Dynamic Transcriptomic Analysis of Breast Muscle Development From the Embryonic to Post-hatching Periods in Chickens

Liu, Jie; Lei, Qiuxia; Li, Fuwei; Zhou, Yan; Gao, Jinbo; Liu, Wei; Han, Haitang; Cao, Deliang

doi:10.3389/fgene.2019.01308

Cited by 19 publications

(16 citation statements)

References 33 publications

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“…In the later stage of embryonic development, the number of differentially expressed genes decreased sharply. A similar gene expression pattern which we employed to assess muscle development after birth [20]. These ndings collectively provide evidence that the embryonic stage is the critical point of muscle development and the most extensive time of gene expression.…”

Section: Discussionmentioning

confidence: 55%

“…Notably, on the 12th day of embryonic development, muscle bers were yet to be formed (in the stage of fusion of multinucleated myotubes to form muscle bers), which was similar to the formation time of intact muscle bers in many local chicken breeds but took longer than fast-large broiler breeds [16]. A wealth of studies had shown that the embryonic period is a critical period for muscle development, during which the expression of muscle development-related genes was most active [17,18]. To elucidate the speci c variation of muscle development, we used the transcriptome analysis to explore the gene regulation network.…”

Section: Discussionmentioning

confidence: 95%

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Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Ren

Liu

Wang

et al. 2020

Preprint

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Background: Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21. Results: Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P<0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,251 (E12vsE16), 4,324 (E12vsE19), and 5,224 (E12vsE21), 1,274 (E16vsE19), 2,735 (E16vsE21) and 857 (E19vsE21) differentially expressed mRNAs were identified. It is worth noting that 6,726 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The downward trend was the most important and was enriched in 3,963 DEGs. GO enrichment analysis provided three significantly enriched categories of the down-trending genes, including 91 cellular components, 53 molecular functions, and 248 biological processes. Through KEGG analysis, we explored the pathway of downtrend genes. A total of 183 KEGG pathways were enriched, including 17 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P<0.05), MAPK signalingpathway, TGF-beta signaling pathway, and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3. Conclusion: Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.

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Section: Discussionmentioning

confidence: 55%

Section: Discussionmentioning

confidence: 95%

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Ren

Liu

Wang

et al. 2020

Preprint

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show abstract

“…In addition, 13 DEGs were enriched in the biosynthesis of amino acid pathway, of which 12 DEGs were upregulated in the breast muscle (Table S4). Another study found that genes related to glycolysis/gluconeogenesis and the biosynthesis of amino acid pathway were gradually upregulated during the growth and development of chicken breast muscle [63]. Therefore, we inferred that these DEGs were activated during fast-twitch muscle fiber formation.…”

mentioning

confidence: 79%

Identification of Differentially Expressed Genes in Different Types of Broiler Skeletal Muscle Fibers Using the RNA-seq Technique

Wang

Shen

Zhou

et al. 2020

BioMed Research International

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The difference in muscle fiber types is very important to the muscle development and meat quality of broilers. At present, the molecular regulation mechanisms of skeletal muscle fiber-type transformation in broilers are still unclear. In this study, differentially expressed genes between breast and leg muscles in broilers were analyzed using RNA-seq. A total of 767 DEGs were identified. Compared with leg muscle, there were 429 upregulated genes and 338 downregulated genes in breast muscle. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in cellular processes, single organism processes, cells, and cellular components, as well as binding and catalytic activity. KEGG analysis shows that a total of 230 DEGs were mapped to 126 KEGG pathways and significantly enriched in the four pathways of glycolysis/gluconeogenesis, starch and sucrose metabolism, insulin signalling pathways, and the biosynthesis of amino acids. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differential expression of 7 selected DEGs, and the results were consistent with RNA-seq data. In addition, the expression profile of MyHC isoforms in chicken skeletal muscle cells showed that with the extension of differentiation time, the expression of fast fiber subunits (types IIA and IIB) gradually increased, while slow muscle fiber subunits (type I) showed a downward trend after 4 days of differentiation. The differential genes screened in this study will provide some new ideas for further understanding the molecular mechanism of skeletal muscle fiber transformation in broilers.

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“…miR-NAs as important post-transcriptional regulators play essential roles in fine tuning gene expression dynamics [15,16]. We previously explored mRNA expression dynamics across chicken muscle developmental stages and found that there were distinct expression profiles in embryonic and post-hatching periods [14]. Therefore, to conduct a comprehensive study of miRNA expression dynamics and highlight key properties of miRNAs during chicken muscle development, we explored the expression patterns of miRNAs in chicken breast muscle from embryonic to post-hatching periods.…”

Section: Discussionmentioning

confidence: 99%

“…In addition to these complex cell developmental processes during myofiber formation and hypertrophy, the fine-tuned regulation of numerous myogenic genes is also important for the development of skeletal muscle [4]. Our previous study also showed that there were distinct gene regulatory mechanisms of chicken muscle development between the embryonic and post-hatching periods, based on RNA sequencing of breast muscle tissue obtained from Shouguang chickens at 12-day embryo (E12), E17 and day 1 (D1), D14, D56 and D98 post-hatching stages [14]. However, a comprehensive study of the dynamics of miRNAs during chicken muscle development is lacking, especially from embryonic to post-hatching period.…”

Section: Introductionmentioning

confidence: 91%

Deciphering the miRNA transcriptome of breast muscle from the embryonic to post-hatching periods in chickens

Liu

et al. 2021

BMC Genomics

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Background miRNAs play critical roles in growth and development. Various studies of chicken muscle development have focused on identifying miRNAs that are important for embryo or adult muscle development. However, little is known about the role of miRNAs in the whole muscle development process from embryonic to post-hatching periods. Here, we present a comprehensive investigation of miRNA transcriptomes at 12-day embryo (E12), E17, and day 1 (D1), D14, D56 and D98 post-hatching stages. Results We identified 337 differentially expressed miRNAs (DE-miRNAs) during muscle development. A Short Time-Series Expression Miner analysis identified two significantly different expression profiles. Profile 4 with downregulated pattern contained 106 DE-miRNAs, while profile 21 with upregulated pattern contained 44 DE-miRNAs. The DE-miRNAs with the upregulated pattern mainly played regulatory roles in cellular turnover, such as pyrimidine metabolism, DNA replication, and cell cycle, whereas DE-miRNAs with the downregulated pattern directly or indirectly contributed to protein turnover metabolism such as glycolysis/gluconeogenesis, pyruvate metabolism and biosynthesis of amino acids. Conclusions The main functional miRNAs during chicken muscle development differ between embryonic and post-hatching stages. miRNAs with an upregulated pattern were mainly involved in cellular turnover, while miRNAs with a downregulated pattern mainly played a regulatory role in protein turnover metabolism. These findings enrich information about the regulatory mechanisms involved in muscle development at the miRNA expression level, and provide several candidates for future studies concerning miRNA-target function in regulation of chicken muscle development.

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Dynamic Transcriptomic Analysis of Breast Muscle Development From the Embryonic to Post-hatching Periods in Chickens

Cited by 19 publications

References 33 publications

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Identification of Differentially Expressed Genes in Different Types of Broiler Skeletal Muscle Fibers Using the RNA-seq Technique

Deciphering the miRNA transcriptome of breast muscle from the embryonic to post-hatching periods in chickens

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