scholarly journals Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

2020 ◽  
Author(s):  
Fuhui Han ◽  
Jing Li ◽  
Nan Liu ◽  
Ranran Zhao ◽  
Lirong Liu ◽  
...  
Keyword(s):  
Unsaturated Fatty Acids ◽  
Structural Characteristics ◽  
Enrichment Analysis ◽  
Intramuscular Fat ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Future Research ◽  
Lipid Deposition ◽  
Alpha Linolenic Acid ◽  
Non Coding Rnas

Abstract Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and its level is affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on lncRNAs involved in sheep intramuscular fat deposition is still in its infancy. Aohan fine-wool sheep (AFWS), China's representative meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of intramuscular fat deposition. We identified lncRNAs by RNA sequencing in sheep longissimus dorsi muscle(LDM) samples at two ages: 2 months (Mth-2) and 12 months (Mth-12).Results: We identified a total of 26,247 genes and 6,935 predicted novel lncRNAs in LDM samples of sheep. Among these, 606 mRNAs and 408 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained targeted genes of differentially expressed lncRNAs and performed an enrichment analysis using Gene Ontology(GO) and the Kyoto Encyclopedia of Genes and Genomes(KEGG). We found these targeted mRNAs were primarily enriched in lipid metabolism, lipid transport, regulation of primary metabolic processes and developmental pathways, such as alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, phosphonate and phosphinate metabolism and cell proliferation. Based on the results of this enrichment analysis, we obtained candidate lncRNAs that potentially regulate lipid deposition and constructed a lncRNA-mRNA co-expression network. We speculated that these lncRNAs have important regulatory roles in intramuscular fat deposition. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of sequencing results by qRT-PCR.Conclusions: Our study provided a list of the lncRNAs and mRNAs related to intramuscular lipid deposition in sheep and lay the foundation for future research on regulatory mechanisms.

scholarly journals Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

2020 ◽  
Author(s):  
Fuhui Han ◽  
Jing Li ◽  
Nan Liu ◽  
Ranran Zhao ◽  
Lirong Liu ◽  
...  
Keyword(s):  
Target Genes ◽  
Structural Characteristics ◽  
Intramuscular Fat ◽  
Differentially Expressed ◽  
Future Research ◽  
Lipid Deposition ◽  
Sequencing Data ◽  
Kegg Pathways ◽  
Longissimus Dorsi Muscle ◽  
Non Coding Rnas

Abstract Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in longissimus dorsi muscle (LDM) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). Results: We identified a total of 26,247 genes and 6,935 novel lncRNAs in LDM samples of sheep. Among these, 606 mRNAs and 408 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were primarily enriched in lipid metabolism, lipid transport, regulation of primary metabolic processes and developmental pathways. Based on the results of important KEGG pathways, we obtained six candidate lncRNAs that potentially regulate lipid deposition and constructed an lncRNA-mRNA co-expression network that included MSTRG.792.1- SCD , MSTRG.8227.1- ACAA2 , MSTRG.10679.1- FADS2 , MSTRG.21942.1- PLA2G4E , MSTRG.21380.1- FZD4 and MSTRG.9270.1- ULK1 . We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR. Conclusions: Our study provided a list of the lncRNAs and mRNAs related to intramuscular lipid deposition in sheep and laid a foundation for future research on regulatory mechanisms.

scholarly journals Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

2020 ◽  
Author(s):  
Fuhui Han ◽  
Jing Li ◽  
Nan Liu ◽  
Ranran Zhao ◽  
Lirong Liu ◽  
...  
Keyword(s):  
Target Genes ◽  
Structural Characteristics ◽  
Intramuscular Fat ◽  
Differentially Expressed ◽  
Future Research ◽  
Lipid Deposition ◽  
Sequencing Data ◽  
Intramuscular Lipid ◽  
Non Coding Rnas

Abstract Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). Results: We identified a total of 26,247 genes and 6,935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. Three pathways were significantly enriched, namely tight junction, glycosaminoglycan biosynthesis-heparan sulfate/heparin and lysosome. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed an lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4,MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1,MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR. Conclusions: Our study provided a list of the lncRNAs and mRNAs related to intramuscular lipid deposition in sheep and laid a foundation for future research on regulatory mechanisms.

scholarly journals Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

2020 ◽  
Author(s):  
Fuhui Han ◽  
Jing Li ◽  
Ranran Zhao ◽  
Lirong Liu ◽  
Lanlan Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Structural Characteristics ◽  
Intramuscular Fat ◽  
Differentially Expressed ◽  
Lipid Deposition ◽  
Sequencing Data ◽  
Dual Purpose ◽  
Intramuscular Lipid ◽  
Non Coding Rnas

Abstract Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). Results: We identified a total of 26,247 genes and 6,935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR.Conclusions: Our study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.

scholarly journals Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

2020 ◽  
Author(s):  
Fuhui Han ◽  
Jing Li ◽  
Nan Liu ◽  
Ranran Zhao ◽  
Lirong Liu ◽  
...  
Keyword(s):  
Target Genes ◽  
Structural Characteristics ◽  
Intramuscular Fat ◽  
Differentially Expressed ◽  
Lipid Deposition ◽  
Sequencing Data ◽  
Dual Purpose ◽  
Intramuscular Lipid ◽  
Non Coding Rnas

Abstract Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). Results: We identified a total of 26,247 genes and 6,935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR.Conclusions: Our study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.

scholarly journals Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fuhui Han ◽  
Jing Li ◽  
Ranran Zhao ◽  
Lirong Liu ◽  
Lanlan Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Structural Characteristics ◽  
Intramuscular Fat ◽  
Differentially Expressed ◽  
Lipid Deposition ◽  
Sequencing Data ◽  
Dual Purpose ◽  
Intramuscular Lipid ◽  
Non Coding Rnas

Abstract Background Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China’s most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). Results We identified a total of 26,247 genes and 6935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR. Conclusions Our study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.

scholarly journals Long-non Coding RNAs Related to Fat Deposition in Pigs Included lncRNA Corresponding to Human MALAT1

2021 ◽  
Author(s):  
Katarzyna Piórkowska ◽  
Kacper Żukowski ◽  
Katarzyna Ropka-Molik ◽  
Mirosław Tyra
Keyword(s):  
Regulatory Elements ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Sequencing Method ◽  
Non Coding Rnas ◽  
Potential Interactions ◽  
Long Non Coding Rna ◽  
Generation Sequencing

Obesity is a problem in the last decades since the development of different technologies forced the submission of a faster pace of life, resulting in nutrition style changes. In turn, domestic pigs are an excellent animal model in recognition of adiposity-related processes, corresponding to the size of individual organs, the distribution of body fat in the organism, and similar metabolism. The present study applied the next-generation sequencing method to identify adipose tissue (AT) transcriptomic signals related to increased fat content by identifying differentially expressed genes (DEGs), included long-non coding RNA molecules. The Freiburg RNA tool was applied to recognise predicting hybridisation energy of RNA-RNA interactions. The results indicated several long non-coding RNAs (lncRNAs) whose expression was significantly positively or negatively associated with fat deposition. lncRNAs play an essential role in regulating gene expression by sponging miRNA, binding transcripts, facilitating translation, or coding other smaller RNA regulatory elements. In the pig fat tissue of obese group, increased expression of lncRNAs corresponding to human MALAT1 was observed that previously recognised in the obesity-related context. Moreover, hybridisation energy analyses pinpointed numerous potential interactions between identified differentially expressed lncRNAs, and obesity-related genes and miRNAs expressed in AT.

scholarly journals Transcriptome analysis of miRNA and mRNA in the livers of pigs with highly diverged backfat thickness

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Xing ◽  
Xitong Zhao ◽  
Hong Ao ◽  
Shaokang Chen ◽  
Ting Yang ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Energy Metabolism ◽  
Differentially Expressed Genes ◽  
Regulatory Network ◽  
Acid Synthesis ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Backfat Thickness ◽  
Lipid Deposition ◽  
Differentially Expressed Mirnas

AbstractFat deposition is very important in pig production, and its mechanism is not clearly understood. MicroRNAs (miRNAs) play critical roles in fat deposition and energy metabolism. In the current study, we investigated the mRNA and miRNA transcriptome in the livers of Landrace pigs with extreme backfat thickness to explore miRNA-mRNA regulatory networks related to lipid deposition and metabolism. A comparative analysis of liver mRNA and miRNA transcriptomes from pigs (four pigs per group) with extreme backfat thickness was performed. We identified differentially expressed genes from RNA-seq data using a Cufflinks pipeline. Seventy-one differentially expressed genes (DEGs), including twenty-eight well annotated on the porcine reference genome genes, were found. The upregulation genes in pigs with higher backfat thickness were mainly involved in fatty acid synthesis, and included fatty acid synthase (FASN), glucokinase (GCK), phosphoglycerate dehydrogenase (PHGDH), and apolipoprotein A4 (APOA4). Cytochrome P450, family 2, subfamily J, polypeptide 34 (CYP2J34) was lower expressed in pigs with high backfat thickness, and is involved in the oxidation of arachidonic acid. Moreover, 13 differentially expressed miRNAs were identified. Seven miRNAs were associated with fatty acid synthesis, lipid metabolism, and adipogenic differentiation. Based on comprehensive analysis of the transcriptome of both mRNAs and miRNAs, an important regulatory network, in which six DEGs could be regulated by differentially expressed miRNAs, was established for fat deposition. The negative correlate in the regulatory network including, miR-545-5p and GRAMD3, miR-338 and FASN, and miR-127, miR-146b, miR-34c, miR-144 and THBS1 indicate that direct suppressive regulation may be involved in lipid deposition and energy metabolism. Based on liver mRNA and miRNA transcriptomes from pigs with extreme backfat thickness, we identified 28 differentially expressed genes and 13 differentially expressed miRNAs, and established an important miRNA-mRNA regulatory network. This study provides new insights into the molecular mechanisms that determine fat deposition in pigs.

scholarly journals Identification of the Genetic Basis for the Large-tailed Phenotypic Trait in Han Sheep Through Integrated mRNA and miRNA Analysis of Tail Fat Tissue Samples

2020 ◽  
Author(s):  
Yang Guangli ◽  
Zhang Huan ◽  
Zhang Shuhong ◽  
Li Zhiqiang ◽  
Gao Fengyi ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Future Research ◽  
Phenotypic Trait ◽  
Fatty Tissue ◽  
Fat Tissue ◽  
Tissue Samples

Abstract Background: While evolution has led certain breeds of sheep to exhibit large tails composed of fatty tissue, the genetic basis for this fatty large-tailed phenotypic trait remains to be defined in breeds of Han sheep. Here, we employed a high-throughput sequencing approach to identify mRNAs and microRNAs (miRNAs) that were differentially expressed in tail fat tissue samples from large-tailed Han (LTH) and small-tailed Han (STH) sheep in order to identify key genetic determinants of the large-tailed phenotype.Results: In total, we identified 521 mRNAs (237 upregulated, 284 downregulated) and 14 miRNAs (6 upregulated, 8 downregulated) that were differentially expressed between these two sheep breeds. Predictive analytical database tools were subsequently utilized to identify 2,409 putative targets of these differentially expressed miRNAs (DEMs), including 65 which were among the list of differentially expressed genes (DEGs) identified in the present study. By specifically focusing on predicted DEM/DEG pairs with appropriate regulatory directionality, we identified DIRF, HSD17B12, LPL, APOBR, INSIGI, THRSP, ACSL5, FAAH, ACSS2, APOA1, ACLY, and ACSM3 through mRNA analyses and ACSL4, FTO, FGF8, IGF2, GNPDA2, LIPG, PRKAA2, ELOVL7, SOAT2, and SIRT1 through miRNA analyses as candidate genes which may regulate fat deposition and fatty acid metabolism in the adipose tissue from the tails of Han sheep. Conclusion: Together, our data provide insight into the potential genetic basis for the large-tailed phenotype of LTH sheep, suggesting that it may be attributable to specific DEMs and DEGs that regulate one another and thereby control lipid metabolism. These data provide a basis for future research regarding the role of these genes in ovine tail fat deposition, and offer preliminary perspectives on the molecular mechanisms governing the fatty large-tailed phenotype in LTH sheep.

scholarly journals Transcriptome Analysis to Identify the Potential Role of Long non-coding RNAs in Enteric Glial Cells under Hyperglycemia

2020 ◽  
Author(s):  
Xuping Zhu ◽  
Yanyu Li ◽  
Xue Zhu ◽  
Yanmin Jiang ◽  
Xiaowei Zhu ◽  
...  
Keyword(s):  
Autonomic Neuropathy ◽  
Glial Cells ◽  
Transcriptome Analysis ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Enteric Glial Cells ◽  
Non Coding Rnas

Abstract Background Long non-coding RNAs (lncRNAs) are important mediators in the pathogenesis of diabetic gastrointestinal autonomic neuropathy, which has just been reported to have a relation to enteric glial cells (EGCs). However, the role of lncRNAs in the pathogenesis of diabetic gastrointestinal autonomic neuropathy, especially EGCs-related gastrointestinal dysfunction, has never been reported. Methods RNA sequencing technology (RNA-Seq) was used to screen the differential lncRNAs and mRNAs in EGCs under hyperglycemia (300 mmol L− 1 high glucose). Results Totally 4678 differentially expressed lncRNAs (DE lncRNAs) and 6244 differentially expressed mRNAs (DE mRNAs) were obtained. GO enrichment analysis and KEGG pathway analysis showed significant differences. 2910 and 1549 co-expressed mRNAs were respectively expressed in up-regulated and down-regulated DE lncRNA target genes. Several up- or down-regulated lncRNAs were at the key junction points of the regulatory network. Protein-protein interaction networks showed highly connected clusters were TP53, AKT1, Casp9, Casp8, Casp3, TNF, etc, which are known closely related to apoptosis. FLRT3, Fras1, and other related target genes, which revealed the potential function of lncRNAs, may be important targets for differential lncRNAs to regulate the apoptosis of glial cells induced by hyperglycemia. Conclusion In this study, the involvement of lncRNAs in EGCs under hyperglycemia was analyzed using transcriptome analysis.

scholarly journals Identification and characterization of circRNAs in the deposition of intramuscular fat in Aohan fine-wool sheep

2020 ◽  
Author(s):  
Le Zhao ◽  
Nan Liu ◽  
Fuhui Han ◽  
Lisheng Zhou ◽  
Lirong Liu ◽  
...  
Keyword(s):  
Interaction Analysis ◽  
Age Groups ◽  
Wnt Signaling Pathway ◽  
Enrichment Analysis ◽  
Circular Rna ◽  
Intramuscular Fat ◽  
Sheep Breed ◽  
Differentially Expressed ◽  
Sphingolipid Metabolism ◽  
Rna Seq

Abstract Background Aohan fine-wool sheep (AFWS) is a high-quality fine-wool sheep breed that supplies both wool and meat. The quality of its meat is affected by many factors. Research is needed on the molecular mechanism of intramuscular fat (IMF) growth, which greatly improves mutton quality. The widely expressed non-coding RNA is used in roles such as competitive endogenous RNAs (ceRNAs), including microRNAs (miRNAs). Although circular RNA (circRNA) was studied in many fields, little research was devoted to IMF in sheep. We used RNA-Seq to analyze tissues associated with IMF in 2-month-old and 12-month-old AFWS rams to understand the role of circRNA in the growth and development of sheep IMF. Results A total of 11,565 candidate circRNAs were identified, of which 104 were differentially expressed in the two age groups. We analyzed these differentially expressed circRNAs. Enrichment analysis was performed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. The enriched pathways included lipid transport (GO:0006869), negative regulation of canonical Wnt signaling pathway (GO:0090090), fat digestion and absorption (ko04975), and sphingolipid metabolism (ko00600). We used the TargetScan and miRanda software programs for interaction analysis, and a network diagram was created. Six circRNAs were randomly selected and verified the RNA-Seq results by quantitative real-time PCR. Conclusion This study provides more information on circRNA regulation in AFWS, and is a useful resource for further research on this sheep breed.

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