scholarly journals Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse

2018 ◽  
Vol 2018 ◽  
pp. 1-13
Author(s):  
Minjung Kim ◽  
Youngseok Yu ◽  
Ji-Hoi Moon ◽  
InSong Koh ◽  
Jae-Hyung Lee
Keyword(s):  
Noncoding Rna ◽  
Osteoblast Differentiation ◽  
Enrichment Analysis ◽  
Osteoblastic Differentiation ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Fuzzy C Means Clustering ◽  
Differentiation Stage ◽  
And Function ◽  
Differential Expression Profiling

Long noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets obtained for 18 days in two-day intervals from neonatal mouse calvarial pre-osteoblast-like cells. Over the course of osteoblast differentiation, 4058 mRNAs and 3948 lncRNAs were differentially expressed, and they were grouped into 12 clusters according to the expression pattern by fuzzy c-means clustering. Using weighted gene coexpression network analysis, we identified 9 modules related to the early differentiation stage (days 2–8) and 7 modules related to the late differentiation stage (days 10–18). Gene ontology and KEGG pathway enrichment analysis revealed that the mRNA and lncRNA upregulated in the late differentiation stage are highly associated with osteogenesis. We also identified 72 mRNA and 89 lncRNAs as potential markers including several novel markers for osteoblast differentiation and activation. Our findings provide a valuable resource for mouse lncRNA study and improves our understanding of the biology of osteoblastic differentiation in mice.

scholarly journals Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu
Keyword(s):  
Pineal Gland ◽  
Expression Pattern ◽  
Noncoding Rna ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Important Regulator ◽  
Gsh Metabolism ◽  
Transcriptome Expression

Abstract Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

scholarly journals Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq

2014 ◽  
Author(s):  
Mar Gonzàlez-Porta ◽  
Alvis Brazma
Keyword(s):  
Enrichment Analysis ◽  
R Package ◽  
Third Party ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Differential Splicing ◽  
Protein Coding ◽  
Downstream Analysis ◽  
Intuitive Manner ◽  
Abundant Transcript

In the past years, RNA sequencing has become the method of choice for the study of transcriptome composition. When working with this type of data, several tools exist to quantify differences in splicing across conditions and to address the significance of those changes. However, the number of genes predicted to undergo differential splicing is often high, and further interpretation of the results becomes a challenging task. Here we present SwitchSeq, a novel set of tools designed to help the users in the interpretation of differential splicing events that affect protein coding genes. More specifically, we provide a framework to identify switch events, i.e., cases where, for a given gene, the identity of the most abundant transcript changes across conditions. The identified events are then annotated by incorporating information from several public databases and third-party tools, and are further visualised in an intuitive manner with the independent R package tviz. All the results are displayed in a self-contained HTML document, and are also stored in txt and json format to facilitate the integration with any further downstream analysis tools. Such analysis approach can be used complementarily to Gene Ontology and pathway enrichment analysis, and can also serve as an aid in the validation of predicted changes in mRNA and protein abundance. The latest version of SwitchSeq, including installation instructions and use cases, can be found at https://github.com/mgonzalezporta/SwitchSeq. Additionally, the plot capabilities are provided as an independent R package at https://github.com/mgonzalezporta/tviz.

scholarly journals Transcriptome Analyses Revealed Adaptive-Responses in Livers of Mice Treated With Hua-Feng-Dan and Its “Guide Drug” Yaomu

2021 ◽  
Author(s):  
Jia-Jia Liu ◽  
Ya Zhang ◽  
Shang-Fu Xu ◽  
Feng Zhang ◽  
Jing-Shan Shi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Toxicity ◽  
Cholesterol Metabolism ◽  
Enrichment Analysis ◽  
Stroke Recovery ◽  
Pathway Enrichment Analysis ◽  
High Dose ◽  
Hepatic Gene Expression ◽  
Rna Seq ◽  
Adaptive Responses

Abstract BackgroundHua-Feng-Dan is a patent Chinese medicine for stroke recovery and is effective against Parkinson’s disease models with modulatory effects on gut microbiota, but its effects on hepatic gene expression are unknown. This study used RNA-Seq to profile hepatic gene expression by Hua-Feng-Dan and its “Guide Drug” Yaomu.MethodsMice received orally Hua-Feng-Dan 1.2 g/kg, Yaomu 0.1-0.3 g/kg, or vehicle for 7 days. Liver pathology was examined, and total RNA was isolated for RNA-Seq. The bioinformatics, including GO and KEGG pathway enrichment analysis, two-dimensional clustering, Ingenuity Pathways Analysis (IPA), and Illumina BaseSpace Correlation Engine were used to analyze differentially expressed genes (DEGs). qPCR was performed to verify selected genes.ResultsHua-Feng-Dan and Yaomu did not produce liver toxicity as evidenced by histopathology and serum ALT and AST. GO Enrichment revealed Hua-Feng-Dan affected lipid homeostasis, protein folding and cell adhesion. KEGG showed activated cholesterol metabolism, bile secretion and PPAR signaling pathways. DEGs were identified by DESeq2 with p < 0.05 compared to controls. Hua-Feng-Dan produced 806 DEGs, Yaomu-0.1 had 235, and Yaomu-0.3 had 92 DEGs. qPCR on selected genes largely verified RNA-Seq results. IPA upstream regulator analysis revealed activation of MAPK and adaptive responses. Yaomu-0.1 had similar effects, but Yaomu-0.3 had little effects. Hua-Feng-Dan-induced DEGs were highly correlated with the GEO database of chemical-induced adaptive transcriptome changes in the liver. ConclusionHua-Feng-Dan at clinical dose did not produce liver pathological changes but induced metabolic and signaling pathway activations. Low dose of its Guide Drug Yaomu produced similar changes to a lesser extent, but high dose of Yaomu had little effects. The effects of Hua-Feng-Dan on liver transcriptome changes may produce adaptive responses to program the liver to produce beneficial or detrimental (over-dosed) pharmacological effects.

scholarly journals ­Transcriptome profiling of non-climacteric ‘Yellow’ melon during ripening: insights on sugar metabolism

2020 ◽  
Author(s):  
Michelle Orane Schemberger ◽  
Marília Aparecida Stroka ◽  
Letícia Reis ◽  
Kamila Karoline de Souza Los ◽  
Gillize Aparecida Telles de Araujo ◽  
...  
Keyword(s):  
Cucumis Melo ◽  
Sugar Content ◽  
Sugar Metabolism ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Sucrose Metabolism ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Pathway Enrichment ◽  
Maturation Stages

Abstract Background: The non-climacteric ‘Yellow’ melon ( Cucumis melo , inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related pathways can contribute to the development of new field management and post-harvest practices, making it possible to deliver better quality fruits to consumers. Results: The RNA-seq associated with RT-qPCR analyses of four maturation stages were performed to identify important enzymes and pathways that are involved in the ripening profile of non-climacteric ‘Yellow’ melon fruit focusing on sugar metabolism. We identified 895 genes 10 days after pollination (DAP)-biased and 909 genes 40 DAP-biased. The KEGG pathway enrichment analysis of these differentially expressed (DE) genes revealed that ‘hormone signal transduction’, ‘carbon metabolism’, ‘sucrose metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘spliceosome’ were the most differentially regulated processes occurring during melon development. In the sucrose metabolism, five DE genes are up-regulated and twelve are down-regulated during fruit ripening. Conclusions: The results demonstrated important enzymes in the sugar pathway that are responsible for the sucrose content and maturation profile in non-climacteric ‘Yellow’ melon. New DE genes were first detected for melon in this study such as invertase inhibitor LIKE 3 ( CmINH3 ), trehalose phosphate phosphatase ( CmTPP1 ) and trehalose phosphate synthases ( CmTPS5 , CmTPS7 , CmTPS9 ). Furthermore, the results of the protein-protein network interaction demonstrated general characteristics of the transcriptome of young and full-ripe melon and provide new perspectives for the understanding of ripening.

scholarly journals ­Transcriptome profiling of non-climacteric ‘Yellow’ melon during ripening: insights on sugar metabolism

2020 ◽  
Author(s):  
Michelle Orane Schemberger ◽  
Marília Aparecida Stroka ◽  
Letícia Reis ◽  
Kamila Karoline de Souza Los ◽  
Gillize Aparecida Telles de Araujo ◽  
...  
Keyword(s):  
Cucumis Melo ◽  
Sugar Content ◽  
Sugar Metabolism ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Sucrose Metabolism ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Pathway Enrichment ◽  
Maturation Stages

Abstract Background: The non-climacteric ‘Yellow’ melon ( Cucumis melo , inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related pathways can contribute to the development of new field management and post-harvest practices, making it possible to deliver better quality fruits to consumers. Results: The RNA-seq associated with RT-qPCR analyses of four maturation stages were performed to identify important enzymes and pathways that are involved in the ripening profile of non-climacteric ‘Yellow’ melon fruit focusing on sugar metabolism. We identified 895 genes 10 days after pollination (DAP)-biased and 909 genes 40 DAP-biased. The KEGG pathway enrichment analysis of these differentially expressed (DE) genes revealed that ‘hormone signal transduction’, ‘carbon metabolism’, ‘sucrose metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘spliceosome’ were the most differentially regulated processes occurring during melon development. In the sucrose metabolism, five DE genes are up-regulated and twelve are down-regulated during fruit ripening. Conclusions: The results demonstrated important enzymes in the sugar pathway that are responsible for the sucrose content and maturation profile in non-climacteric ‘Yellow’ melon. New DE genes were first detected for melon in this study such as invertase inhibitor LIKE 3 ( CmINH3 ), trehalose phosphate phosphatase ( CmTPP1 ) and trehalose phosphate synthases ( CmTPS5 , CmTPS7 , CmTPS9 ). Furthermore, the results of the protein-protein network interaction demonstrated general characteristics of the transcriptome of young and full-ripe melon and provide new perspectives for the understanding of ripening.

scholarly journals Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

2020 ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu
Keyword(s):  
Pineal Gland ◽  
Expression Pattern ◽  
Noncoding Rna ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Important Regulator ◽  
Gsh Metabolism ◽  
Transcriptome Expression

Abstract Background: long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified.Results: Overall, 135 DE lncRNAs and 1,360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included.Conclusion: All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

scholarly journals Transcriptomics Analysis ofCandida albicansTreated with Huanglian Jiedu Decoction Using RNA-seq

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Qianqian Yang ◽  
Lei Gao ◽  
Maocan Tao ◽  
Zhe Chen ◽  
Xiaohong Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Antifungal Agents ◽  
Enrichment Analysis ◽  
Trichophyton Mentagrophytes ◽  
Inhibition Mechanism ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Genes Encoding ◽  
Life Threatening ◽  
Systemic Infections

Candida albicansis the major invasive fungal pathogen of humans, causing diseases ranging from superficial mucosal infections to disseminated, systemic infections that are often life-threatening. Resistance ofC. albicansto antifungal agents and limited antifungal agents has potentially serious implications for management of infections. As a famous multiherb prescription in China, Huanglian Jiedu Decoction (HLJJD,Orengedokutoin Japan) is efficient againstTrichophyton mentagrophytesandC. albicans. But the antifungal mechanism of HLJDD remains unclear. In this study, by using RNA-seq technique, we performed a transcriptomics analysis of gene expression changes forC. albicansunder the treatment of HLJDD. A total of 6057 predicted protein-encoding genes were identified. By gene expression analysis, we obtained a total of 735 differentially expressed genes (DEGs), including 700 upregulated genes and 35 downregulated genes. Genes encoding multidrug transporters such as ABC transporter and MFS transporter were identified to be significantly upregulated. Meanwhile, by pathway enrichment analysis, we identified 26 significant pathways, in which pathways of DNA replication and transporter activity were mainly involved. These results might provide insights for the inhibition mechanism of HLJDD againstC. albicans.

scholarly journals SAT0008 INDIVIDUAL FUNCTIONS OF THE HISTONE-ACETYLTRANSFERASES CBP AND P300 IN REGULATING THE INFLAMMATORY RESPONSE BY AFFECTING HISTONE ACETYLATION AND MRNA STABILITY

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 934.1-934
Author(s):  
M. Krosel ◽  
M. Gabathuler ◽  
K. Walker ◽  
M. Tomsic ◽  
O. Distler ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Signaling Pathway ◽  
Mrna Stability ◽  
Biological Process ◽  
Enrichment Analysis ◽  
Histone Acetyltransferases ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Research Support ◽  
Pathway Enrichment

Background:Prolonged TNF-induced H3K27 acetylation (H3K27ac) and increased mRNA stability in rheumatoid arthritis (RA) synovial fibroblasts (SF) are leading to a sustained inflammatory response. Underlying enzymes coordinately regulating these pathways have not been identified so far. The histone acetyltransferases cAMP-response element binding protein binding protein (CBP) and p300 are writers of activating H3K27ac marks and close homologues with widely accepted redundant functions.Objectives:To analyze individual functions of CBP and p300 in regulating the inflammatory response of RA SF.Methods:SF were isolated from patients with RA undergoing joint replacement surgery. The expression of CBP and p300 was silenced by transfection of antisense LNA gapmeRs (12.5 nM). SF were stimulated with TNF (10 ng/ml) for 24h. Actinomycin D (10 µg/ml) was added 4h after TNF-treatment for 2h and 4h (n=3) to test mRNA stability. Transcriptomes were determined by RNA-seq (Illumina NovaSeq 6000, n=6). We mapped raw reads from RNA-seq reference genome using STAR. Counts for genes were obtained using Feature counts. We searched for differential expression genes (DEG) across experimental conditions using general linear models (glm) implemented in ‘edgeR’ package of R. Significantly affected genes (± fold change > 1.5, FDR < 0.05, top 3000 genes included) entered pathway enrichment analysis for Gene Ontology (GO) biological process, and KEGG pathways in DAVID. Changes in the mRNA (n=12-14) and protein expression (n=6-12) were confirmed by quantitative Real-time PCR and ELISA. The levels of activating histone marks H3K27ac and nuclear localization of p50 and p65 were analyzed by Western blotting.Results:DEG revealed that silencing of p300 affected the expression of 6026 and 5138 genes in unstimulated and stimulated SF, respectively. In contrast, only 285 and 1911 genes were affected by CBP silencing in unstimulated and stimulated SF, respectively. In TNF-stimulated SF, pathway enrichment analysis of DEG revealed a key role of CBP in regulating the “type I interferon signaling pathway” (p=2.12x10-6). Both, silencing of CBP and p300 regulated genes enriched in the “TNF signaling pathway” (CBP: p=0.005; p300: p=0.031). In contrast to CBP silencing that had anti-inflammatory effects, silencing of p300 had pro-and anti-inflammatory effects. ELISA experiments suggested that silencing of CBP reduced the secretion of IL6 (p<0.01), CCL2, CXC3L1 (p<0.05), and CXCL12 (p<0.001). Silencing of p300 reduced the secretion of CCL2 (p<0.001) and CXC3L1 (p<0.05) but increased the expression of IL8 (p<0.001) and CXCL2 (p<0.05). Western blotting revealed that neither CBP, nor p300 silencing affected the nuclear expression of the NF-ĸB subunits p65 and p50. Silencing of p300 reduced the levels of H3K27ac by 30% in unstimulated SF, and by 61.4% (p<0.05) in presence of TNF. In addition to regulating H3K27ac, silencing of p300 regulated the expression of TNF-induced cytokines by increasing the mRNA stability of IL8, IL6 and CCL2 mRNA but not of CXCL2. Silencing of CBP reduced H3K27ac by 43.5% only in presence of TNF and did not affect TNF-induced mRNA stability of cytokines. This is in line with the enrichment of the GO biological process “regulation of mRNA stability” (p=2.61x10-8) being enriched only after silencing of p300.Conclusion:Our results suggested that p300 is the major writer for H3K27ac marks in SF. Additionally, p300 regulated cytokine expression by affecting mRNA stability in a target-specific manner. We identified overlapping and distinct functions for CBP and p300 in regulating the inflammatory response of SF.Disclosure of Interests:Monika Krosel: None declared, Marcel Gabathuler: None declared, Kellie Walker: None declared, Matija Tomsic: None declared, Oliver Distler Grant/research support from: Grants/Research support from Actelion, Bayer, Boehringer Ingelheim, Competitive Drug Development International Ltd. and Mitsubishi Tanabe; he also holds the issued Patent on mir-29 for the treatment of systemic sclerosis (US8247389, EP2331143)., Consultant of: Consultancy fees from Actelion, Acceleron Pharma, AnaMar, Bayer, Baecon Discovery, Blade Therapeutics, Boehringer, CSL Behring, Catenion, ChemomAb, Curzion Pharmaceuticals, Ergonex, Galapagos NV, GSK, Glenmark Pharmaceuticals, Inventiva, Italfarmaco, iQvia, medac, Medscape, Mitsubishi Tanabe Pharma, MSD, Roche, Sanofi and UCB, Speakers bureau: Speaker fees from Actelion, Bayer, Boehringer Ingelheim, Medscape, Pfizer and Roche, Caroline Ospelt Consultant of: Consultancy fees from Gilead Sciences., Kerstin Klein: None declared

scholarly journals Diagnosis of thyroid neoplasm using support vector machine algorithms based on platelet RNA-seq

Endocrine ◽  
2020 ◽  
Author(s):  
Yuling Shen ◽  
Yi Lai ◽  
Dong Xu ◽  
Le Xu ◽  
Lin Song ◽  
...  
Keyword(s):  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Thyroid Neoplasm ◽  
Support Vector ◽  
Pathway Enrichment Analysis ◽  
Papillary Thyroid ◽  
Rna Seq ◽  
Training Set ◽  
Pathway Enrichment ◽  
Validation Set

Abstract Objective To assess the capacity of support vector machine (SVM) algorithms that are developed based on platelet RNA-seq data in identifying thyroid neoplasm patients and differentiating patients with thyroid adenomas, papillary thyroid cancer and metastasized papillary thyroid cancer. Methods Platelets were collected and isolated from 109 patients and 63 healthy controls. RNA-seq was performed to find transcripts with differential levels. Genes corresponding to these altered transcripts were identified using R packages. All samples were subsampled into a training set and a validation set. Two SVM algorithms were developed and trained with the training set, using the genes with differential transcript levels (GDTLs) as classifiers, and validated with the validation set. GO and KEGG pathway enrichment analysis were performed using the R package clusterProfiler. Results We detected 765 GDTLs (442 up-regulated and 323 down-regulated) in platelets of patients and healthy controls. The algorithm identifying thyroid neoplasm patients achieved an accuracy of 97%, with an AUC (area under curve) of 0.998. The other algorithm differentiating patients with multiclass thyroid neoplasms had an average accuracy of 80.5%. GO analysis showed that GDTLs were strongly involved in biological processes such as neutrophil degranulation, neutrophil activation, autophagy and regulation of multi-organism process. KEGG pathway enrichment analysis revealed that GDTLs were mainly enriched in NOD-like receptor signaling pathway and pathways in endocytosis, osteoclast differentiation, human cytomegalovirus infection and tuberculosis. Conclusion Our results indicated that the combination of SVM algorithms and platelet RNA-seq data allowed for thyroid neoplasm diagnostics and multiclass thyroid neoplasm classification.

scholarly journals Identification of Candidate Circular RNAs Underlying Intramuscular Fat Content in the Donkey

2020 ◽  
Vol 11 ◽  
Author(s):  
Bojiang Li ◽  
Chunyu Feng ◽  
Shiyu Zhu ◽  
Junpeng Zhang ◽  
David M. Irwin ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Intramuscular Fat ◽  
Circular Rnas ◽  
Pathway Enrichment Analysis ◽  
Beta Oxidation ◽  
Longissimus Dorsi Muscle ◽  
And Function ◽  
Fatty Acid Beta Oxidation ◽  
Imf Content ◽  
Host Genes

Intramuscular fat (IMF) content is a crucial indicator of meat quality. Circular RNAs (circRNAs) are a large class of endogenous RNAs that are involved in many physiological processes. However, the expression and function of circRNA in IMF in the donkey remains unresolved. Here we performed an expression profiling of circRNAs in the donkey longissimus dorsi muscle and identified 12,727 candidate circRNAs. Among these, 70% were derived from the exons of protein genes. Furthermore, a total of 127 differentially expressed (DE) circRNAs were identified in high (H) and low (L) IMF content groups, including 63 upregulated and 64 downregulated circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the host genes of the DE circRNAs showed that the host genes were enriched in lipid metabolism related GO terms (e.g., fatty acid beta-oxidation using acyl-CoA dehydrogenase and MLL3/4 complex), and signaling pathways (e.g., TGF-beta and lysine degradation signaling pathway). Further analyses indicated that 127 DE circRNAs were predicted to potentially interact with miRNAs, leading to the construction of circRNA-miRNA regulatory network. Multiple circRNAs can potentially function as sponges of miRNAs that regulate the differentiation of adipocytes. Our results provide valuable expression profile information for circRNA in the donkey and new insight into the regulatory mechanisms of circRNAs in the regulation of IMF content.

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