Comprehensive Analysis of lncRNAs and circRNAs Reveals the Metabolic Specialization in Oxidative and Glycolytic Skeletal Muscles

The biochemical and functional differences between oxidative and glycolytic muscles could affect human muscle health and animal meat quality. However, present understanding of the epigenetic regulation with respect to lncRNAs and circRNAs is rudimentary. Here, porcine oxidative and glycolytic skeletal muscles, which were at the growth curve inflection point, were sampled to survey variant global expression of lncRNAs and circRNAs using RNA-seq. A total of 4046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including the oxidation-reduction process, glycolytic process, and fatty acid metabolic. All these were closely related to different phenotypes between oxidative and glycolytic muscles. Additionally, 810 circRNAs were identified, of which 137 were differentially expressed (p < 0.05). Interestingly, some circRNA-miRNA-mRNA networks were found, which were closely linked to muscle fiber-type switching and mitochondria biogenesis in muscles. Furthermore, 44.69%, 39.19%, and 54.01% of differentially expressed mRNAs, lncRNAs, and circRNAs respectively were significantly enriched in pig quantitative trait loci (QTL) regions for growth and meat quality traits. This study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological functions, which may improve understanding of muscle metabolism and development from an epigenetic perspective.

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Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy

Scientific Reports ◽

10.1038/s41598-021-96870-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Candice P. Chu ◽

Shiguang Liu ◽

Wenping Song ◽

Ethan Y. Xu ◽

Mary B. Nabity

Keyword(s):

Small Rna ◽

Target Genes ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Rna Seq ◽

Ckd Progression ◽

Critical Pathways ◽

Qrt Pcr ◽

Hereditary Nephropathy ◽

Differentially Expressed Mirnas

AbstractDogs with X-linked hereditary nephropathy (XLHN) are an animal model for Alport syndrome in humans and progressive chronic kidney disease (CKD). Using mRNA sequencing (mRNA-seq), we have characterized the gene expression profile affecting the progression of XLHN; however, the microRNA (miRNA, miR) expression remains unknown. With small RNA-seq and quantitative RT-PCR (qRT-PCR), we used 3 small RNA-seq analysis tools (QIAGEN OmicSoft Studio, miRDeep2, and CPSS 2.0) to profile differentially expressed renal miRNAs, top-ranked miRNA target genes, and enriched biological processes and pathways in CKD progression. Twenty-three kidney biopsies were collected from 5 dogs with XLHN and 4 age-matched, unaffected littermates at 3 clinical time points (T1: onset of proteinuria, T2: onset of azotemia, and T3: advanced azotemia). We identified up to 23 differentially expressed miRNAs at each clinical time point. Five miRNAs (miR-21, miR-146b, miR-802, miR-142, miR-147) were consistently upregulated in affected dogs. We identified miR-186 and miR-26b as effective reference miRNAs for qRT-PCR. This study applied small RNA-seq to identify differentially expressed miRNAs that might regulate critical pathways contributing to CKD progression in dogs with XLHN.

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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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Gene Profiling of Bone around Orthodontic Mini-Implants by RNA-Sequencing Analysis

BioMed Research International ◽

10.1155/2015/538080 ◽

2015 ◽

Vol 2015 ◽

pp. 1-14 ◽

Cited By ~ 3

Author(s):

Kyung-Yen Nahm ◽

Jung Sun Heo ◽

Jae-Hyung Lee ◽

Dong-Yeol Lee ◽

Kyu-Rhim Chung ◽

...

Keyword(s):

Bone Formation ◽

Rna Sequencing ◽

Cell Fate ◽

Reduction Process ◽

Gene Profiling ◽

Sequencing Analysis ◽

Rna Seq ◽

Mini Implants ◽

Oxidation Reduction ◽

The Times

This study aimed to evaluate the genes that were expressed in the healing bones around SLA-treated titanium orthodontic mini-implants in a beagle at early (1-week) and late (4-week) stages with RNA-sequencing (RNA-Seq). Samples from sites of surgical defects were used as controls. Total RNA was extracted from the tissue around the implants, and an RNA-Seq analysis was performed with Illumina TruSeq. In the 1-week group, genes in the gene ontology (GO) categories of cell growth and the extracellular matrix (ECM) were upregulated, while genes in the categories of the oxidation-reduction process, intermediate filaments, and structural molecule activity were downregulated. In the 4-week group, the genes upregulated included ECM binding, stem cell fate specification, and intramembranous ossification, while genes in the oxidation-reduction process category were downregulated. GO analysis revealed an upregulation of genes that were related to significant mechanisms, including those with roles in cell proliferation, the ECM, growth factors, and osteogenic-related pathways, which are associated with bone formation. From these results, implant-induced bone formation progressed considerably during the times examined in this study. The upregulation or downregulation of selected genes was confirmed with real-time reverse transcription polymerase chain reaction. The RNA-Seq strategy was useful for defining the biological responses to orthodontic mini-implants and identifying the specific genetic networks for targeted evaluations of successful peri-implant bone remodeling.

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SAT-455 Mouse Thyroid Responds to Iodine Overload by Transcriptionally Enhancing the Keap1/Nrf2 Antioxidant Response and by Upregulating Nrf2-Dependent and Independent Inflammatory and Fibrosis Pathways

Journal of the Endocrine Society ◽

10.1210/jendso/bvaa046.1262 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

Author(s):

Dionysios V Chartoumpekis ◽

Panos Ziros ◽

Ioannis Habeos ◽

Venetsana Kyriazopoulou ◽

Adam Smith ◽

...

Keyword(s):

Pathway Analysis ◽

Sodium Iodide ◽

Target Genes ◽

Rna Extraction ◽

Xenobiotic Metabolism ◽

Antioxidant Response ◽

Differentially Expressed ◽

P Value ◽

Rna Seq ◽

Thyroid Cells

Abstract Nrf2 (Nfe2l2) is a transcription factor that regulates a series of cytoprotective and antioxidant enzymes. Its cytoplasmic inhibitor Keap1 senses the presence of oxidative or electrophilic stress though the interaction of sulfhydryl groups of its cysteines with reactive species and ceases to bind Nrf2. Thus, Nrf2 can transfer to the nucleus and induce its target genes. Follicular thyroid cells have physiologically high levels of reactive oxygen species as oxidation of iodine is essential for iodination of thyroglobulin and thyroid hormones synthesis. We have shown previously that Nrf2 pathway is active in thyroid and regulates the transcription of thyroglobulin. We thus hypothesized that the response of thyroid to iodine excess should comprise Nrf2-dependent and -independent pathways. To this end, 3 months-old male C57Bl6J WT or Nrf2 knockout (KO) mice were exposed to 0.05% sodium iodide in their water for 7 days. Thyroids were excised and used for RNA extraction; RNA-seq was performed by Exiqon, with a fold-change cutoff set at 2. Selected representative genes of the enriched pathways were quantified by real-time qPCR to validate RNA-seq results. Pathway analysis of the differentially expressed genes was performed using the Ingenuity Pathway Analysis (IPA) software. Pathways that were enriched with a p-value<0.05 were considered significant. 828 genes were differentially expressed in response to iodine exposure; 66% were upregulated, as were most of the highly enriched pathways (related to inflammatory-immune response, antioxidant response, xenobiotic metabolism, platelet activation and calcium signaling). About 300 genes were differentially expressed between WT and KO mice; highly enriched pathways were related to glutathione and xenobiotic metabolism, Ahr signaling and Nrf2 signaling and were all downregulated in KO mice. Analysis of the potential upstream regulators of these highly enriched pathways revealed that Nrf2 and NfkB are major regulators of the antioxidant and inflammatory response induction upon iodine exposure and that Tgfβ-Smad cascade regulates the induction of fibrosis signaling. Last, we performed an analysis limited to already known thyroid pathways. A few genes were enriched following this method; upregulation of Duoxa1 (hydrogen peroxide generator) and downregulation of Nis (sodium iodide symporter) upon iodine exposure, which are expected responses, and the downregulation of thyroglobulin and upregulation of Duoxa1 in KO mice that confirm our previous findings. In conclusion, Nrf2-driven cytoprotective response is upregulated after iodine overload along with induction of inflammatory pathways. Nrf2 regulates transcriptomic responses in the thyroid, including a small but significant part of the response to iodine challenge. Hence, Nrf2 can be considered a novel player in the frontiers of thyroid antioxidant response and thyroid economy.

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Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages

Animals ◽

10.3390/ani10071198 ◽

2020 ◽

Vol 10 (7) ◽

pp. 1198 ◽

Cited By ~ 2

Author(s):

Guofang Wu ◽

Lin Ma ◽

Lei Wang ◽

Jiping Zhou ◽

Yuhong Ma ◽

...

Keyword(s):

Skeletal Muscle ◽

Meat Quality ◽

Molecular Mechanisms ◽

Target Genes ◽

Developmental Stages ◽

Enrichment Analysis ◽

Rna Seq ◽

Developmental Processes ◽

Citrate Cycle ◽

Molecular Approaches

The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding.

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RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

Animals ◽

10.3390/ani9121077 ◽

2019 ◽

Vol 9 (12) ◽

pp. 1077 ◽

Cited By ~ 2

Author(s):

Chengchuang Song ◽

Yongzhen Huang ◽

Zhaoxin Yang ◽

Yulin Ma ◽

Buren Chaogetu ◽

...

Keyword(s):

Adipose Tissue ◽

Meat Quality ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Cell Metabolism ◽

Differentially Expressed ◽

Receptor Interaction ◽

Control Group ◽

Rna Seq ◽

Angus Cattle

In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different breeds of cattle would facilitate cattle breeding. Compared to Angus cattle adipose tissue, a total of 4167 DEGs were identified in cattle-yak adipose tissue and 3269 DEGs were identified in Qaidamford cattle adipose tissue. Considering cattle-yak as a control group, 154 DEGs were identified in Qaidamford cattle adipose tissue. GO analysis indicated the significant enrichment of some DEGs related to lipid metabolism. The KEGG pathway database was also used to map DEGs and revealed that most annotated genes were involved in ECM-receptor interaction and the PI3K-Akt signal pathway, which are closely related to cell metabolism. Eight selected DEGs related to adipose tissue development or metabolism were verified by RT-qPCR, indicating the reliability of the RNA-seq data. The results of this comparative transcriptome analysis of adipose tissue and screening DEGs suggest several candidates for further investigations of meat quality in different cattle breeds.

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Dietary Olive Oil Intake Improves Running Endurance with Intramuscular Triacylglycerol Accumulation in Mice

Nutrients ◽

10.3390/nu13041164 ◽

2021 ◽

Vol 13 (4) ◽

pp. 1164

Author(s):

Yusuke Komiya ◽

Makoto Sugiyama ◽

Masaru Ochiai ◽

Nanako Osawa ◽

Yuto Adachi ◽

...

Keyword(s):

Olive Oil ◽

Functional Food ◽

Skeletal Muscles ◽

Gastrocnemius Muscle ◽

Fiber Type ◽

Muscle Metabolism ◽

Treadmill Running ◽

Endurance Capacity ◽

Growth Profiles ◽

Triacylglycerol Accumulation

Olive oil is a functional food shown to have a variety of bioactive effects. Therefore, we expect it to be a novel functional food with an exercise-mimetic effect on skeletal muscles. This study aimed to investigate the effect of olive oil on the endurance capacity and muscle metabolism in mice. Mice fed a 7% (w/w) olive oil diet for eight weeks showed improved treadmill running endurance and increased intramuscular triacylglycerol (IMTG) accumulation in the gastrocnemius muscle compared to soybean oil diet-fed controls. The increase in running endurance with olive oil intake was independent of the muscle fiber type. To elucidate underlying the mechanism of elevated IMTG levels, we examined the expression levels of the genes related to lipid metabolism. We found that the expression of diacylglycerol O-acyltransferase1 (DGAT1) was significantly upregulated in the muscle of olive oil diet-fed mice. In addition, the olive oil diet-fed mice showed no metabolic impairment or differences in growth profiles compared to the controls. These results suggest that dietary olive oil intake affects muscle metabolism and muscle endurance by increasing energy accumulation.

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Identification of differentially expressed long noncoding RNAs and pathways in liver tissues from rats with hepatic fibrosis

PLoS ONE ◽

10.1371/journal.pone.0258194 ◽

2021 ◽

Vol 16 (10) ◽

pp. e0258194

Author(s):

Yan Wang ◽

Xiong Xiao ◽

Xiaobo Wang ◽

Feng Guo ◽

Xiaozhong Wang

Keyword(s):

Hepatic Fibrosis ◽

Rat Liver ◽

Target Gene ◽

Target Genes ◽

Differentially Expressed ◽

Akt Signaling Pathway ◽

Oxidation Reduction ◽

Non Coding Rnas ◽

Polymerase Chain ◽

Liver Tissues

To identify long non-coding RNAs (lncRNAs) and their potential roles in hepatic fibrosis in rat liver issues induced by CCl4, lncRNAs and genes were analyzed in fibrotic rat liver tissues by RNA sequencing and verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Differentially expressed (DE) lncRNAs (DE-lncRNAs) and genes were subjected to bioinformatics analysis and used to construct a co-expression network. We identified 10 novel DE-lncRNAs that were downregulated during the hepatic fibrosis process. The cis target gene of DE-lncRNA, XLOC118358, was Met, and the cis target gene of the other nine DE-lncRNAs, XLOC004600, XLOC004605, XLOC004610, XLOC004611, XLOC004568, XLOC004580 XLOC004598, XLOC004601, and XLOC004602 was Nox4. The results of construction of a pathway-DEG co-expression network show that lncRNA-Met and lncRNAs-Nox4 were involved in oxidation-reduction processes and PI3K/Akt signaling pathway. Our results identified 10 DE-lncRNAs related to hepatic fibrosis, and the potential roles of DE-lncRNAs and target genes in hepatic fibrosis might provide new therapeutic strategies for hepatic fibrosis.

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Identification of CircRNA-Associated ceRNA Networks Using Longissimus Thoracis of Pigs of Different Breeds and Growth Stages

10.21203/rs.3.rs-852221/v1 ◽

2021 ◽

Author(s):

Xiaona Zhuang ◽

Zekun Lin ◽

Junyi Luo ◽

Ting Chen ◽

Qianyun Xi ◽

...

Keyword(s):

Meat Quality ◽

Fiber Type ◽

Biological Activities ◽

Differentially Expressed ◽

Integrated Analysis ◽

Growth Stages ◽

Muscle Tissues ◽

Genome Wide ◽

Key Factor ◽

Pathway Analyses

Abstract Background: Long-term artificial selection for growth rate and lean meat rate has eventually led to meat quality deterioration. Muscle fiber type is a key factor that markedly affects meat quality. circRNAs have been reported to participate in diverse biological activities, including myofiber growth and development; thus, we herein compared porcine circRNA transcriptome between oxidative and glycolytic muscle tissues. Results: Longissimus thoracis muscle tissues were obtained from Lantang and Landrace pigs at birth (LT1D and LW1D, respectively) and 90 postnatal days (LT90D and LW90D, respectively). Hematoxylin and eosin staining and quantitative real-time PCR revealed that all structural traits of the muscle showed large variations between different breeds and growth stages. In total, 329 known miRNAs and 42,081 transcript candidates were identified; 6,962 differentially expressed transcripts were found to play a key role in myogenesis by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In addition, 3,352 circRNAs were identified using five predicting algorithms, and 104 circRNA candidates were differentially expressed. Integrated analysis of differentially expressed miRNAs, mRNAs, and circRNAs led to the identification of 777, 855, and 22 convincing ceRNA interactions in LT1D vs. LT90D, LW1D vs. LW90D, and LT90D vs. LW90D, respectively. Finally, we identified a circRNA candidate circKANSL1L, which showed high homology between mice and pigs, and it was found to inhibit the proliferation of C2C12 cells but promote their differentiation.Conclusions: We identified genome-wide circRNAs in 0- and 90-day-old Lantang and Landrace pigs by RNA-seq and found that circRNAs were abundant, differentially expressed, and associated with myogenesis. Our results should serve as a reference for future studies on pork quality.

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MiRNA biomarkers and potential critical genes associated with the prognosis of gastric cancer

10.21203/rs.3.rs-406855/v1 ◽

2021 ◽

Author(s):

Zhou Chen ◽

Hao Xu ◽

Zhongtian Bai ◽

Shi Dong ◽

Jian Zhang ◽

...

Keyword(s):

Gastric Cancer ◽

Target Genes ◽

Cox Model ◽

Differential Expression Analysis ◽

Differentially Expressed ◽

Rna Seq ◽

Diagnosis And Prognosis ◽

Kaplan Meier ◽

Differentially Expressed Mirnas ◽

Pathway Analyses

Abstract Background Dysregulated expression of miRNAs in gastric cancer (GC) is associated with tumor progression. MiRNA markers are important for the prognosis and therapeutic targeting of GC patients. Methods To detect differentially expressed miRNAs in GC from the TCGA database and predict their target genes. We downloaded RNA sequencing (RNA-seq), miRNA-seq and clinical data of GC from TCGA. Differential expression analysis of RNA-seq and miRNA-seq data was performed by R 3.6.1. MiRNAs associated with prognosis were evaluated with the Cox model, and differentially expressed miRNAs were assessed by Kaplan–Meier curve analysis. Risk factors were identified in the Cox model. Target genes of differentially expressed miRNAs were searched in three databases. GO enrichment and KEGG pathway analyses were used to evaluate the biological functions of these target genes.Results Five miRNAs (hsa-miR-135b-3p, hsa-miR-143-5p, hsa-miR-196b-3p, hsa-miR-942-3p, hsa-miR-9-3p) were related to survival. Eight target genes (AKAP12, AR, DZIP1, PCDHA11, PCDHA12, PI15, SH3BGRL and TMEM108) were closely correlated with patient overall survival (OS). Conclusion Differentially expressed miRNAs and their target genes have an important influence on the diagnosis and prognosis of GC and may be used as tumor biomarkers in further studies and as potential therapeutic targets.

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