scholarly journals Differentially Expressed MiRNAs of Goat Submandibular Glands Among Three Developmental Stages Are Involved in Immune Functions

2021 ◽  
Vol 12 ◽  
Author(s):  
Aili Wang ◽  
Zhibin Ji ◽  
Rong Xuan ◽  
Xiaodong Zhao ◽  
Lei Hou ◽  
...  
Keyword(s):  
Growth And Development ◽  
Target Genes ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Biologically Active ◽  
Differentially Expressed ◽  
Immune Functions ◽  
Submandibular Glands ◽  
Differentially Expressed Mirnas ◽  
Old Adult

Submandibular glands (SMGs) are one of the primary components of salivary glands in goats. The proteins and biologically active substances secreted by the SMGs change with growth and development. Our previous studies showed that most of the differentially expressed genes in the SMGs of goats at different developmental stages are involved in immune-related signaling pathways, but the miRNA expression patterns in the same tissues are unknown. The aim of this study was to reveal the expression profile of miRNAs at three different developmental stages, detect differentially expressed miRNAs (DE miRNAs) and predict disease-related DE miRNAs. SMG tissue samples were collected from groups of 1-month-old kids, 12-month-old maiden goats and 24-month-old adult goats (three samples from each group), and high-throughout transcriptome sequencing was conducted. A total of 178, 241 and 7 DE miRNAs were discovered between 1-month-old kids and 12-month-old maiden goats, between 1-month-old kids and 24-month-old adult goats, and between 12-month-old maiden goats and 24-month-old adult goats, respectively. Among these DE miRNAs, 88 DE miRNAs with medium or high expression levels (TPM ≥50) were classified into five expression pattern clusters. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that some of the predicted target genes of the DE miRNAs in the five clusters were enriched in disease-related GO terms and pathways. MiRNA target genes in significant pathways were significantly enriched in Hepatitis B (FDR = 9.03E-10) and Pathways in cancer (FDR = 4.2E-10). Further analysis was performed with a PPI network, and 10 miRNAs were predicted to play an important role in the occurrence and prevention of diseases during the growth and development of goats.

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

Animals ◽  
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.

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 Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 483 ◽  
Author(s):  
Sun ◽  
Luo ◽  
Chang ◽  
Li ◽  
Zhou ◽  
...  
Keyword(s):  
Small Rna ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Complex Biological Process ◽  
Cucumber Fruit ◽  
Differentially Expressed Mirnas

Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA–mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.

An integrated analysis of mRNA and miRNA in skeletal muscle from myostatin-edited Meishan pigs

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 305-315 ◽  
Author(s):  
Shanshan Xie ◽  
Xiang Li ◽  
Lili Qian ◽  
Chunbo Cai ◽  
Gaojun Xiao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Growth And Development ◽  
Target Genes ◽  
Muscle Growth ◽  
Genetically Engineered ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Signal Pathways ◽  
Skeletal Muscle Growth ◽  
Differentially Expressed Mirnas

Myostatin (MSTN) is a key muscle factor that negatively regulates skeletal muscle growth and development. Our laboratory recently produced genetically engineered Meishan pigs containing a ZFN-edited MSTN loss-of-function mutation (MSTN−/−, MKO) that led to the hypertrophy of skeletal muscles. In this study, we performed transcriptome sequencing and miRNA sequencing in skeletal muscle samples from MKO and wildtype Meishan (MWT) pigs to investigate the effect of MSTN−/− on expression of mRNA and miRNA. Our results indicated that, compared to MWT pigs, there were 200 genes and 4 miRNAs being significantly up-regulated, and 238 genes and 5 miRNAs being significantly down-regulated in MKO pigs. Analysis by GO and KEGG pathways revealed that differentially expressed miRNAs and their target genes of those differentially expressed miRNAs were involved in the signal pathways of skeletal muscle growth and development such as AMPK, mTOR, and TGF-beta. An integrated analysis of the correlation between miRNA-mRNA and transcriptome predicated that XK and METTL8 were target genes for miR-499-5p, while LRP4 was a target gene for miR-490-3p. Our results provide important clues to help us further investigate MSTN′s regulatory mechanisms during skeletal muscle growth and development.

scholarly journals Comparative Transcriptomics Analysis of Testicular miRNA from Cryptorchid and Normal Horses

Animals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 338
Author(s):  
Haoyuan Han ◽  
Qiuming Chen ◽  
Yuan Gao ◽  
Jun Li ◽  
Wantao Li ◽  
...  
Keyword(s):  
Metal Ion ◽  
Target Genes ◽  
Expression Patterns ◽  
Osteoclast Differentiation ◽  
Zinc Ion ◽  
Differentially Expressed ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Expression Levels ◽  
Differentially Expressed Mirnas

In the biological process of testicular spermatogenesis, the expression and interaction of many genes are regulated by microRNAs (miRNAs). However, comparisons of miRNA expression between descended testes (DTs) and undescended testes (UDTs) are rarely done in horses. In this study, we selected two UDTs (CKY2b and GU4b) from Chakouyi (CKY) and Guanzhong (GU) horses and eight DTs (GU1–3, CKY1, CKY3, CKY2a, GU4a, and GU5). Three groups were compared to evaluate expression patterns of testicular miRNA in stallion testes. Group 1 compared normal CKY horses and GU horses (CKY1 and CKY3 vs. GU1–3). Group 2 (CKY2a and GU4a (DTs) vs. CKY2b and GU4b (UDTs)) and group 3 (GU1–3, CKY1, CKY3 (DTs) vs. CKY2b and GU4b (UDTs)) compared the expression levels in unilateral retained testes to normal testes. The results show that 42 miRNAs (7 upregulated and 35 downregulated) had significantly different expression levels in both comparisons. The expression levels of eca-miR-545, eca-miR-9084, eca-miR-449a, eca-miR-9024, eca-miR-9121, eca-miR-8908e, eca-miR-136, eca-miR-329b, eca-miR-370, and eca-miR-181b were further confirmed by quantitative real-time PCR assay. The target genes of differentially expressed miRNAs in three comparisons were predicted, and the functions were annotated. The putative target genes of the 42 co-differentially expressed miRNAs were annotated to 15 functional terms, including metal ion binding, GTPase activator activity, zinc ion binding, intracellular, cytoplasm, and cancer pathways, and osteoclast differentiation. Our data indicate that the differentially expressed miRNAs in undescended testis suggests a potential role in male fertility and a relationship with cryptorchidism in horses. The discovery of miRNAs in stallion testes might contribute to a new direction in the search for biomarkers of stallion fertility.

scholarly journals Deep Sequencing Discovery and Profiling of Known and Novel miRNAs Produced in Response to DNA Damage in Rice

2021 ◽  
Vol 22 (18) ◽  
pp. 9958
Author(s):  
Jianxiang Zhang ◽  
Cheng Xu ◽  
Kangwei Liu ◽  
Yaoqinq Li ◽  
Mengna Wang ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Gene Transcription ◽  
Target Genes ◽  
Expression Patterns ◽  
Dna Damage Repair ◽  
Repair Process ◽  
Differentially Expressed ◽  
Damage Repair ◽  
Differentially Expressed Mirnas

Under extreme environmental conditions such as ultraviolet and ionizing radiation, plants may suffer DNA damage. If these damages are not repaired accurately and rapidly, they may lead to chromosomal abnormalities or even cell death. Therefore, organisms have evolved various DNA repair mechanisms to cope with DNA damage which include gene transcription and post-translational regulation. MicroRNA (miRNA) is a type of non-coding single-stranded RNA molecule encoded by endogenous genes. They can promote DNA damage repair by regulating target gene transcription. Here, roots from seedlings of the japonica rice cultivar ‘Yandao 8’ that were treated with bleomycin were collected for transcriptome-level sequencing, using non-treated roots as controls. A total of 14,716,232 and 17,369,981 reads mapping to miRNAs were identified in bleomycin-treated and control groups, respectively, including 513 known and 72 novel miRNAs. Compared with the control group, 150 miRNAs showed differential expression levels. Target predictions of these differentially expressed miRNAs yielded 8731 potential gene targets. KEGG annotation and a gene ontology analysis indicated that the highest-ranked target genes were classified into metabolic processes, RNA degradation, DNA repair, and so on. Notably, the DNA repair process was significantly enriched in both analyses. Among these differentially expressed miRNAs, 58 miRNAs and 41 corresponding potential target genes were predicted to be related to DNA repair. RT-qPCR results confirmed that the expression patterns of 20 selected miRNAs were similar to those from the sequencing results, whereas four miRNAs gave opposite results. The opposing expression patterns of several miRNAs with regards to their target genes relating to the DNA repair process were also validated by RT-qPCR. These findings provide valuable information for further functional studies of miRNA involvement in DNA damage repair in rice.

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

2021 ◽  
Vol 12 ◽  
Author(s):  
Jie Yang ◽  
Xuejiao Xu ◽  
Sujie Lin ◽  
Shiyao Chen ◽  
Guifang Lin ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Plutella Xylostella ◽  
Target Genes ◽  
Expression Patterns ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Sequencing Analysis ◽  
Bt Resistance ◽  
Differentially Expressed Mirnas

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.

scholarly journals Comprehensive microRNA analysis in bleomycin-induced pulmonary fibrosis identifies multiple sites of molecular regulation

2011 ◽  
Vol 43 (9) ◽  
pp. 479-487 ◽  
Author(s):  
Ting Xie ◽  
Jiurong Liang ◽  
Rishu Guo ◽  
Ningshan Liu ◽  
Paul W. Noble ◽  
...  
Keyword(s):  
Lung Fibrosis ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Toll Like Receptor ◽  
Mirna Array ◽  
Differentially Expressed Mirnas ◽  
Mouse Lungs ◽  
Insight Into

The molecular mechanisms of lung injury and fibrosis are incompletely understood. MicroRNAs (miRNAs) are crucial biological regulators that act by suppressing their target genes and are involved in a variety of pathophysiological processes. To gain insight into miRNAs in the regulation of lung fibrosis, total RNA was isolated from mouse lungs harvested at different days after bleomycin treatment, and miRNA array with 1,810 miRNA probes was performed thereafter. MiRNAs expressed in lungs with bleomycin treatment at different time points were compared with miRNAs expressed in lungs without bleomycin treatment, resulting in 161 miRNAs differentially expressed. Furthermore, miRNA expression patterns regulated in initial and late periods after bleomycin were identified. Target genes were predicted in silico for differentially expressed miRNAs, including let-7f, let-7g, miR-196b, miR-16, miR-195, miR-25, miR-144, miR-351, miR-153, miR-468, miR-449b, miR-361, miR-700, miR-704, miR-717, miR-10a, miR-211, miR-34a, miR-367, and miR-21. Target genes were then cross-referenced to the molecular pathways, suggesting that the differentially expressed miRNAs regulate apoptosis, Wnt, Toll-like receptor, and TGF-β signaling. Our study demonstrated a relative abundance of miRNA levels in bleomycin-induced lung fibrosis. The miRNAs and their potential target genes identified may contribute to the understanding of the complex transcriptional program of lung fibrosis.

Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

2021 ◽  
Vol 15 (8) ◽  
pp. 927-936 ◽  
Author(s):  
Yan Peng ◽  
Yuewu Liu ◽  
Xinbo Chen
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Hot Spot ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Promising Tool ◽  
Differentially Expressed Mirnas ◽  
Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identified. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

scholarly journals Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Peirong Li ◽  
Tongbing Su ◽  
Deshuang Zhang ◽  
Weihong Wang ◽  
Xiaoyun Xin ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Leaf Development ◽  
Target Genes ◽  
Expression Patterns ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Leaf Morphogenesis ◽  
Expression Levels ◽  
Parental Lines

AbstractHeterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.

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