scholarly journals Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition

2018 ◽  
Author(s):  
Roberta Davoli ◽  
Enrico Gaffo ◽  
Martina Zappaterra ◽  
Stefania Bortoluzzi ◽  
Paolo Zambonelli
Keyword(s):  
Mirna Expression ◽  
Small Rnas ◽  
Genetic Improvement ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Large White ◽  
The Impact

SummaryThe identification of the molecular mechanisms regulating pathways associated to the potential of fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. MicroRNAs (miRNAs) interactions with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is well far from saturation and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations are still fragmentary. We characterized by RNAseq the small RNAs (sRNAs) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs, 14 up-regulated (including ssc-miR-132, ssc-miR-146b, sscmiR-221–5p, ssc-miR-365–5p, and the moRNA ssc-moR-21–5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p, and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network resulted to be expressed from backfat related pig QTLs. These results are informative on the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs, and facilitate the perspective implementation of innovative strategies of pig genetic improvement based on genomic markers.

scholarly journals Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White Pigs

2020 ◽  
Author(s):  
Dawei Zhang ◽  
Wenjing Wu ◽  
Xin Huang ◽  
Ke Xu ◽  
Cheng Zheng ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Fat Deposition ◽  
Mapk Signaling Pathway ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Domestic Pig ◽  
Large White ◽  
Pig Breeds

Abstract Background: Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of SC fat tissue is necessary for the rational selection of Chinese domestic pig breeds. In the present study, SC adipocytes were isolated from Jiaxing Black pigs (a Chinese indigenous pig breed with redundant SC fat deposition) and Large White pigs (a lean-type pig breed with relatively low SC fat deposition) and the expression profiles of mRNAs and lncRNAs were compared by RNA-seq analysis to identify biomarkers correlated with the differences of SC fat deposition between the two breeds.Results: A total of 3,371 differentially expressed genes (DEGs) and 1,182 differentially expressed lncRNAs (DELs) were identified in SC adipocytes between Jiaxing Black (JX) and Large White (LW) pigs, which included 797 upregulated mRNAs, 2,574 downregulated mRNAs, 461 upregulated lncRNAs and 721 downregulated lncRNAs. Gene Ontology and KEGG pathway analyses revealed that the DEGs and DELs were mainly involved in the immune response, cell fate determination, PI3K-Akt signaling pathway and MAPK signaling pathway, which are known to be related to adipogenesis and lipid metabolism. The expression levels of DEGs and DELs according to the RNA-seq data were verified by quantitative PCR, which showed 81.8% consistency. The differences in MAPK pathway activity between JX and LW pigs was confirmed by western blot analysis, with <100-fold elevated p38 phosphorylation in JX pigs.Conclusions: This study offers a detailed characterization of mRNAs and lncRNAs in fat- and lean-type pig breeds. The activity of the MAPK signaling pathway was found to be associated with subcutaneous adipogenesis. These results greatly enhance our understanding of the molecular mechanisms regulating SC fat deposition in pigs.

scholarly journals Integrated analysis of sex-biased mRNA and miRNA expression profiles in the gonad of the discus fish (Symphysodon aequifasciatus)

2018 ◽  
Author(s):  
yuanshuai Fu ◽  
Zhe Xu ◽  
Zaizhong Chen ◽  
Bin Wen ◽  
Jianzhong Gao
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
High Efficiency ◽  
Expression Profiles ◽  
Gonad Development ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Integrated Analysis ◽  
Illumina Hiseq ◽  
Differentially Expressed Mirnas

The discus fish (Symphysodon aequifasciatus) is an ornamental fish that is well-known around the world. Phenotype investigation indicated that there are no significant differences in appearance between males and females of the discus fish. To better understand the sexual development mechanisms and obtain a high efficiency sex identification method in the artificial reproduction process of the discus fish, we constructed six cDNA libraries from three adult testes and three adult ovaries, and perform RNA-sequencing for identifying sex-biased candidate genes, microRNA (miRNA), and metabolic pathway using the Illumina Hiseq 4000. A total of 50,082 non-redundant genes (unigenes) were identified, of which 18,570 unigenes were significantly overexpressed in testes, and 11,182 unigenes were significantly overexpressed in ovaries, and 8 differentially expressed unigenes were validated by quantitative Real-Time PCR (qPCR). A total of 551 miRNAs were identified, of which 47 miRNAs were differentially expressed between testes and ovaries, and 7 differentially expressed miRNAs and one non-differential miRNA were validated by qPCR. Twenty-four of these differentially expressed miRNAs and their 15 predicted target genes constituted 41 important miRNA-mRNA interaction pairs, which may be important candidates for sex-related miRNAs and sex-related genes in the discus fish. Some of vital sex-related metabolic pathways were also identified that may play key roles in regulating gonad development of the discus fish. These results can provide important insights to better understand molecular mechanisms for sexual dimorphism in gonads development.

scholarly journals Effects of Short-time Exposure to Atrazine on miRNA Expression Profiles in the Gonad of Common Carp (Cyprinus carpio)

2018 ◽  
Author(s):  
Fang Wang ◽  
Qian-wen Yang ◽  
Wen-Jie Zhao ◽  
Qi-Yan Du ◽  
Zhong-Jie Chang
Keyword(s):  
Common Carp ◽  
Cyprinus Carpio ◽  
Mirna Expression ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Endocrine Disrupting Chemical ◽  
Endocrine Disrupting ◽  
Mirna Expression Profiles

ABSTRACTMicroRNAs (miRNAs) are endogenous small non-coding RNAs that negatively regulate gene expression by targeting specific mRNAs; they are involved in the modulation of important mRNA networks involved in toxicity. Atrazine is a known endocrine-disrupting chemical, whose molecular mechanisms are unknown. In this study, common carp (Cyprinus carpio) gonads at two key developmental stages were exposed to 0.428 ppb atrazine for 24 h in vitro. MiRNA expression profiles were analysed to identify miRNAs related to gonad development and to reveal the atrazine mechanisms interfering with gonad differentiation. Atrazine exposure caused significant alteration of multiple miRNAs. Compared with the juvenile ovary, more miRNAs were down-regulated in juvenile testis, some of these down-regulated miRNAs target the steroid hormone biosynthesis pathway related-genes. Predicted target genes of differently-expressed miRNAs after exposure to atrazine were involved in many reproductive biology signalling pathways. We suggest that these target genes may have important roles in atrazine-induced reproductive toxicity by altering miRNAs expression. Our results also indicate that atrazine can up-regulate aromatase expression through miRNAs, which supports the hypothesis that atrazine has endocrine-disrupting activity by altering the expression of genes of the Hypothalamus-Pituitary-Gonad axis through its corresponding miRNAs. This study tells us the following conclusions: 1. Atrazine exposure results in significant alterations of miRNAs whose predicted target genes are associated with reproductive processes. 2. In the primordial gonad, atrazine promoted the expression of early gonad-determining genes by decreasing specific miRNAs. 3. In the juvenile gonad, atrazine promoted the biosynthesis of steroid hormones.

scholarly journals A systemic study of indoxacarb resistance in Spodoptera litura revealed complex expression profiles and regulatory mechanism

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Li Shi ◽  
Yao Shi ◽  
Ya Zhang ◽  
Xiaolan Liao
Keyword(s):  
Spodoptera Litura ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Resistance Mechanisms ◽  
Differentially Expressed ◽  
Glutathione S Transferase ◽  
Differentially Expressed Mirnas ◽  
Important Pest ◽  
Resistant Strains

Abstract The tobacco cutworm, Spodoptera litura, is an important pest of crop and vegetable plants worldwide, and its resistance to insecticides have quickly developed. However, the resistance mechanisms of this pest are still unclear. In this study, the change in mRNA and miRNA profiles in the susceptible, indoxacarb-resistant and field indoxacarb-resistant strains of S. litura were characterized. Nine hundred and ten co-up-regulated and 737 co-down-regulated genes were identified in the resistant strains. Further analysis showed that 126 co-differentially expressed genes (co-DEGs) (cytochrome P450, carboxy/cholinesterase, glutathione S-transferase, ATP-binding cassette transporter, UDP-glucuronosyl transferase, aminopeptidase N, sialin, serine protease and cuticle protein) may play important roles in indoxacarb resistance in S. litura. In addition, a total of 91 known and 52 novel miRNAs were identified, and 10 miRNAs were co-differentially expressed in the resistant strains of S. litura. Furthermore, 10 co-differentially expressed miRNAs (co-DEmiRNAs) had predicted co-DEGs according to the expected miRNA-mRNA negative regulation pattern and 37 indoxacarb resistance-related co-DEGs were predicted to be the target genes. These results not only broadened our understanding of molecular mechanisms of insecticide resistance by revealing complicated profiles, but also provide important clues for further study on the mechanisms of miRNAs involved in indoxacarb resistance in S. litura.

scholarly journals Profiling the microRNA Expression in Human iPS and iPS-derived Retinal Pigment Epithelium

2014 ◽  
Vol 13s5 ◽  
pp. CIN.S14074 ◽  
Author(s):  
Heuy-Ching Wang ◽  
Whitney A. Greene ◽  
Ramesh R. Kaini ◽  
Jane Shen-Gunther ◽  
Hung-I H Chen ◽  
...  
Keyword(s):  
Retinal Pigment Epithelium ◽  
Mirna Expression ◽  
Cell Cycle Progression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Ips Cells ◽  
Differentially Expressed ◽  
Induced Pluripotent

The purpose of this study is to characterize the microRNA (miRNA) expression profiles of induced pluripotent stem (iPS) cells and retinal pigment epithelium (RPE) derived from induced pluripotent stem cells (iPS-RPE). MiRNAs have been demonstrated to play critical roles in both maintaining pluripotency and facilitating differentiation. Gene expression networks accountable for maintenance and induction of pluripotency are linked and share components with those networks implicated in oncogenesis. Therefore, we hypothesize that miRNA expression profiling will distinguish iPS cells from their iPS-RPE progeny. To identify and analyze differentially expressed miRNAs, RPE was derived from iPS using a spontaneous differentiation method. MiRNA microarray analysis identified 155 probes that were statistically differentially expressed between iPS and iPS-RPE cells. Up-regulated miRNAs including miR-181c and miR-129–5p may play a role in promoting differentiation, while down-regulated miRNAs such as miR-367, miR-18b, and miR-20b are implicated in cell proliferation. Subsequent miRNA-target and network analysis revealed that these miRNAs are involved in cellular development, cell cycle progression, cell death, and survival. A systematic interrogation of temporal and spatial expression of iPS-RPE miRNAs and their associated target mRNAs will provide new insights into the molecular mechanisms of carcinogenesis, eye differentiation and development.

scholarly journals Genome-wide profiling of miRNA expression patterns in tubal endometriosis

Reproduction ◽  
2019 ◽  
Vol 157 (6) ◽  
pp. 525-534 ◽  
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.

scholarly journals Construction of potential periodontitis-related miRNA-mRNA regulatory network

2020 ◽  
Author(s):  
Zheng Zhang ◽  
Youli Zheng ◽  
Xiaowei Bian ◽  
Mingguang Jin
Keyword(s):  
Candidate Genes ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Multivariate Logistic Regression Analysis ◽  
Gene Expression Profiles ◽  
Mirna Expression Profile ◽  
Differentially Expressed ◽  
B Cell Differentiation

Abstract Background MicroRNAs (miRNAs) are found to be involved in the pathogenesis of periodontitis, a major cause of tooth loss in adults. However, a comprehensive miRNA-mRNA regulatory network has still not been established. Methods One miRNA expression profile and 2 gene expression profiles were downloaded from the GEO database and analyzed using GEO2R. Candidate genes commonly appeared in differentially expressed mRNAs (DE-mRNAs) and target genes of differentially expressed miRNAs (DE-miRNAs) were selected for functional and pathway enrichment analyses using Enrichr database. Multivariate Logistic regression analysis was used to screen independent variables among candidate genes. The diagnostic values of screened genes were determined by the area under the receiver operating characteristic (ROC) curve (AUC). Results A total of 5 DE-miRNAs (4 upregulated and 1 downregulated) and 11 candidate genes (3 upregulated and 8 downregulated) were screened. After the construction of miRNA-mRNA regulatory network, 12 miRNA-mRNA pairs were identified. In the network, the upregulated genes were significantly enriched in cellular triglyceride homeostasis and positive regulation of B cell differentiation, whereas the downregulated genes were enriched in vesicle organization, negative regulation of lymphocyte and leukocyte migration. EPCAM and RAB30 were screened as risk factors of periodontitis. The combined AUC of these 2 genes was 0.896 (GSE10334) and 0.916 (GSE16134). Conclusion In this study, we established a potential periodontitis-related miRNA-mRNA regulatory network, which brings new insights into the molecular mechanisms and provides key clues in seeking novel therapeutic targets for periodontitis. In the future, more experiments need to be carried out to validate our current findings.

scholarly journals Identification of Differentially Expressed Genes and Pathways for Abdominal Fat Deposition in Ovariectomized and Sham-Operated Chickens

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 155 ◽  
Author(s):  
Xiaopeng Mu ◽  
Xiaoyan Cui ◽  
Ranran Liu ◽  
Qinghe Li ◽  
Maiqing Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Abdominal Fat ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Feed Conversion ◽  
Fat Percentage ◽  
Steroid Biosynthesis

Ovariectomy results in improved meat quality (growth rate, tenderness, and flavor) of broilers. However, some negative effects increased (abdominal fat (AF) deposition, low feed conversion, etc.) have also been reported. In this study, the gene expression profiles of AF tissue in ovariectomized and sham-operated chickens were determined to identify differentially expressed genes (DEGs) and pathways to explore the molecular mechanisms underlying AF accumulation. Comparing the ovariectomized group and the sham-operated group, the abdominal fat weight (AFW) and abdominal fat percentage (AFP) were increased significantly (p < 0.05) at 14 and 19 weeks after ovariectomy. According to the gene expression profiling analysis, 108 DEGs of fat metabolism were screened from 1461 DEGs. Among them, ABCA1, ABCACA, LPL, CREB1, PNPLA2, which are involved in glycerolipid—or steroid—associated biological processes, and the hormone receptor genes, ESR1 and PRLR, were down-regulated significantly in the ovariectomized group compared to the sham-operated group (p < 0.05). Conversely, CETP, DGAT2, DHCR24, HSD17B7 and MSMO1, were significantly up-regulated (p < 0.05) after ovariectomy. Based on the DEGs, the glycerolipid metabolism, steroid biosynthesis, and other signaling pathways (MAPK, TGF-β, and adhesion pathways, etc.) were enriched, which may also contribute to the regulation of AF deposition. Our data suggest that AF deposition was significantly increased in ovariectomized chickens by the down-regulation of the decomposition genes of glycerolipid metabolism, which inhibits AF degradation, and the up-regulation of steroid biosynthesis genes, which increases fat accumulation. These findings provide new insights into the molecular mechanisms of fat deposition in the ovariectomized chickens.

Integration of small RNAs, degradome, and transcriptome sequencing in Populus × euramericana “Neva” provides insights into the allelopathic interference of para-hydroxybenzoic acid

2020 ◽  
Vol 50 (4) ◽  
pp. 422-437 ◽  
Author(s):  
Guoting Liang ◽  
Jing Guo ◽  
Shuyong Zhang ◽  
Guangcan Zhang
Keyword(s):  
Small Rnas ◽  
Mirna Target ◽  
Target Genes ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Hydroxybenzoic Acid ◽  
Differentially Expressed Mirnas ◽  
Leaves And Roots

Allelopathy is a hot topic of research; however, little is known regarding microRNA (miRNA) expression profiles in plants in response to allelochemicals. In this study, we combined the analyses of the transcriptome, small RNAs (sRNAs), and the degradome to identify key regulatory miRNA-targeted circuits under para-hydroxybenzoic acid (pHBA) stress. A total of 739 and 673 miRNAs were identified in leaves and roots, respectively. Of those, 214 and 148 miRNAs were significantly differentially expressed and identified as pHBA-responsive miRNAs in leaves and roots, respectively. The target genes for the pHBA-responsive miRNAs are involved in signal transduction, response to stress, and secondary metabolite pathways. Furthermore, an integrated analysis of the miRNA–target expression profiles was used to screen the 60 differentially expressed target genes from the 46 differentially expressed miRNAs in the leaves and the 51 differentially expressed target genes from the 36 differentially expressed miRNAs in roots. This integrated analysis revealed 17 and 30 pairs of miRNA targets in the leaves and roots, respectively, which had negatively correlated expression profiles. According to a real-time quantitative polymerase chain reaction (PCR) analysis, 14 miRNA–target pairs also exhibited negative correlations. Moreover, four coexpression regulatory networks were constructed based on the profiles of the differentially expressed miRNA–target pairs. These results suggest that comprehensive analyses of transcriptomes, sRNAs, and the degradome provide a useful platform for investigating the molecular mechanism underlying the pHBA-induced stress response in plants.

scholarly journals Identification and characterization of mRNAs and lncRNAs in the uterus of polytocous and monotocous Small Tail Han sheep (Ovis aries)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6938 ◽  
Author(s):  
Yongfu La ◽  
Jishun Tang ◽  
Xiaoyun He ◽  
Ran Di ◽  
Xiangyu Wang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Ovis Aries ◽  
Differentially Expressed ◽  
Retinol Metabolism ◽  
Two Phases

Background Long non-coding RNAs (lncRNAs) regulate endometrial secretion and uterine volume. However, there is little research on the role of lncRNAs in the uterus of Small Tail Han sheep (FecB++). Herein, RNA-seq was used to comparatively analyze gene expression profiles of uterine tissue between polytocous and monotocous sheep (FecB++) in follicular and luteal phases. Methods To identify lncRNA and mRNA expressed in the uterus, the expression of lncRNA and mRNA in the uterus of Small Tail Han sheep (FecB++) from the polytocous group (n = 6) and the monotocous group (n = 6) using RNA-sequencing and real-time polymerase chain reaction (RT-PCR). Identification of differentially expressed lncRNAs and mRNAs were performed between the two groups and two phases . Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for the differentially expressed mRNAs. LncRNA-mRNA co-expression network was constructed to further analyses the function of related genes. Results In the follicular phase, 473 lncRNAs and 166 mRNAs were differentially expressed in polytocous and monotocous sheep; in the luteal phase, 967 lncRNAs and 505 mRNAs were differentially expressed in polytocous and monotocous sheep. GO and KEGG enrichment analysis showed that the differentially expressed lncRNAs and their target genes are mainly involved in ovarian steroidogenesis, retinol metabolism, the oxytocin signaling pathway, steroid hormone biosynthesis, and the Foxo signaling pathway. Key lncRNAs may regulate reproduction by regulating genes involved in these signaling pathways and biological processes. Specifically, UGT1A1, LHB, TGFB1, TAB1, and RHOA, which are targeted by MSTRG.134747, MSTRG.82376, MSTRG.134749, MSTRG.134751, and MSTRG.134746, may play key regulatory roles. These results offer insight into molecular mechanisms underlying sheep prolificacy.

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