Dataset Information

The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken.

ABSTRACT: Scope: As DNA methylation is one of the key epigenetic mechanisms involved in embryonic muscle development, elucidating its relationship with non-coding RNAs and genes is essential for understanding early muscle development. The methylome profiles of pre-hatching chicken across multiple developmental stages remain incomplete although several related studies have been reported. Methods: In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq of broilers and layers in different embryonic development points (E10, E13, E16 and E19) to explore the genetic basis of embryonic muscle development in chicken. The differential methylated regions and novel lncRNAs were identified for association analyses. Through genomic position and correlation analysis between DMRs and lncRNAs, the target lncRNAs were detected to participate in the embryonic muscle formation and the results were then verified in vitro experiments. Results: Comparison of methylome profiles between two chicken lines revealed that lower methylation in broilers might contribute to muscle development in embryonic period. Differential methylated region analysis showed that the majority of differential methylated regions were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, we identified a long non-coding RNA MyH1-AS that potentially regulated embryonic muscle development, proved by the regulatory network construction and further in vitro experiments. Conclusion: Our study revealed an integrative landscape of middle- to late-stage of embryonic myogenesis in chicken, gave rise to a comprehensive understanding of epigenetic and transcriptional regulation in muscle development. Moreover, we provided a reliable data resource for further embryonic muscle development studies.

SUBMITTER: Liu Z

PROVIDER: S-EPMC6643139 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken.

Liu Zihao Z Han Shunshun S Shen Xiaoxu X Wang Yan Y Cui Can C He Haorong H Chen Yuqi Y Zhao Jing J Li Diyan D Zhu Qing Q Yin Huadong H

International journal of biological sciences 20190602 7

<b>Scope</b>: As DNA methylation is one of the key epigenetic mechanisms involved in embryonic muscle development, elucidating its relationship with non-coding RNAs and genes is essential for understanding early muscle development. The methylome profiles of pre-hatching chicken across multiple developmental stages remain incomplete although several related studies have been reported. <b>Methods</b>: In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq of ...[more]

PMID: 31337971

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Project description:The embryogenesis period is critical for epigenetic reprogramming and is thus of great significance in the research field of poultry epigenetics for elucidation of the trends in DNA methylation variations during the embryonic development of birds, particularly due to differences in embryogenesis between birds and mammals. Here, we first examined the variations in genomic DNA methylation during chicken embryogenesis through high-performance liquid chromatography using broilers as the model organism. We then identified the degree of DNA methylation of the promoters and gene bodies involved in two specific genes (IGF2 and TNF-?) using the bisulfite sequencing polymerase chain reaction method. In addition, we measured the expression levels of IGF2, TNF-? and DNA methyltransferase (DNMT) 1, 3a and 3b. Our results showed that the genomic DNA methylation levels in the liver, heart and muscle increased during embryonic development and that the methylation level of the liver was significantly higher in mid-anaphase. In both the muscle and liver, the promoter methylation levels of TNF-? first increased and then decreased, whereas the gene body methylation levels remained lower at embryonic ages E8, 11 and 14 before increasing notably at E17. The promoter methylation level of IGF2 decreased persistently, whereas the methylation levels in the gene body showed a continuous increase. No differences in the expression of TNF-? were found among E8, 11 and 14, whereas a significant increase was observed at E17. IGF2 showed increasing expression level during the examined embryonic stages. In addition, the mRNA and protein levels of DNMTs increased with increasing embryonic ages. These results suggest that chicken shows increasing genomic DNA methylation patterns during the embryonic period. Furthermore, the genomic DNA methylation levels in tissues are closely related to the genes expression levels, and gene expression may be simultaneously regulated by promoter hypomethylation and gene body hypermethylation.

Project description:BackgroundMuscle 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.ResultsDiameter 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, 2,262 in E12vsE16, 5,058 in E12vsE19, 6139 in E12vsE21, 1,282 in E16vsE19, 2,920 in E16vsE21, and 646 in E19vsE21differentially expressed mRNAs were identified. It is worth noting that 7,572 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 significant enrichment trends included 3,150 DEGs. GO enrichment analysis provided three significantly enriched categories of significantly enriched differential genes, including 65 cellular components, 88 molecular functions, and 453 biological processes. Through KEGG analysis, we explored the biological metabolic pathways involved in differentially expressed genes. A total of 177 KEGG pathways were enriched, including 19 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, PI3K-Akt 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.ConclusionsOur 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.

Project description:BACKGROUND:Genetically selected modern broiler chickens have acquired outstanding production efficiency through rapid growth and improved feed efficiency compared to unselected chicken breeds. Recently, we analyzed the transcriptome of breast muscle tissues obtained from modern pedigree male (PeM) broilers (rapid growth and higher efficiency) and foundational Barred Plymouth Rock (BPR) chickens (slow growth and poorer efficiency). This study was designed to investigate microRNAs that play role in rapid growth of the breast muscles in modern broiler chickens. RESULTS:In this study, differential abundance of microRNA (miRNA) was analyzed in breast muscle of PeM and BPR chickens and the results were integrated with differentially expressed (DE) mRNA in the same tissues. A total of 994 miRNA were identified in PeM and BPR chicken lines from the initial analysis of small RNA sequencing data. After filtering and statistical analyses, the results showed miR-2131-5p, miR-221-5p, miR-126-3p, miR-146b-5p, miR-10a-5p, let-7b, miR-125b-5p, and miR-146c-5p up-regulated whereas miR-206 down-regulated in PeM compared to BPR breast muscle. Based on inhibitory regulations of miRNAs on the mRNA abundance, our computational analysis using miRDB, an online software, predicated that 118 down-regulated mRNAs may be targeted by the up-regulated miRNAs, while 35 up-regulated mRNAs appear to be due to a down-regulated miRNA (i.e., miR-206). Functional network analyses of target genes of DE miRNAs showed their involvement in calcium signaling, axonal guidance signaling, and NRF2-mediated oxidative stress response pathways suggesting their involvement in breast muscle growth in chickens. CONCLUSION:From the integrated analyses of differentially expressed miRNA-mRNA data, we were able to identify breast muscle specific miRNAs and their target genes whose concerted actions can contribute to rapid growth and higher feed efficiency in modern broiler chickens. This study provides foundation data for elucidating molecular mechanisms that govern muscle growth in chickens.

Project description:BackgroundChicken provides humans with a large amount of animal protein every year, in which skeletal muscle plays a leading role. The embryonic skeletal muscle development determines the number of muscle fibers and will affect the muscle production of chickens. CircRNAs are involved in a variety of important biological processes, including muscle development. However, studies on circRNAs in the chicken embryo muscle development are still lacking.ResultsIn the study, we collected chicken leg muscles at 14 and 20-day embryo ages both in the fast- and slow-growing groups for RNA-seq. We identified 245 and 440 differentially expressed (DE) circRNAs in the comparison group F14vsF20 and S14vsS20 respectively. GO enrichment analysis for the host genes of DE circRNAs showed that biological process (BP) terms in the top 20 related to growth in F14vsF20 were found such as positive regulation of transcription involved in G1/S phase of mitotic cell cycle, multicellular organismal macromolecule metabolic process, and multicellular organismal metabolic process. In group S14vsS20, we also found some BP terms associated with growth in the top 20 including actomyosin structure organization, actin cytoskeleton organization and myofibril assembly. A total of 7 significantly enriched pathways were obtained, containing Adherens junction and Tight junction. Further analysis of those pathways found three crucial host genes MYH9, YBX3, IGF1R in both fast- and slow-growing groups, three important host genes CTNNA3, AFDN and CREBBP only in the fast-growing group, and six host genes FGFR2, ACTN2, COL1A2, CDC42, DOCK1 and MYL3 only in the slow-growing group. In addition, circRNA-miRNA network also revealed some key regulation pairs such as novel_circ_0007646-miR-1625-5p, novel_circ_0007646-miR-1680-5p, novel_circ_0008913-miR-148b-5p, novel_circ_0008906-miR-148b-5p and novel_circ_0001640-miR-1759-3p.ConclusionsComprehensive analysis of circRNAs and their targets would contribute to a better understanding of the molecular mechanisms in poultry skeletal muscle and it also plays an important guiding role in the next research.

Dataset Information

The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken.

Publications

The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken.

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