Transcriptome Analysis of mRNAs and Long Non-Coding RNAs During Subsequent Embryo Development of Porcine Cloned Zygotes After Vitrification

Cryopreservation of porcine cloned zygotes has important implications for biotechnology and biomedicine research; however, lower embryo developmental potential remains an urgent problem to be resolved. For exploring the sublethal cryodamages during embryo development, this study was designed to acquire the mRNA and long non-coding RNA (lncRNA) profiles of 2-cells, 4-cells and blastocysts derived from vitrified porcine cloned zygotes using transcriptome sequencing. We identified 167 differentially expressed (DE) mRNAs and 516 DE lncRNAs in 2-cell stage, 469 DE mRNAs and 565 lncRNAs in 4-cell stage, and 389 DE mRNAs and 816 DE lncRNAs in blastocyst stage. Functional enrichment analysis revealed that the DE mRNAs during embryo development were involved in many regulatory mechanisms related to cell cycle, cell proliferation, apoptosis, metabolism and others. Moreover, the target genes of DE lncRNAs in the three embryonic stages were also enriched in many key GO terms or pathways such as “defense response”, “linoleic acid metabolic process”, “embryonic axis specification”, “negative regulation of protein neddylation”, etc., In conclusion, the present study provided comprehensive transcriptomic data about mRNAs and lncRNAs for the vitrified porcine cloned zygotes during different developmental stages, which contributed to further understand the potential cryodamage mechanisms responsible for impaired embryo development.

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Regulatory role of non-coding RNA in ginseng rusty root symptom tissue

Scientific Reports ◽

10.1038/s41598-021-88709-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xingbo Bian ◽

Pengcheng Yu ◽

Ling Dong ◽

Yan Zhao ◽

He Yang ◽

...

Keyword(s):

Fatty Acid ◽

Regulatory Networks ◽

Target Genes ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Circular Rnas ◽

Primary Metabolism ◽

Non Coding Rna

AbstractGinseng rusty root symptom (GRS) is one of the primary diseases of ginseng. It leads to a severe decline in the quality of ginseng and significantly affects the ginseng industry. The regulatory mechanism of non-coding RNA (ncRNA) remains unclear in the course of disease. This study explored the long ncRNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) in GRS tissues and healthy ginseng (HG) tissues and performed functional enrichment analysis of the screened differentially expressed ncRNAs. Considering the predictive and regulatory effects of ncRNAs on mRNAs, we integrated ncRNA and mRNA data to analyze and construct relevant regulatory networks. A total of 17,645 lncRNAs, 245 circRNAs, and 299 miRNAs were obtained from HG and GRS samples, and the obtained ncRNAs were characterized, including the classification of lncRNAs, length and distribution of circRNA, and the length and family affiliations of miRNAs. In the analysis of differentially expressed ncRNA target genes, we found that lncRNAs may be involved in the homeostatic process of ginseng tissues and that lncRNAs, circRNAs, and miRNAs are involved in fatty acid-related regulation, suggesting that alterations in fatty acid-related pathways may play a key role in GRS. Besides, differentially expressed ncRNAs play an essential role in regulating transcriptional translation processes, primary metabolism such as starch and sucrose, and secondary metabolism such as alkaloids in ginseng tissues. Finally, we integrated the correlations between ncRNAs and mRNAs, constructed corresponding interaction networks, and identified ncRNAs that may play critical roles in GRS. These results provide a basis for revealing GRS's molecular mechanism and enrich our understanding of ncRNAs in ginseng.

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Identification of Tumorigenic and Prognostic Biomarkers in Colorectal Cancer Based on microRNA Expression Profiles

BioMed Research International ◽

10.1155/2020/7136049 ◽

2020 ◽

Vol 2020 ◽

pp. 1-8

Author(s):

Yuntao Shi ◽

Yingying Zhuang ◽

Jialing Zhang ◽

Mengxue Chen ◽

Shangnong Wu

Keyword(s):

Target Genes ◽

Cox Regression ◽

Expression Profiles ◽

Survival Rates ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Risk Groups ◽

Normal Mucosa ◽

Microrna Expression ◽

Functional Enrichment

Objective. Although noncoding RNAs, especially the microRNAs, have been found to play key roles in CRC development in intestinal tissue, the specific mechanism of these microRNAs has not been fully understood. Methods. GEO and TCGA database were used to explore the microRNA expression profiles of normal mucosa, adenoma, and carcinoma. And the differential expression genes were selected. Computationally, we built the SVM model and multivariable Cox regression model to evaluate the performance of tumorigenic microRNAs in discriminating the adenomas from normal tissues and risk prediction. Results. In this study, we identified 20 miRNA biomarkers dysregulated in the colon adenomas. The functional enrichment analysis showed that MAPK activity and MAPK cascade were highly enriched by these tumorigenic microRNAs. We also investigated the target genes of the tumorigenic microRNAs. Eleven genes, including PIGF, TPI1, KLF4, RARS, PCBP2, EIF5A, HK2, RAVER2, HMGN1, MAPK6, and NDUFA2, were identified to be frequently targeted by the tumorigenic microRNAs. The high AUC value and distinct overall survival rates between the two risk groups suggested that these tumorigenic microRNAs had the potential of diagnostic and prognostic value in CRC. Conclusions. The present study revealed possible mechanisms and pathways that may contribute to tumorigenesis of CRC, which could not only be used as CRC early detection biomarkers, but also be useful for tumorigenesis mechanism studies.

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miRNA Mediated Noise Making of 3′UTR Mutations in Cancer

Genes ◽

10.3390/genes9110545 ◽

2018 ◽

Vol 9 (11) ◽

pp. 545 ◽

Cited By ~ 5

Author(s):

Wei Wu ◽

Lingxiang Wu ◽

Mengyan Zhu ◽

Ziyu Wang ◽

Min Wu ◽

...

Keyword(s):

Somatic Mutations ◽

Target Genes ◽

Expression Profiles ◽

Tumor Development ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Messenger Rnas ◽

Cellular Functions ◽

Mrna Binding

Somatic mutations in 3′-untranslated regions (3′UTR) do not alter amino acids and are considered to be silent in cancers. We found that such mutations can promote tumor progression by altering microRNA (miRNA) targeting efficiency and consequently affecting miRNA–mRNA interactions. We identified 67,159 somatic mutations located in the 3′UTRs of messenger RNAs (mRNAs) which can alter miRNA–mRNA interactions (functional somatic mutations, funcMutations), and 69.3% of these funcMutations (the degree of energy change > 12 kcal/mol) were identified to significantly promote loss of miRNA-mRNA binding. By integrating mRNA expression profiles of 21 cancer types, we found that the expression of target genes was positively correlated with the loss of absolute affinity level and negatively correlated with the gain of absolute affinity level. Functional enrichment analysis revealed that genes carrying funcMutations were significantly enriched in the MAPK and WNT signaling pathways, and analysis of regulatory modules identified eighteen miRNA modules involved with similar cellular functions. Our findings elucidate a complex relationship between miRNA, mRNA, and mutations, and suggest that 3′UTR mutations may play an important role in tumor development.

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3131 ONCOSTREAMS: NOVEL DYNAMICS PATHOLOGICAL MULTICELLULAR STRUCTURES INVOLVED IN GLIOBLATOMA GROWTH AND INVASION

Journal of Clinical and Translational Science ◽

10.1017/cts.2019.253 ◽

2019 ◽

Vol 3 (s1) ◽

pp. 111-111 ◽

Cited By ~ 2

Author(s):

Andrea Comba ◽

Patrick Dunn ◽

Anna E Argento ◽

Padma Kadiyala ◽

Sebastien Motsch ◽

...

Keyword(s):

Extracellular Matrix ◽

Target Genes ◽

Collective Motion ◽

Malignant Tumors ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Genetically Engineered ◽

Functional Enrichment ◽

Low Grade ◽

Normal Brain

OBJECTIVES/SPECIFIC AIMS: Oncostreams represent a novel growth pattern of GBM. In this study we uncovered the cellular and molecular mechanism that regulates the oncostreams function in GBM growth and invasion. METHODS/STUDY POPULATION: We studied oncostreams organization and function using genetically engineered mouse gliomas models (GEMM), mouse primary patient derived GBM model and human glioma biopsies. We evaluated the molecular landscape of oncostreams by laser capture microdissection (LCM) followed by RNA-Sequencing and bioinformatics analysis. RESULTS/ANTICIPATED RESULTS: Oncostreams are multicellular structures of 10-20 cells wide and 2-400 μm long. They are distributed throughout the tumors in mouse and human GBM. Oncostreams are heterogeneous structures positive for GFAP, Nestin, Olig2 and Iba1 cells and negative for Neurofilament. Using GEMM we found a negative correlation between oncostream density and animal survival. Moreover, examination of patient’s glioma biopsies evidenced that oncostreams are present in high grade but no in low grade gliomas. This suggests that oncostreams may play a role in tumor malignancy. Our data also indicated that oncostreams aid local invasion of normal brain. Transcriptome analysis of oncostreams revealed 43 differentially expressed (DE) genes. Functional enrichment analysis of DE genes showed that “collagen catabolic processes”, “positive regulation of cell migration”, and “extracellular matrix organization” were the most over-represented GO biological process. Network analysis indicated that Col1a1, ACTA2, MMP9 and MMP10 are primary target genes. These genes were also overexpressed in more malignant tumors (WT-IDH) compared to the less malignant (IDH1- R132H) tumors. Confocal time lapse imagining of 3D tumor slices demonstrated that oncostreams display a collective motion pattern within gliomas that has not been seen before. DISCUSSION/SIGNIFICANCE OF IMPACT: In summary, oncostreams are anatomically and molecularly distinctive, regulate glioma growth and invasion, display collective motion and are regulated by the extracellular matrix. We propose oncostreams as novel pathological markers valuable for diagnosis, prognosis and designing therapeutics for GBM patients.

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MISIM v2.0: a web server for inferring microRNA functional similarity based on microRNA-disease associations

Nucleic Acids Research ◽

10.1093/nar/gkz328 ◽

2019 ◽

Vol 47 (W1) ◽

pp. W536-W541 ◽

Cited By ~ 12

Author(s):

Jianwei Li ◽

Shan Zhang ◽

Yanping Wan ◽

Yingshu Zhao ◽

Jiangcheng Shi ◽

...

Keyword(s):

Web Server ◽

Enrichment Analysis ◽

Fold Increase ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Rna Molecules ◽

Novel Mirna ◽

Non Coding Rna ◽

Disease Associations ◽

Data Content

Abstract MicroRNAs (miRNAs) are one class of important small non-coding RNA molecules and play critical roles in health and disease. Therefore, it is important and necessary to evaluate the functional relationship of miRNAs and then predict novel miRNA-disease associations. For this purpose, here we developed the updated web server MISIM (miRNA similarity) v2.0. Besides a 3-fold increase in data content compared with MISIM v1.0, MISIM v2.0 improved the original MISIM algorithm by implementing both positive and negative miRNA-disease associations. That is, the MISIM v2.0 scores could be positive or negative, whereas MISIM v1.0 only produced positive scores. Moreover, MISIM v2.0 achieved an algorithm for novel miRNA-disease prediction based on MISIM v2.0 scores. Finally, MISIM v2.0 provided network visualization and functional enrichment analysis for functionally paired miRNAs. The MISIM v2.0 web server is freely accessible at http://www.lirmed.com/misim/.

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Downregulation of miRNA-205 Expression and Biological Mechanism in Prostate Cancer Tumorigenesis and Bone Metastasis

BioMed Research International ◽

10.1155/2020/6037434 ◽

2020 ◽

Vol 2020 ◽

pp. 1-17

Author(s):

Yu Sun ◽

Sheng-Hua Li ◽

Ji-Wen Cheng ◽

Gang Chen ◽

Zhi-Guang Huang ◽

...

Keyword(s):

Prostate Cancer ◽

Bone Metastasis ◽

Protein Level ◽

Target Genes ◽

Mrna Level ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Forest Plot ◽

Biological Mechanism

Background. The expression and mechanism of microRNA-205 (miRNA-205) in prostate cancer (PCa) and its bone metastasis remain controversial. Materials and Methods. The expression and discriminating capability of miRNA-205 were assessed by drawing a forest plot and a summarized receiver operating characteristic (SROC) curve, using data available from 27 miRNA-array and miRNA-sequencing datasets. The miRNA-205 target genes were acquired from online prediction tools, differentially upregulated genes in PCa, and differentially expressed genes (DEGs) after miRNA-205 transfection into PCa cell lines. Functional enrichment analysis was conducted to explore the biological mechanism of miRNA-205 targets. Immunohistochemistry (IHC) was applied to verify the protein level of the hub gene. Results. The expression of miRNA-205 in the PCa group (1,461 samples) was significantly lower than that in the noncancer group (510 samples), and the downregulation of miRNA-205 showed excellent sensitivity and specificity in differentiating between the two groups. In bone metastatic PCa, the miRNA-205 level was further reduced than in nonbone metastatic PCa, and it showed a good capability in distinguishing between the two groups. In total, 153 miRNA-205 targets were screened through the three aforementioned methods. Based on the results of functional enrichment analysis, the targets of miRNA-205 were mainly enriched during chromosome segregation and phospholipid-translocating ATPase activity and in the spindle microtubule and the p53 signaling pathway. CDK1 had the highest connectivity in the PPI network analysis and was screened as one of the hub genes. A statistically significant negative correlation between miRNA-205 and CDK1 was observed. The expression of CDK1 in PCa samples was pronouncedly upregulated in terms of both the mRNA level and the protein level when compared with noncancer samples. Conclusion. miRNA-205 may play a vital role in PCa tumorigenesis and bone metastasis by targeting CDK1.

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System Analysis of MIRNAs in Maize Internode Elongation

Biomolecules ◽

10.3390/biom9090417 ◽

2019 ◽

Vol 9 (9) ◽

pp. 417

Author(s):

Chuanxi Peng ◽

Xing Wang ◽

Tianyu Feng ◽

Rui He ◽

Mingcai Zhang ◽

...

Keyword(s):

Target Genes ◽

System Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Internode Elongation ◽

Differentially Expressed Mirnas ◽

Post Transcriptional Regulation

MicroRNAs (miRNAs), the post-transcriptional gene regulators, are known to play an important role in plant development. The identification of differentially expressed miRNAs could better help us understand the post-transcriptional regulation that occurs during maize internode elongation. Accordingly, we compared the expression of MIRNAs between fixed internode and elongation internode samples and classified six differentially expressed MIRNAs as internode elongation-responsive miRNAs including zma-MIR160c, zma-MIR164b, zma-MIR164c, zma-MIR168a, zma-MIR396f, and zma-MIR398b, which target mRNAs supported by transcriptome sequencing. Functional enrichment analysis for predictive target genes showed that these miRNAs were involved in the development of internode elongation by regulating the genes respond to hormone signaling. To further reveal how miRNA affects internode elongation by affecting target genes, the miRNA–mRNA–PPI (protein and protein interaction) network was constructed to summarize the interaction of miRNAs and these target genes. Our results indicate that miRNAs regulate internode elongation in maize by targeting genes related to cell expansion, cell wall synthesis, transcription, and regulatory factors.

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Circular RNA screening identifies circMYLK4 as a regulator of fast/slow myofibers in porcine skeletal muscles

10.21203/rs.3.rs-62413/v1 ◽

2020 ◽

Author(s):

Haigang Cao ◽

Jieming Liu ◽

Tianning Du ◽

Yihao Liu ◽

Xiaoyu Zhang ◽

...

Keyword(s):

Muscle Development ◽

Target Genes ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Circular Rna ◽

Functional Enrichment ◽

Differentially Expressed ◽

Marker Genes ◽

Type Conversion ◽

Myofiber Type

Abstract Background: The myofiber type is related to the quality of meat; specifically, slow-oxidized myofiber helps to increase the tenderness and juiciness of meat. An increasing number of studies have shown that circRNAs play a key role in skeletal muscle development. However, the key circRNAs that regulate myofiber types and their roles are still poorly understood.Results: A total of 40757 circRNAs were identified from the longissimus dorsi (LD) and the soleus (Sol) muscles, of which 10388 were co-expressed in the two muscles. Further analysis found 181 differentially expressed circRNAs in the LD compared with Sol. Functional enrichment analysis showed that target genes of differentially expressed circRNA-sponge miRNAs were enriched in the AMPK, FoxO and PI3K-Akt signaling pathways. In addition, we focused on a novel circRNA—circMYLK4. CircMYLK4 significantly increased the mRNA and protein levels of slow muscle marker genes and caused the flesh to turn red.Conclusion: Our study laid an essential foundation for further research on circRNAs in myofiber type conversion and the achievement of higher meat quality.

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Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks

Nucleic Acids Research ◽

10.1093/nar/gkz332 ◽

2019 ◽

Vol 47 (W1) ◽

pp. W206-W211 ◽

Cited By ~ 15

Author(s):

Shaojuan Li ◽

Changxin Wan ◽

Rongbin Zheng ◽

Jingyu Fan ◽

Xin Dong ◽

...

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Transcription Factor ◽

Target Genes ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Differential Gene ◽

Direct Target ◽

Human And Mouse

AbstractCharacterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate the TF’s biological role. Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data. Cistrome-GO is freely available at http://go.cistrome.org/.

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131 GENE SILENCING IN BOVINE ZYGOTES: SIRNA TRANSFECTION v. MICROINJECTION

Reproduction Fertility and Development ◽

10.1071/rdv22n1ab131 ◽

2010 ◽

Vol 22 (1) ◽

pp. 224 ◽

Cited By ~ 1

Author(s):

C. M. O'Meara ◽

J. D. Murray ◽

J. F. Roche ◽

S. Mamo ◽

E. Gallagher ◽

...

Keyword(s):

Gene Silencing ◽

Embryo Development ◽

Relative Abundance ◽

Gene Function ◽

Developmental Stages ◽

Analysis Data ◽

Blastocyst Stage ◽

Cell Stage ◽

E Cadherin

Ribonucleic acid interference (RNAi) has become an effective tool for studying gene function in a variety of cells. The objective of this study was to compare the efficiency of gene silencing when siRNA were introduced into bovine zygotes by microinjection (as done previously; Tesfaye D et al. 2007 Mol. Reprod. Dev. 74, 978-988) v. a novel method of transfection in terms of gene knockdown and embryo development. For microin-jection, in vitro-produced bovine zygotes (16 h post insemination) were randomly assigned to 1 of 3 groups over 2 experiments. In Experiment 1, E-cadherin siRNA was injected at 100 μM (n = 168) and compared with PBS-injected (n = 180) and noninjected controls (n = 152). In Experiment 2, E-cadherin siRNA was injected at 375 μM (n = 154) and compared with PBS-injected (n = 136) and noninjected controls (n = 151). Embryos were subsequently cultured in vitro until Day 7 (day of IVF = Day 0). For transfection, the zona pellucida was removed from in vitro-produced zygotes. Zona-free zygotes were randomly assigned to 1 of 4 groups (i) GAPDH (n = 67), (ii) scrambled (n = 66), (iii) E-cadherin (n = 69) siRNA treatments at 100 nM or (iv) nontransfected controls (n = 66). Zygotes were incubated in transfection medium with siRNA for 1 h at 39°C, cultured individually in the well-of-the-well system to Day 7. The proportion of zygotes undergoing cleavage and developing to the blastocyst stage was recorded, and Day 7 embryos were frozen individually for mRNA analysis. Data for mRNA expression were fitted to a general linear model, and developmental stages were tested using ANOVA. Microinjection of 100 μM E-cadherin siRNA had no effect on phenotype (P > 0.05). Injection of PBS or 375 μM E-cadherin siRNA resulted in a decrease in the number of embryos reaching the 8-cell stage (51.5%, 45.5%, and 62.9%, respectively) and blastocyst stage (39.0%, 32.5%, and 45%, respectively) compared with noninjected controls (P < 0.05). The mRNA abundance of the target gene was suppressed by 36 and 46% when siRNA targeting E-cadherin was injected at 100 μM and 375 μM compared with control and PBS-injected groups (P < 0.05). Transfection with E-cadherin siRNA decreased development of 8-cell embryos (20.3 v. 53.0%, respectively) and blastocysts (7.2 v. 18.2%, respectively) compared with controls (P < 0.05). The mRNA relative abundance was not different between controls (nontransfected, or transfected with GAPDH or scrambled siRNA). However, transfection of zygotes with 100nM E-cadherin siRNA led to a 70% reduction in E-cadherin mRNA relative abundance in Day 7 blastocysts compared with controls (P < 0.05). Zona removal and transfection resulted in decreased embryo development compared with microinjection (P < 0.05). However, transfection yielded more efficient gene silencing of E-cadherin mRNA with reduced embryo development compared with microinjection. This technique of gene silencing could improve the efficiency of gene function studies in early bovine embryogenesis. Supported by Science Foundation Ireland.

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