scholarly journals Comparative Genome-Wide Alternative Splicing Analysis of Longissimus Dorsi Muscles Between Japanese Black (Wagyu) and Chinese Red Steppes Cattle

2021 ◽  
Vol 8 ◽  
Author(s):  
Xibi Fang ◽  
Lixin Xia ◽  
Haibin Yu ◽  
Wei He ◽  
Zitong Bai ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Beef Cattle ◽  
Splice Site ◽  
Muscle Development ◽  
Single Gene ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Longissimus Dorsi ◽  
Transcriptional Level ◽  
Japanese Black Cattle

Alternative splicing is a ubiquitous regulatory mechanism in gene expression that allows a single gene generating multiple messenger RNAs (mRNAs). Significant differences in fat deposition ability and meat quality traits have been reported between Japanese black cattle (Wagyu) and Chinese Red Steppes, which presented a unique model for analyzing the effects of transcriptional level on marbling fat in livestock. In previous studies, the differentially expressed genes (DGEs) in longissimus dorsi muscle (LDM) samples between Wagyu and other breeds of beef cattle have been reported. In this study, we further investigated the differences in alternative splicing in LDM between Wagyu and Chinese Red Steppes cattle. We identified several alternative splicing types including cassette exon, mutually exclusive exons, alternative 5′ splice site, alternative 3′ splice site, alternative start exon, and intron retention. In total, 115 differentially expressed alternatively spliced genes were obtained, of which 17 genes were enriched in the metabolic pathway. Among the 17 genes, 5 genes, including MCAT, CPT1B, HADHB, SIRT2, and DGAT1, appeared to be the novel spliced candidates that affect the lipid metabolism in cattle. Additionally, another 17 genes were enriched in the Gene Ontology (GO) terms related to muscle development, such as NR4A1, UQCC2, YBX3/CSDA, ITGA7, etc. Overall, altered splicing and expression levels of these novel candidates between Japanese black cattle and Chinese Red Steppes revealed by RNA-seq suggest their potential involvement in the muscle development and fat deposition of beef cattle.

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

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.

scholarly journals Differentially expressed extracellular vesicle, exosome and non-exosome miRNA profile in high and low tick-resistant beef cattle

2021 ◽  
Author(s):  
Pevindu Abeysinghe ◽  
Natalie Turner ◽  
Hassendrini Peiris ◽  
Kanchan Vaswani ◽  
Nick Cameron ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Blood Plasma ◽  
Noncoding Rna ◽  
Extracellular Vesicle ◽  
Micro Rna ◽  
Differentially Expressed ◽  
Economic Losses ◽  
Transcriptional Level ◽  
Beef Industry ◽  
Tick Resistance

Abstract Heavy tick burden on beef cattle account for huge economic losses globally, with an estimated value of US$22-30 billion per annum. In Australia, ticks cost the northern beef industry approximately A$170-200 million. Methods to evaluate and predict tick resistance would therefore be of great value to the global cattle trade. Exosomes (EX) are small extracellular vesicles (EVs) of ~30-150nm diameter and have gained popularity for their diagnostic and prognostic potential. EX contain, among other biomolecules, various types of RNA including micro-RNA (miRNA) and long noncoding RNA (lncRNA). MiRNA specifically have been validated as therapeutic biomarkers as they perform regulatory functions at the post-transcriptional level and are differentially expressed between divergent groups. The objective of the present study was to evaluate the miRNA profiles of EV and fractionated exosomal samples of high and low tick-resistant beef cattle to highlight potential miRNA biomarkers of tick resistance. Cows (n = 3/group) were classified into high or low tick resistant groups according to a novel scoring system. EVs and EX were isolated and fractionated from the blood plasma of high and low tick resistant cattle using established isolation and enrichment protocols. The resultant EX and non-EX samples were processed for next generation miRNA sequencing. Offspring of the cows in each high and low tick resistant group underwent the same processing for blood plasma EX, non-EX and miRNA analysis to evaluate the heritability of miRNA associated with tick resistance.A total of 2631 miRNAs were identified in EX and non-EX fractionated samples from high and low tick-resistant beef cattle. MiR-449a was highly expressed in maternal high tick-resistant EX samples. Of these, 174 were novel miRNAs, and 10 were differentially expressed (DE) (FDR < 0.05). These 10 DE miRNAs were also present in EVs, and three miRNAs were highly expressed: miR-2419-3p, miR-7861-3p and miR-2372-5p. Although 196 novel miRNAs were identified in fractionated samples of offspring, no miRNA were differentially expressed in these animals.

scholarly journals Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq

2021 ◽  
Vol 12 ◽  
Author(s):  
Chaoyun Yang ◽  
Liyun Han ◽  
Peng Li ◽  
Yanling Ding ◽  
Yun Zhu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Differentially Expressed Genes ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Muscle Development ◽  
Dietary Factors ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Biological Regulation ◽  
Key Genes

Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = −0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.

scholarly journals Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun Huang ◽  
Fei Ge ◽  
Xiaoming Ma ◽  
Rongfeng Dai ◽  
Renqing Dingkao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Basis ◽  
Muscle Development ◽  
Expression Profiles ◽  
Economic Benefits ◽  
Production Performance ◽  
Differentially Expressed ◽  
Myoblast Differentiation ◽  
Longissimus Dorsi ◽  
Non Coding Rnas

Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. Male hybrid sterility has been focused on for a long time; however, the mRNAs and non-coding RNAs related to muscle development as well as their regulatory networks remain unclear. The phenotypic data showed that the production performance (i.e., body weight, withers height, body length, and chest girth) of cattle-yak was significantly better than that of the yak, and the economic benefits of the cattle-yak were higher under the same feeding conditions. Then, we detected the expression profiles of the longissimus dorsi muscle of cattle-yak and yak to systematically reveal the molecular basis using the high-throughput sequencing technology. Here, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs were identified to be differentially expressed between cattle-yaks and yaks in the longissimus dorsi muscle. These mRNAs, lncRNA targeted genes, and circRNA host genes were significantly enriched in myoblast differentiation and some signaling pathways related to muscle development (such as HIF-1 signaling pathway and PI3K-Akt signaling pathway). We constructed a competing endogenous RNA (ceRNA) network and found that some non-coding RNAs differentially expressed may be involved in the regulation of muscle traits. Taken together, this study may be used as a reference tool to provide the molecular basis for studying muscle development.

scholarly journals Differentially Expressed Extracellular Vesicle, Exosome and Non-Exosome miRNA Profile in High and Low Tick-Resistant Beef Cattle

2021 ◽  
Vol 11 ◽  
Author(s):  
Pevindu Abeysinghe ◽  
Natalie Turner ◽  
Hassendrini Peiris ◽  
Kanchan Vaswani ◽  
Nick Cameron ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Blood Plasma ◽  
Noncoding Rna ◽  
Extracellular Vesicle ◽  
Micro Rna ◽  
Differentially Expressed ◽  
Economic Losses ◽  
Transcriptional Level ◽  
Beef Industry ◽  
Tick Resistance

Heavy tick burden on beef cattle account for huge economic losses globally, with an estimated value of US$22-30 billion per annum. In Australia, ticks cost the northern beef industry approximately A$170-200 million. Methods to evaluate and predict tick resistance would therefore be of great value to the global cattle trade. Exosomes (EX) are small extracellular vesicles (EVs) of ~30-150nm diameter and have gained popularity for their diagnostic and prognostic potential. EX contain, among other biomolecules, various types of RNA including micro-RNA (miRNA) and long noncoding RNA (lncRNA). MiRNA specifically have been validated as therapeutic biomarkers as they perform regulatory functions at the post-transcriptional level and are differentially expressed between divergent groups. The objective of the present study was to evaluate the miRNA profiles of EV and fractionated exosomal samples of high and low tick-resistant beef cattle to highlight potential miRNA biomarkers of tick resistance. Cows (n = 3/group) were classified into high or low tick resistant groups according to a novel scoring system. EVs and EX were isolated and fractionated from the blood plasma of high and low tick resistant cattle using established isolation and enrichment protocols. The resultant EX and non-EX samples were processed for next generation miRNA sequencing. Offspring of the cows in each high and low tick resistant group underwent the same processing for blood plasma EX, non-EX and miRNA analysis to evaluate the heritability of miRNA associated with tick resistance. A total of 2631 miRNAs were identified in EX and non-EX fractionated samples from high and low tick-resistant beef cattle. MiR-449a was highly expressed in maternal high tick-resistant EX samples. Of these, 174 were novel miRNAs, and 10 were differentially expressed (DE) (FDR &lt; 0.05). These 10 DE miRNAs were also present in EVs, and three miRNAs were highly expressed: miR-2419-3p, miR-7861-3p and miR-2372-5p. Although 196 novel miRNAs were identified in fractionated samples of offspring, no miRNA were differentially expressed in these animals.

scholarly journals Comprehensive analysis of differentially expressed circRNAs and ceRNA regulatory network in porcine skeletal muscle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Meng Li ◽  
Na Zhang ◽  
Wanfeng Zhang ◽  
Wei Hei ◽  
Chunbo Cai ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Regulatory Network ◽  
Growth Regulation ◽  
Muscle Development ◽  
Muscle Growth ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Large White ◽  
Skeletal Muscle Growth ◽  
Cerna Network

Abstract Background Circular RNA (circRNA), a novel class of non-coding RNA, has a closed-loop structure with important functions in skeletal muscle growth. The purpose of this study was to investigate the role of differentially expressed circRNAs (DEcircRNAs), as well as the DEcircRNA-miRNA-mRNA regulatory network, at different stages of porcine skeletal muscle development. Here, we present a panoramic view of circRNA expression in porcine skeletal muscle from Large White and Mashen pigs at 1, 90, and 180 days of age. Results We identified a total of 5819 circRNAs. DEcircRNA analysis at different stages showed 327 DEcircRNAs present in both breeds. DEcircRNA host genes were concentrated predominately in TGF-β, MAPK, FoxO, and other signaling pathways related to skeletal muscle growth and fat deposition. Further prediction showed that 128 DEcircRNAs could bind to 253 miRNAs, while miRNAs could target 945 mRNAs. The constructed ceRNA network plays a vital role in skeletal muscle growth and development, and fat deposition. Circ_0015885/miR-23b/SESN3 in the ceRNA network attracted our attention. miR-23b and SESN3 were found to participate in skeletal muscle growth regulation, also playing an important role in fat deposition. Using convergent and divergent primer amplification, RNase R digestion, and qRT-PCR, circ_0015885, an exonic circRNA derived from Homer Scaffold Protein 1 (HOMER1), was confirmed to be differentially expressed during skeletal muscle growth. In summary, circ_0015885 may further regulate SESN3 expression by interacting with miR-23b to function in skeletal muscle. Conclusions This study not only enriched the circRNA library in pigs, but also laid a solid foundation for the screening of key circRNAs during skeletal muscle growth and intramural fat deposition. In addition, circ_0015885/miR-23b/SESN3, a new network regulating skeletal muscle growth and fat deposition, was identified as important for increasing the growth rate of pigs and improving meat quality.

Genome-wide identification and characterization of long non-coding RNAs in Longissimus dorsi skeletal muscle of Shandong black cattle and Luxi cattle

2020 ◽  
Author(s):  
Ruili Liu ◽  
Xianxun Liu ◽  
Kun Yu ◽  
Xuejin Bai ◽  
Yajuan Dong
Keyword(s):  
Skeletal Muscle ◽  
Cell Differentiation ◽  
Muscle Cell ◽  
Muscle Development ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Longissimus Dorsi ◽  
Protein Coding ◽  
Non Coding Rnas

Abstract Background There is increasing understanding of the possible regulatory role of long non-coding RNAs (LncRNA). Studies on livestock have mainly focused on the regulation of cell differentiation, fat synthesis, and embryonic development. However, there has been little study of skeletal muscle of domestic animals and the potential role of lncRNA. Results RNA samples were collected from longissimus dorsi muscle samples of Shandong black cattle and Luxi cattle and libraries were constructed and sequenced. A total of 1415 transcripts (of which 480 were LncRNAs) were differentially expressed (P < 0.05) in the different breeds, and fourteen of these RNAs were randomly selected and validated by qPCR. We found that the most differentially expressed LncRNAs were found on chromosome 9, with 1164 within 50 kb of a protein-coding gene. In addition, Pearson's correlation coefficients of co-expression levels indicated a potential trans regulatory relationship between the differentially expressed LncRNAs and 43844 mRNAs (r > 0.9). The identified co-expressed mRNAs (MYORG, Dll1, EFNB2, SOX6, MYOCD, and MYLK3) are related to the formation of muscle structure, and enriched in muscle system process, strained muscle cell differentiation, muscle cell development, striated muscle tissue development, calcium signaling, and AMPK signaling. Additionally, we also found that some LncRNAs (LOC112444238, LOC101903367, LOC104975788, LOC112441863, LOC112449549, and LOC101907194) may interact with miRNAs related to cattle muscle growth and development. Based on this, we constructed a LncRNAs-miRNA-mRNA interaction network as the putative basis for biological regulation in cattle skeletal muscle. Interestingly, a candidate differential LncRNA (LOC104975788) and a protein-coding gene (Pax7) contain miR-133a binding sites and binding was confirmed by luciferase reporter assay. LOC104975788 may bind miR-133a competitively with Pax7, thus relieving the inhibitory effect of miR-133a on Pax7 to regulate skeletal muscle development. These results will provide the theoretical basis for further study of LncRNA regulation and activity in different cattle breeds. Conclusions The data obtained in this study were used to predict muscle-related LncRNAs-miRNA-mRNA interaction networks, which can help elucidate the molecular mechanism of cattle muscle development. These results can be used to facilitate livestock breeding and improve livestock production.

scholarly journals PSI-B-14 Late-Breaking: Evaluation of mRNA isoforms expression profile using two approaches to measure meat tenderness from Longissimus thoracis muscle in beef cattle

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 318-319
Author(s):  
Maria Malane M Muniz ◽  
Angela Cánovas ◽  
Larissa Fernanda Simielli Fonseca ◽  
Danielly Beraldo dos Santos Silva ◽  
Ana Fabrícia Braga Magalhães ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Beef Cattle ◽  
Muscle Development ◽  
Trinucleotide Repeat ◽  
Biological Marker ◽  
Differentially Expressed ◽  
Meat Tenderness ◽  
Mrna Isoforms ◽  
Beef Tenderness ◽  
Mrna Isoform

Abstract The Warner-Bratzler shear force (WBSF) and myofibrillar fragmentation index (MFI) are complementary methodologies commonly used to measure beef tenderness. To identify mRNA isoforms differentially expressed became an important tool to provide new insights to better understand the transcripts involved in the regulation of the meat tenderness, using MFI and WBSF measures in Nellore beef cattle. Longissimus thoracis muscle samples from the 20 most extreme bulls (out of 80 bulls set) for WBSF [tender (n = 9) and tough (n = 10) groups] and MFI [high (n = 10) and low (n = 10) groups] traits were collected to perform transcriptomic analysis using RNA-Sequencing. The CLC Genomics Workbench v.12.0 was used to align the fragments of each sample to the bovine reference genome ARS.UCD1.2. An average of 37 million transcripts were expressed in the Nellore muscle transcriptome. A total of 41 and 31 mRNA isoforms were differentially expressed (q≤0.05 and Fold Change greater than 2) between the two groups of divergent bulls for WBSF and MFI traits, respectively. The RPL14-202 mRNA isoform was the only isoform differentially expressed in common between both traits and is one of two known transcripts of the RPL14 gene. The RPL14 gene contains a trinucleotide repeat tract whose length is highly polymorphic and has several biochemical functions. Bulls with tender meat have one base insertion inside this region and possibly has splice site disruption effects. The RPL14-202 mRNA isoform could be used as potential biological marker for beef tenderness. The identified differentially expressed mRNA isoforms (ACTA1-202, ACTN3-201, MYL6-202, MYL6-201, MYBPC2-202) were involved with skeletal muscle cell differentiation, negative regulation of sarcomere organization and regulation of skeletal muscle contraction. mRNA isoforms directly associated with muscle development were identified using different approaches to measure beef tenderness suggesting potential key regulator genes and biomarkers associated with an important consumer valued trait for the beef industry.

scholarly journals Comprehensive Analysis of Differentially Expressed CircRNAs and CeRNA Regulatory Network in Porcine Skeletal Muscle

2020 ◽  
Author(s):  
Meng Li ◽  
Na Zhang ◽  
Wanfeng Zhang ◽  
Wei Hei ◽  
Chunbo Cai ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Regulatory Network ◽  
Growth Regulation ◽  
Muscle Development ◽  
Muscle Growth ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Large White ◽  
Skeletal Muscle Growth ◽  
Cerna Network

Abstract Background: Circular RNA (circRNA), a novel class of non-coding RNA, has a closed-loop structure with important functions in skeletal muscle growth. The purpose of this study was to investigate the role of differentially expressed circRNAs (DEcircRNAs), as well as the DEcircRNA-miRNA-mRNA regulatory network, at different stages of porcine skeletal muscle development. Here, we present a panoramic view of circRNA expression in porcine skeletal muscle from Large White and Mashen pigs at 1, 90, and 180 days of age. Results: We identified a total of 5,819 circRNAs. DEcircRNA analysis at different stages showed 327 DEcircRNAs present in both breeds. DEcircRNA host genes were concentrated predominately in TGF-β, MAPK, FoxO, and other signaling pathways related to skeletal muscle growth and fat deposition. Further prediction showed that 128 DEcircRNAs could bind to 253 miRNAs, while miRNAs could target 945 mRNAs. The constructed ceRNA network plays a vital role in skeletal muscle growth and development, and fat deposition. Circ_0015885/miR-23b/SESN3 in the ceRNA network attracted our attention. miR-23b and SESN3 were found to participate in skeletal muscle growth regulation, also playing an important role in fat deposition. Using convergent and divergent primer amplification, RNase R digestion, and qRT-PCR, circ_0015885, an exonic circRNA derived from Homer Scaffold Protein 1 (HOMER1), was confirmed to be differentially expressed during skeletal muscle growth. In summary, circ_0015885 may further regulate SESN3 expression by interacting with miR-23b to function in skeletal muscle. Conclusions: This study not only enriched the circRNA library in pigs, but also laid a solid foundation for the screening of key circRNAs during skeletal muscle growth and intramural fat deposition. In addition, circ_0015885/miR-23b/SESN3, a new network regulating skeletal muscle growth and fat deposition, was identified as important for increasing the growth rate of pigs and improving meat quality.

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