scholarly journals Analyses of MicroRNA and mRNA Expression Profiles Reveal the Crucial Interaction Networks and Pathways for Regulation of Chicken Breast Muscle Development

2019 ◽  
Vol 10 ◽  
Author(s):  
Yuanfang Li ◽  
Yi Chen ◽  
Wenjiao Jin ◽  
Shouyi Fu ◽  
Donghua Li ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Muscle Development ◽  
Expression Profiles ◽  
Interaction Networks ◽  
Breast Muscle ◽  
Chicken Breast

scholarly journals Comprehensive Proteomic Characterization of the Pectoralis Major at Three Chronological Ages in Beijing-You Chicken

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Zhang ◽  
Jing Cao ◽  
Ailian Geng ◽  
Haihong Wang ◽  
Qin Chu ◽  
...  
Keyword(s):  
Meat Quality ◽  
Muscle Development ◽  
Expression Profiles ◽  
Pectoralis Major ◽  
Breast Muscle ◽  
Differentially Expressed ◽  
Chronological Age ◽  
Chicken Breast ◽  
Group 13 ◽  
Oocyte Meiosis

Chronological age is one of the important factors influencing muscle development and meat quality in chickens. To evaluate the protein expression profiles during skeletal muscle development, we performed a tandem mass tag (TMT)-based quantitative proteomic strategy in pectoralis major (breast muscle) of Beijing-You chicken (BYC) at the chronological age of 90, 120, and 150 days. Each chronological age contained 3 pooling samples or 15 birds (five birds per pooling sample). A total of 1,413 proteins were identified in chicken breast muscle with FDR < 1% and 197 of them were differentially expressed (fold change ≥1.2 or ≤0.83 and p < 0.05). There were 110 up- and 71 down-regulated proteins in 120 d vs 90 d group, 13 up- and 10 down-regulated proteins in 150 d vs 120 d group. The proteomic profiles of BYC at 120 d were very similar to those at 150 d and highly different from those at 90 d, suggesting that 120 d might be an important chronological age for BYC. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these differentially expressed proteins were mainly involved in the pathway of glycolysis/gluconeogenesis, adrenergic signaling in cardiomyocytes, focal adhesion, oocyte meiosis and phagosome. Furthermore, some DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. In summary, these results provided some candidate protein-coding genes for further functional validation and contribute to a comprehensive understanding of muscle development and age-dependent meat quality regulation by proteins in chickens.

scholarly journals Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler

2021 ◽  
Vol 9 ◽  
Author(s):  
Weihua Tian ◽  
Zhang Wang ◽  
Dandan Wang ◽  
Yihao Zhi ◽  
Jiajia Dong ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Intramuscular Fat ◽  
Breast Muscle ◽  
Chromatin Interaction ◽  
Chicken Breast ◽  
Meat Production ◽  
Skeletal Muscle Development ◽  
Significant Difference ◽  
Imf Content

Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken.

scholarly journals Effects of exercise on carcass composition, meat quality, and mRNA expression profiles in breast muscle of a Chinese indigenous chicken breed

2019 ◽  
Vol 98 (11) ◽  
pp. 5241-5246 ◽  
Author(s):  
Xing Guo ◽  
Jiangxian Wang ◽  
Hong Chen ◽  
Hu Su ◽  
Zhicheng Wang ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Meat Quality ◽  
Expression Profiles ◽  
Carcass Composition ◽  
Breast Muscle ◽  
Indigenous Chicken ◽  
Chicken Breed

scholarly journals LncRNAs and their regulatory networks in breast muscle tissue of Chinese Gushi chickens during late postnatal development

2021 ◽  
Author(s):  
Yuanfang Li ◽  
Wenjiao Jin ◽  
Bin Zhai ◽  
Yi Chen ◽  
Guoxi Li ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Muscle Development ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Breast Muscle ◽  
Chicken Breast ◽  
Ppi Networks ◽  
Comparison Groups ◽  
Late Stages ◽  
Go Terms

Abstract Background: Chicken skeletal muscle is an important economic product. The late stages of chicken development constitute the main period that affects meat production. LncRNAs play important roles in controlling the epigenetic process of growth and development. However, studies on the role of lncRNAs in the late stages of chicken breast muscle development are still lacking. In this study, to investigate the expression characteristics of lncRNAs during chicken muscle development, 12 cDNA libraries were constructed from Gushi chicken breast muscle samples from 6-, 14-, 22-, and 30-week-old chickens.Results: A total of 1,252 new lncRNAs and 1,376 annotated lncRNAs were identified. Furthermore, 53, 61, 50, 153, 117, and 78 DE-lncRNAs were found in the W14 vs. W6, W22 vs. W14, W22 vs. W6, W30 vs. W6, W30 vs. W14, and W30 vs. W22 comparison groups, respectively. After GO enrichment analysis of the DE-lncRNAs, several muscle development-related GO terms were found in the W22 vs. W14 comparison group. Moreover, it was found that the MAPK signaling pathway was one of the most frequently enriched pathways in the different comparison groups. In addition, 12 common target DE-miRNAs of DE-lncRNAs were found in different comparison groups, some of which were muscle-specific miRNAs, such as gga-miR-206, gga-miR-1a-3p, and miR-133a-3p. Interestingly, the precursors of four newly identified miRNAs were found to be homologous to lncRNAs. Additionally, we found some ceRNA networks associated with muscle development-related GO terms. For example, the ceRNA networks contained the DYNLL2 gene with 12 lncRNAs that targeted 2 miRNAs. We also constructed PPI networks, such as IGF-I-EGF and FZD6-WNT11.Conclusions: This study revealed, for the first time, the dynamic changes in lncRNA expression in Gushi chicken breast muscle at different periods and revealed that the MAPK signaling pathway plays a vital role in muscle development. Furthermore, MEF2C and its target lncRNA may be involved in muscle regulation through the MAPK signaling pathway. This research provided valuable resources for elucidating posttranscriptional regulatory mechanisms to promote the development of chicken breast muscles after hatching.

scholarly journals LncRNAs and their regulatory networks in breast muscle tissue of Chinese Gushi chickens during late postnatal development

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yuanfang Li ◽  
Wenjiao Jin ◽  
Bin Zhai ◽  
Yi Chen ◽  
Guoxi Li ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Muscle Development ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Breast Muscle ◽  
Chicken Breast ◽  
Ppi Networks ◽  
Comparison Groups ◽  
Late Stages ◽  
Go Terms

Abstract Background Chicken skeletal muscle is an important economic product. The late stages of chicken development constitute the main period that affects meat production. LncRNAs play important roles in controlling the epigenetic process of growth and development. However, studies on the role of lncRNAs in the late stages of chicken breast muscle development are still lacking. In this study, to investigate the expression characteristics of lncRNAs during chicken muscle development, 12 cDNA libraries were constructed from Gushi chicken breast muscle samples from 6-, 14-, 22-, and 30-week-old chickens. Results A total of 1252 new lncRNAs and 1376 annotated lncRNAs were identified. Furthermore, 53, 61, 50, 153, 117, and 78 DE-lncRNAs were found in the W14 vs. W6, W22 vs. W14, W22 vs. W6, W30 vs. W6, W30 vs. W14, and W30 vs. W22 comparison groups, respectively. After GO enrichment analysis of the DE-lncRNAs, several muscle development-related GO terms were found in the W22 vs. W14 comparison group. Moreover, it was found that the MAPK signaling pathway was one of the most frequently enriched pathways in the different comparison groups. In addition, 12 common target DE-miRNAs of DE-lncRNAs were found in different comparison groups, some of which were muscle-specific miRNAs, such as gga-miR-206, gga-miR-1a-3p, and miR-133a-3p. Interestingly, the precursors of four newly identified miRNAs were found to be homologous to lncRNAs. Additionally, we found some ceRNA networks associated with muscle development-related GO terms. For example, the ceRNA networks contained the DYNLL2 gene with 12 lncRNAs that targeted 2 miRNAs. We also constructed PPI networks, such as IGF-I-EGF and FZD6-WNT11. Conclusions This study revealed, for the first time, the dynamic changes in lncRNA expression in Gushi chicken breast muscle at different periods and revealed that the MAPK signaling pathway plays a vital role in muscle development. Furthermore, MEF2C and its target lncRNA may be involved in muscle regulation through the MAPK signaling pathway. This research provided valuable resources for elucidating posttranscriptional regulatory mechanisms to promote the development of chicken breast muscles after hatching.

scholarly journals LncRNAs and their regulatory networks in breast muscle tissue of Chinese Gushi chicken during postnatal late development

2020 ◽  
Author(s):  
Yuanfang Li ◽  
Wenjiao Jin ◽  
Bin Zhai ◽  
Yi Chen ◽  
Guoxi Li ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Muscle Development ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Breast Muscle ◽  
Chicken Breast ◽  
Ppi Networks ◽  
Comparison Groups ◽  
Late Stages ◽  
Go Terms

Abstract Background: Chicken skeletal muscle is an important economic product. Late stages of chicken development are the main period that affects meat production. LncRNAs play important roles in controlling the epigenetic process of growth and development. However, studies on the role of lncRNAs in the late stages of chicken breast muscle development are still lacking. In this study, in order to study the expression characteristics of lncRNAs during chicken muscle development, 12 cDNA libraries were constructed from Gushi chicken breast muscle samples from 6-, 14-, 22-, and 30-week-old chickens.Results: Therefore, a total of 1,252 new lncRNAs and 1,376 annotated lncRNAs were identified. Furthermore, 53, 61, 50, 153, 117, and 78 DE-lncRNAs were found in the W14 vs. W6, W22 vs. W14, W22 vs. W6, W30 vs. W6, W30 vs. W14, and W30 vs. W22 comparison groups, respectively. After GO enrichment analysis of the DE-lncRNAs, several muscle development-related GO terms were found in the W22 vs. W14 comparison group. Furthermore, it was found that the MAPK signaling pathway was one of the most frequently enriched pathways in the different comparison groups. In addition, 12 common target DE-miRNAs of DE-lncRNAs were found in different comparison groups, some of which were muscle-specific miRNAs, such as gga-miR-206, gga-miR-1a-3p, and miR-133a-3p. Interestingly, the precursors of four newly identified miRNAs were found to be homologous to lncRNAs. Furthermore, we found some ceRNA networks associated with muscle development-related GO terms. For example, the ceRNA networks containing the DYNLL2 gene with 12 lncRNAs that targeted 2 miRNAs. In addition, we also constructed PPI networks, such as IGF-I-EGF and FZD6-WNT11, etc.Conclusions: This study for the first time revealed the dynamic changes of lncRNA expression in Gushi chicken breast muscle at different periods, and reveal the MAPK signaling pathway play a vital role in muscle development. Furthermore, MEF2C and its target lncRNA may be involved in muscle regulation through the MAPK signaling pathway. This research provided valuable resources for elucidating post-transcriptional regulatory mechanisms to promote the development of chicken breast muscles after hatching.

scholarly journals LncRNAs and their regulatory networks in breast muscle tissue of Chinese Gushi chicken during postnatal late development

2020 ◽  
Author(s):  
Yuanfang Li ◽  
Yi Chen ◽  
Wenjiao Jin ◽  
Bin Zhai ◽  
Guoxi Li ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Muscle Development ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Breast Muscle ◽  
Chicken Breast ◽  
Ppi Networks ◽  
Comparison Groups ◽  
Late Stages ◽  
Go Terms

Abstract Background: Chicken skeletal muscle is an important economic product. Late stages of chicken development are the main period that affects meat production. LncRNAs play important roles in controlling the epigenetic process of growth and development. However, studies on the role of lncRNAs in the late stages of chicken breast muscle development are still lacking. In this study, in order to study the expression characteristics of lncRNAs during chicken muscle development, 12 cDNA libraries were constructed from Gushi chicken breast muscle samples from 6-, 14-, 22-, and 30-week-old chickens. Results: Therefore, a total of 1,252 new lncRNAs and 1,376 annotated lncRNAs were identified. Furthermore, 53, 61, 50, 153, 117, and 78 DE-lncRNAs were found in the W14 vs. W6, W22 vs. W14, W22 vs. W6, W30 vs. W6, W30 vs. W14 , and W30 vs. W22 comparison groups, respectively. After GO enrichment analysis of the DE-lncRNAs, several muscle development-related GO terms were found in the W22 vs. W14 comparison group. Furthermore, it was found that the MAPK signaling pathway was one of the most frequently enriched pathways in the different comparison groups. In addition, 12 common target DE-miRNAs of DE-lncRNAs were found in different comparison groups, some of which were muscle-specific miRNAs, such as gga-miR-206, gga-miR-1a-3p, and miR-133a-3p. Interestingly, the precursors of four newly identified miRNAs were found to be homologous to lncRNAs. Furthermore, we found some ceRNA networks associated with muscle development-related GO terms. For example, the ceRNA networks containing the DYNLL2 gene with 12 lncRNAs that targeted 2 miRNAs. In addition, we also constructed PPI networks, such as IGF-I - EGF and FZD6 - WNT11 , etc. Conclusions: This study for the first time revealed the dynamic changes of lncRNA expression in Gushi chicken breast muscle at different periods, and reveal the MAPK signaling pathway play a vital role in muscle development. Furthermore, MEF2C and its target lncRNA may be involved in muscle regulation through the MAPK signaling pathway. This research provided valuable resources for elucidating post-transcriptional regulatory mechanisms for postpartum development of chicken breast muscle.

Sign in / Sign up

Export Citation Format

Share Document