Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality

Luo, Yuzhu; Wang, Jiqing; Hu, Jiang; Liu, Xiu; Li, Shaobin; Hao, Zhiyun; Li, Mingna; Zhao, Zhidong; Zhang, Yuting; Yang, Shutong; Wang, Longbin; Gu, Yuanhua

doi:10.1007/s10142-023-00987-4

Cited by 4 publications

(3 citation statements)

References 57 publications

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“…These results showed that there were many The ceRNA regulatory network is centered on miRNAs, linking mRNAs with lncRNAs/circRNAs to form a network of mutual influence and regulation (Poliseno et al, 2010;Salmena et al, 2011). Recently, numerous studies have shown that lncRNA-miRNA-mRNA is involved in the regulation of skeletal muscle growth and development (Cui et al, 2022;Shen et al, 2023).…”

Section: Discussionmentioning

confidence: 97%

“…The ceRNA regulatory network is centered on miRNAs, linking mRNAs with lncRNAs/circRNAs to form a network of mutual influence and regulation ( Poliseno et al, 2010 ; Salmena et al, 2011 ). Recently, numerous studies have shown that lncRNA–miRNA–mRNA is involved in the regulation of skeletal muscle growth and development ( Cui et al, 2022 ; Shen et al, 2023 ). Therefore, we constructed a ceRNA regulatory network associated with skeletal muscle growth and development to better clarify the molecular mechanisms underlying skeletal muscle growth and development in chickens.…”

Section: Discussionmentioning

confidence: 99%

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Transcriptome analysis of mRNAs, lncRNAs, and miRNAs in the skeletal muscle of Tibetan chickens at different developmental stages

Chen

Zhao

et al. 2023

Front. Physiol.

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Introduction: As a valuable genetic resource, native birds can contribute to the sustainable development of animal production. Tibetan chickens, known for their special flavor, are one of the important local poultry breeds in the Qinghai–Tibet Plateau. However, Tibetan chickens have a slow growth rate and poor carcass traits compared with broilers. Although most of the research on Tibetan chickens focused on their hypoxic adaptation, there were fewer studies related to skeletal muscle development.Methods: Here, we performed the transcriptional sequencing of leg muscles from Tibetan chicken embryos at E (embryonic)10, E14, and E18.Results: In total, 1,600, 4,610, and 2,166 DE (differentially expressed) mRNAs, 210, 573, and 234 DE lncRNAs (long non-coding RNAs), and 52, 137, and 33 DE miRNAs (microRNAs) were detected between E10 and E14, E10 and E18, and E14 and E18, respectively. Functional prediction showed several DE mRNAs and the target mRNAs of DE lncRNAs and DE miRNAs were significantly enriched in sarcomere organization, actin cytoskeleton organization, myofibril, muscle fiber development, and other terms and pathways related to muscle growth and development. Finally, a lncRNA–miRNA–mRNA ceRNA (competing endogenous RNA) network associated with muscle growth and development, which contained 6 DE lncRNAs, 13 DE miRNAs, and 50 DE mRNAs, was constructed based on the screened DE RNAs by Gene Ontology (GO) enrichment. These DE RNAs may play a critical regulatory role in the skeletal muscle development of chickens.Discussion: The results provide a genomic resource for mRNAs, lncRNAs, and miRNAs potentially involved in the skeletal muscle development of chickens, which lay the foundation for further studies of the molecular mechanisms underlying skeletal muscle growth and development in Tibetan chickens.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of mRNAs, lncRNAs, and miRNAs in the skeletal muscle of Tibetan chickens at different developmental stages

Chen

Zhao

et al. 2023

Front. Physiol.

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“…Based on our previously published ovine preadipocyte mRNA data (SRR19917845-SRR19917856) and miRNA data from the same samples as those used in the study 43 , 44 , a lncRNA associated ceRNA network was constructed according to the ceRNA construction method established by Shen et al 52 . (1) Spearman rank correlation coefficient (SCC) was used to evaluate the expression association between mRNA-miRNA or lncRNA-miRNA.…”

Section: Methodsmentioning

confidence: 99%

Screening and identification of lncRNAs in preadipocyte differentiation in sheep

Hao,

Jin,

Hickford

et al. 2024

Sci Rep

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Studies of preadipocyte differentiation and fat deposition in sheep have mainly focused on functional genes, and with no emphasis placed on the role that long non-coding RNAs (lncRNAs) may have on the activity of those genes. Here, the expression profile of lncRNAs in ovine preadipocyte differentiation was investigated and the differentially expressed lncRNAs were screened on day 0 (D0), day 2(D2) and day 8(D8) of ovine preadipocyte differentiation, with their target genes being predicted. The competing endogenous RNA (ceRNA) regulatory network was constructed by GO and KEGG enrichment analysis for functional annotation, and some differentially expressed lncRNAs were randomly selected to verify the RNA-Seq results by RT-qPCR. In the study, a total of 2517 novel lncRNAs and 3943 known lncRNAs were identified from ovine preadipocytes at the three stages of differentiation, with the highest proportion being intergenic lncRNAs. A total of 3455 lncRNAs were expressed at all three stages of preadipocyte differentiation, while 214, 226 and 228 lncRNAs were uniquely expressed at day 0, day 2 and day 8, respectively. By comparing the expression of the lncRNAs between the three stages of differentiation stages, a total of 405, 272 and 359 differentially expressed lncRNAs were found in D0-vs-D2, D0-vs-D8, and D2-vs-D8, respectively. Functional analysis revealed that the differentially expressed lncRNAs were enriched in signaling pathways related to ovine preadipocyte differentiation, such as mitogen-activated protein kinase (MAPK) pathway, the phosphoinositide 3-kinase protein kinase B (PI3K-Akt) pathway, and the transforming growth factor beta (TGF-β) pathway. In summary, lncRNAs from preadipocytes at different stages of differentiation in sheep were identified and screened using RNA-Seq technology, and the regulatory mechanisms of lncRNAs in preadipocyte differentiation and lipid deposition were explored. This study provides a theoretical reference for revealing the roles of lncRNAs in ovine preadipocyte differentiation and also offers a theoretical basis for further understanding the regulatory mechanisms of ovine preadipocyte differentiation.

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Integrated metabolomics and transcriptomics analyses reveal the key genes regulating differential metabolites of longissimus dorsi muscle in castrated South Sichuan black goats (Capra hircus)

Zhang

Xing

Wang

et al. 2023

Funct Integr Genomics

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Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality

Cited by 4 publications

References 57 publications

Transcriptome analysis of mRNAs, lncRNAs, and miRNAs in the skeletal muscle of Tibetan chickens at different developmental stages

Transcriptome analysis of mRNAs, lncRNAs, and miRNAs in the skeletal muscle of Tibetan chickens at different developmental stages

Screening and identification of lncRNAs in preadipocyte differentiation in sheep

Integrated metabolomics and transcriptomics analyses reveal the key genes regulating differential metabolites of longissimus dorsi muscle in castrated South Sichuan black goats (Capra hircus)

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