdU, wound healing and Transwell assays were conducted to compare the proliferation, migration and invasion abilities of GC cells in the different groups. Results We identified 11 SRDEMs and 233 DETGs, from which we selected miR-137-3p and its target gene COL5A1 for further research because of their key roles in the results of the bioinformatics analyses. Then, we showed that miR-137-3p was significantly downregulated in GC and that overexpression of miR-137-3p suppressed the proliferation, invasion and migration of GC cells by targeting COL5A1. Furthermore, we found that COL5A1 could regulate the expression of FSTL1 and GC progression by sponging miR-137-3p. Finally, bioinformatics analyses showed that FSTL1 might promote GC progression by regulating the immune infiltration of GC. Conclusions miR-137-3p played a tumor-suppressive role in GC, and its target gene COL5A1 could competitively bind miR-137-3p to upregulate the expression of FSTL1, which affects immune infiltration.

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