High-throughput Analysis of CircRNA in Cows with Naturally Infected Staphylococcus aureus Mammary Gland

Abstract Circular RNAs (CircRNA) is a special type of non-coding RNA molecule with a closed ring structure and is not affected by RNA exonucases. It has stable expression and is not easy to degrade, and exists in most eukaryotes. However, circRNA regulation of cow mastitis has not been widely recognized. Mammary epithelial tissues were collected from healthy Holstein cows (HCN) and mastitis Holstein cows (HCU). RNA sequencing (RNA SEQ) was performed for the differentially expressed circRNAs, and analysis results showed that 19 differentially expressed circRNAs were identified in HCN and HCU, among which 6 circRNAs were up-regulated and 13 circRNAs were down-regulated. We randomly selected 9 circRNAs for Q-PCR verification, and the results showed consistent expression. Three circRNAs: circRNA2860, circRNA5323 and circRNA4027 were confirmed to be significantly differentially expressed circRNAs in cow mastitis. Furthermore, RNA polymerase transcription factor binding and tight junction are most enriched in GO and KEGG pathways, respectively. In addition, the regulatory network of circRNA-miRNA has been inferred from a bioinformatics perspective, which may help to understand the underlying molecular mechanism of circRNAs involved in regulating mastitis in cows.

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Machine learning reduced gene/non-coding RNA features that classify Schizophrenia patients accurately and highlight insightful gene clusters

10.1101/2020.06.08.20125906 ◽

2020 ◽

Author(s):

Yichuan Liu ◽

Hui-Qi Qu ◽

Xiao Chang ◽

Lifeng Tian ◽

Joseph Glessner ◽

...

Keyword(s):

Machine Learning ◽

Neurodevelopmental Disorder ◽

Wnt Signaling Pathway ◽

Gene Clusters ◽

Differentially Expressed ◽

Cell Junction ◽

Mrna Levels ◽

Rna Seq ◽

Non Coding Rna ◽

Non Coding Rnas

AbstractSchizophrenia (SCZ) is a chronic and severely disabling neurodevelopmental disorder that affects people worldwide. RNA-seq has been a powerful method to detect the differentially expressed genes/non-coding RNAs in patients; however, due to overfitting problems differentially expressed targets (DETs) cannot be used properly as biomarkers. In this study, dorsolateral prefrontal cortex (dlpfc) RNA-seq data from 254 individuals’ was obtained from the CommonMind consortium and analyzed with machine learning methods, including random forest, forward feature selection (ffs), and factor analysis, to reduce the numbers of gene/non-coding RNA feature vectors to overcome overfitting problem and explore involved functional clusters. In 2-fold shuffle testing, the average predictive accuracy for SCZ patients was 67% based on coding genes, and the 96% based on long non-coding RNAs (lncRNAs). Coding genes were further clustered into 14 factors and lncRNAs were clustered into 45 factors to represent the underlying features. The largest contribution factor for coding genes contains number of genes critical in neurodevelopment and previously reported in relation with various brain disorders. Genomic loci of lncRNAs were more insightful, enriched for genes critical in synapse function (p=7.3E-3), cell junction (p=0.017), neuron differentiation (p=8.3E-3), phosphorylation (8.2E-4), and involving the Wnt signaling pathway (p=0.029). Taken together, machine learning is a powerful algorithm to reduce functional biomarkers in SCZ patients. The lncRNAs capture the characteristics of SCZ tissue more accurately than mRNA as the formers regulate every level of gene expression, not limited to mRNA levels.

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Identification and Characterization of Circular RNAs in Longissimus Dorsi Muscle Tissue from Two Goat Breeds using RNA-Seq

10.21203/rs.3.rs-944970/v1 ◽

2021 ◽

Author(s):

Jiyuan Shen ◽

Huimin Zhen ◽

Lu Li ◽

Yuting Zhang ◽

Jiqing Wang ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Fiber ◽

Muscle Development ◽

Production Performance ◽

Differentially Expressed ◽

Circular Rnas ◽

Longissimus Dorsi ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Fiber Size

Abstract Background: Circular RNAs (circRNAs) are a class of non-coding RNA that play crucial roles in the development of skeletal muscle. However, little is known about the role of circRNAs in caprine skeletal muscle. In this study, the muscle fiber size and expression profiles of circRNAs were compared in Longissimus dorsi muscle of Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotypic differences in meat production performance, using hematoxylin and eosin staining and RNA-Seq, respectively.Results: The muscle fiber size in LC goats were larger than those in ZB goats (P < 0.05). A total of 10,875 circRNAs were identified and 214 of these were differentially expressed between the two caprine breeds. The authentication and expression levels of 20 circRNAs were confirmed using reverse transcriptase-polymerase chain reaction (RT-PCR) and DNA sequencing. The parent genes of differentially expressed circRNAs were mainly enriched in connective tissue development, Rap1, cGMP-PKG, cAMP and Ras signaling pathway. Some miRNAs reportedly associated with skeletal muscle development and intramuscular fat deposition would be targeted by several differentially expressed circRNAs and the most highly expressed circRNA (circ_001086).Conclusion: These results provide an improved understanding of the functions of circRNAs in skeletal muscle development of goats.

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

Animals ◽

10.3390/ani10091565 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1565

Author(s):

Zhiyun Hao ◽

Yuzhu Luo ◽

Jiqing Wang ◽

Jiang Hu ◽

Xiu Liu ◽

...

Keyword(s):

Mammary Gland ◽

Signaling Pathway ◽

Target Genes ◽

Mammary Epithelial Cells ◽

Expression Profiles ◽

Wnt Signaling Pathway ◽

Mammary Epithelial ◽

Differentially Expressed ◽

Rna Seq ◽

Non Coding Rnas

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

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Identification of Non-coding RNA Biomarkers in Stress-induced Depression via Comprehensive Analysis of Competing Endogenous RNA Network

10.21203/rs.3.rs-100243/v1 ◽

2020 ◽

Author(s):

xuanjun liu ◽

Lan Yan ◽

Chun Lin ◽

Yiliang Zhang ◽

Haofei Miao ◽

...

Keyword(s):

Molecular Mechanisms ◽

Comprehensive Analysis ◽

Differentially Expressed ◽

Psychiatric Disease ◽

Circular Rnas ◽

Messenger Rnas ◽

Competing Endogenous Rna ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Promising Perspective

Abstract BackgroundDepression is one of the most common psychiatric disease worldwide. Although the research about the pathogenesis of depression have achieved progress, the detailed effect of non-coding RNAs (ncRNAs) in depression are still not clearly elucidated. This study was aimed to identify non-coding RNA biomarkers in stress-induced depression via comprehensive analysis of competing endogenous RNA networkMethodsIn this present study, we acquired RNA expression from RNA seq expression profile in three mice with depressive-like behaviors using chronic restraint stress paradigm and three C57BL/6J wild-type mice as control mice. ResultsA total of 41 differentially expressed circular RNAs (circRNAs) and 181 differentially expressed messenger RNAs (mRNAs) were up-regulated, and 65 differentially expressed circRNAs and 289 differentially expressed mRNAs were down-regulated, which were selected by a threshold of fold change ≥2 and a p-value < 0.05. Gene Ontology was performed to analyze the biological functions, and we predicted potential signaling pathways based on Kyoto Encyclopedia of Genes and Genomes pathway database. In addition, we constructed a circRNA-microRNA (miRNA)-mRNA regulatory network to further identify non-coding RNAs biomarkers. ConclusionsOur findings provide a promising perspective for further research into molecular mechanisms of depression, and targeting circRNA -mediated competing endogenous RNA (ceRNA) network is a useful strategy to early recognize the depression.

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RNA-Seq Profiling of Circular RNAs During Development of Hindgut in Rat Embryos With Ethylenethiourea-Induced Anorectal Malformations

Frontiers in Genetics ◽

10.3389/fgene.2021.605015 ◽

2021 ◽

Vol 12 ◽

Author(s):

Si Ying Li ◽

Chen Yi Wang ◽

Yun Xia Xiao ◽

Xiao Bing Tang ◽

Zheng Wei Yuan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Transforming Growth Factor ◽

Quantitative Polymerase Chain Reaction ◽

Anorectal Malformations ◽

Normal Group ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Circular Rnas ◽

Rna Seq ◽

Pregnant Rats

Anorectal malformations (ARMs) are among the most common congenital terminal digestive tract malformations. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play roles in the development of the digestive system; however, their contributions to the pathogenesis of ARMs are not well-established. In this study, we explored the mechanism underlying ethylenethiourea (ETU)-induced ARMs by profiling circRNA expression via RNA-seq and constructing a regulatory circRNA-miRNA-mRNA network. Nine pregnant rats were gavage-fed a single dose of 125 mg/kg 1% ETU (ARM group) on gestational day 10 (GD10), and another 9 pregnant rats received a similar dose of saline (normal group) as a control. Embryos were obtained by cesarean section on the key time-points of anorectal development (GD14, GD15, and GD16). Hindgut samples isolated from the fetuses were evaluated by high-throughput sequencing and differentially expressed circRNAs were validated by reverse transcription-quantitative polymerase chain reaction, agarose gel electrophoresis, and Sanger cloning and sequencing. A total of 18295 circRNAs were identified in the normal and ARM groups. Based on the 425 differentially expressed circRNAs (|Fc| > 2, p < 0.05), circRNA-miRNA and miRNA-mRNA pairs were predicted using miREAP, miRanda, and TargetScan. A total of 55 circRNAs (14 up- and 41 downregulated in the ARM group compared to the normal group) were predicted to bind to 195 miRNAs and 947 mRNAs. Competing endogenous RNA networks and a Kyoto Encyclopedia of Genes and Genomes analysis revealed that novel_circ_001042 had the greatest connectivity and was closely related to ARM-associated signaling pathways, such as the Wingless Type MMTV integration site family, mitogen-activated protein kinase, and transforming growth factor-β pathways. These results provide original insight into the roles of circRNAs in ARMs and provide a valuable resource for further analyses of molecular mechanisms and signaling networks.

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Super-enhancer Associated Long Non-coding RNA AC005592.2 Promotes Tumor Progression by Regulating OLFM4 in Colorectal Cancer

10.21203/rs.3.rs-60449/v1 ◽

2020 ◽

Author(s):

Linping Yan ◽

Huanhuan Chen ◽

Li Tang ◽

Pan Jiang ◽

Feng Yan

Keyword(s):

Colorectal Cancer ◽

Biological Effects ◽

Differentially Expressed ◽

Rna Seq ◽

Invasion And Migration ◽

Super Enhancer ◽

Non Coding Rna ◽

Attractive Therapeutic Target ◽

And Migration ◽

Long Non Coding Rna

Abstract Background: Super-enhancer-associated long non-coding RNAs (SE-lncRNAs) have been reported to play essential roles in tumorigenesis, but the fundamental mechanism of SE-lncRNAs in colorectal cancer (CRC) remains largely unknown. Methods: A microarray was performed to identify the differentially expressed SE-lncRNAs between CRC tissues and peritumoral tissues. A novel SE-lncRNA AC005592.2 was selected from these differentially expressed SE-lncRNAs to explore its effects in the CRC development. Fluorescence quantitative real-time PCR (qRT-PCR) was used to assay the expression of AC005592.2 in CRC tissues and cell lines. Functional assays were applied to identify the biological effects of AC005592.2 in CRC cells. Furthermore, RNA-seq was employed to predict potential targets of AC005592.2. Results: AC005592.2 was significantly increased in CRC tissues and cells. And the high expression of AC005592.2 was significantly associated with TNM stage and tumor differentiation of CRC patients. Knockdown of AC005592.2 suppressed CRC cell proliferation, invasion and migration, but promoted apoptosis, while AC005592.2 overexpression exerted precisely the opposite effects on CRC cells. Besides, AC005592.2 positively regulated the expression of olfactomedin 4 (OLFM4), which was also up-regulation in CRC tissues. Conclusion: The findings suggested that AC005592.2 is a crucial promoter of CRC progression, and may serve as an attractive therapeutic target for CRC.

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Comprehensive Analysis of Differentially Expressed mRNA, Non-coding RNA, and Their Competitive Endogenous RNA Network of Pacific Oyster Crassostrea gigas With Different Glycogen Content Between Different Environments

Frontiers in Marine Science ◽

10.3389/fmars.2021.725628 ◽

2021 ◽

Vol 8 ◽

Author(s):

Xue Wang ◽

Weijun Wang ◽

Zan Li ◽

Guohua Sun ◽

Tao Xu ◽

...

Keyword(s):

Environmental Factors ◽

Signaling Pathway ◽

Crassostrea Gigas ◽

Glycogen Content ◽

Pacific Oyster ◽

Functional Enrichment ◽

Differentially Expressed ◽

Rna Seq ◽

Non Coding Rna ◽

Huanghai Sea

Glycogen content is a quantitative trait, its phenotype differences are found between individual oysters due to genetic effects and environmental factors which were including food, water temperature, salinity, and so on. In this study, a full sibling family of Pacific oyster Crassostrea gigas showed different phenotypes with high and low glycogen content between South Huanghai Sea (Rizhao offshore area, RZ) and North Huanghai Sea (Kongtong Dao area, KTD), respectively. At the same time, the content of 11 glucogenic amino acids and 13 fatty acids were also significant differences between RZ and KTD. RNA-seq and small RNA-seq technologies were used for transcriptome sequencing and functional enrichment analysis of differentially expressed RNA were used by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. A total of 2,084 mRNAs, 1,080 long non-coding RNAs (lncRNAs), 34 circular RNAs (circRNAs), and 7 microRNAs (miRNAs) were differentially expressed. Based on these differentially expressed genes (DEGs), miRNA target interactions (lncRNA/circRNA–miRNA pairs and miRNA–mRNA pairs) were predicted using the miRanda software. The differentially expressed mRNAs in this network were mainly shown to be involved in calcium signaling pathway and insulin signaling pathway. These findings could help to speculate that environmental factors may be epigenetically regulated by non-coding RNA in C. gigas, thereby further affecting glycogen content.

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Identification of circular RNAs in the immature and mature rat anterior pituitary

Journal of Endocrinology ◽

10.1530/joe-18-0540 ◽

2019 ◽

Vol 240 (3) ◽

pp. 393-402 ◽

Cited By ~ 1

Author(s):

Dong-Xu Han ◽

Chang-Jiang Wang ◽

Xu-Lei Sun ◽

Jian-Bo Liu ◽

Hao Jiang ◽

...

Keyword(s):

Pituitary Adenomas ◽

Anterior Pituitary ◽

Differentially Expressed ◽

Circular Rnas ◽

Illumina Platform ◽

Immature Rat ◽

Kegg Pathways ◽

New Class ◽

Rat Pituitary ◽

Mirna Sponges

Circular RNAs (circRNAs) are a new class of RNA that have a stable structure characterized by covalently closed circular molecules and are involved in invasive pituitary adenomas and recurrent clinically nonfunctioning pituitary adenomas. However, information on circRNAs in the normal pituitary, especially in rats, is limited. In this study, we identified 4123 circRNAs in the immature (D15) and mature (D120) rat anterior pituitary using the Illumina platform, and 32 differentially expressed circRNAs were found. A total of 150 Gene Ontology terms were significantly enriched, and 16 KEGG pathways were found to contain differentially expressed genes. Moreover, we randomly selected eight highly expressed circRNAs and detected their relative expression levels in the mature and immature rat pituitary by qPCR. In addition, we predicted 90 interactions between 53 circRNAs and 57 miRNAs using miRanda. Notably, circ_0000964 and circ_0001303 are potential miRNA sponges that may regulate the Fshb gene. The expression profile of circRNAs in the immature and mature rat anterior pituitary may provide more information about the roles of circRNAs in the development and reproduction in mammals.

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Insight of Transcriptional Regulators reveals the Tolerance Mechanism of Carpet-grass (Axonopus compressus) Against Drought

10.21203/rs.3.rs-41830/v4 ◽

2021 ◽

Author(s):

Mohsin Nawaz ◽

Liao Li ◽

Farrukh Azeem ◽

Samina Shabbir ◽

Ali Zohaib ◽

...

Keyword(s):

Drought Stress ◽

Perennial Grass ◽

Warm Season ◽

Transcriptional Response ◽

Differentially Expressed ◽

Rna Seq ◽

Kegg Pathways ◽

Public Data ◽

Validation Experiment ◽

Environmental Adaptations

Abstract Background: Carpet grass [Axonopus compressus (L.)] is an important warm-season perennial grass around the world and is known for its adaptability to varied environmental conditions. However, Carpet grass lacks enough data in public data banks, which confined our comprehension of the mechanisms of environmental adaptations, gene discovery, and development of molecular markers. In current study, the DEGs (differentially expressed genes) in Axonopus compressus under drought stress (DS) were identified and compared with CK (control) by RNA-Seq. Results: A total of 263,835 unigenes were identified in Axonopus compressus, and 201,303 (also added to the numbers of the remaining 2 databases) a sequence of unigenes significantly matched in at least one of the seven databases. A total of 153697 (58.25%) unigenes classified to 144 KEGG pathways, and 7,444 unigenes were expressed differentially between DS and CK, of which 4,249 were up-regulated and 3,195 were down-regulated unigenes. Of the 50 significantly enriched GO terms, 18, 6, and 14 items were related to BP, CC, and MF respectively. Analysis of KEGG enrichment revealed 2569 DEGs involved in 143 different pathways, under drought stress. 2,747 DEGs were up-regulated and 2,502 DEGs were down-regulated. Moreover, we identified 352 transcription factors (TFs) in Axonopus compressus, of which 270 were differentially expressed between CK and DS. The qRT-PCR validation experiment also supports the transcriptional response of Axonopus compressus against drought. Accuracy of transcriptome unigenes of Axonopus compressus was assessed with BLAST, which showed 3,300 sequences of Axonopus compressus in the NCBI.Conclusion: The 7,444 unigenes were found to be between DS and CK treatments, which indicate the existence of a strong mechanism of drought tolerance in Axonopus compressus. The current findings provide the first framework for further investigations for the particular roles of these unigenes in Axonopus compressus in response to drought.

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RNA-Seq Whole Transcriptome Analysis of Bovine Mammary Epithelial Cells in Response to Intracellular Staphylococcus aureus

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.00642 ◽

2020 ◽

Vol 7 ◽

Author(s):

Xiaozhou Wang ◽

Feng Su ◽

Xiaohui Yu ◽

Na Geng ◽

Liping Li ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Epithelial Cells ◽

Defense Mechanism ◽

Mammary Epithelial Cells ◽

Treated Group ◽

Mammary Epithelial ◽

Differentially Expressed ◽

Receptor Interaction ◽

Rna Seq ◽

Bovine Mammary Epithelial Cells

Staphylococcus aureus (S. aureus), a common mastitis pathogen widespread in the natural environment of dairy farms, is capable of invading mammary epithelial cells making treatment difficult. However, the mechanism of the response of bovine mammary epithelial cell to S. aureus invasion remains elusive. In this study, transcriptomic analysis and bioinformatics tools were applied to explore the differentially expressed RNAs in bovine mammary epithelial cells (bMECs) between the control and S. aureus-treated group. A total of 259 differentially expressed mRNAs (DEmRNAs), 27 differentially expressed microRNAs (DEmiRNAs), and 21 differentially expressed long non-coding RNAs (DElncRNAs) were found. These RNAs mainly enrich the inflammatory response, immune response, endocytosis, and cytokine-cytokine receptor interaction. qRT-PCR was used to analyze the quality of the RNA-seq results. In particular, to the defense mechanism of bovine mammary epithelial cells against intracellular S. aureus, the PPAR signaling pathway and the genes (ACOX2, CROT, and NUDT12) were found to be up-regulated to promote the production of peroxisomes and ROS, DRAM1 expression was also up-regulated to facilitate the activation of autophagy, indicating that the above mechanisms were involved in the elimination of intracellular S. aureus in bovine mammary epithelial cells.

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