scholarly journals The Landscape of Chromatin Accessibility in Skeletal Muscle During Embryonic Development in Pigs

2020 ◽  
Author(s):  
Jingwei Yue ◽  
Xinhua Hou ◽  
Xin Liu ◽  
Ligang Wang ◽  
Hongmei Gao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factors ◽  
Embryonic Development ◽  
Muscle Development ◽  
Chromatin Accessibility ◽  
Regulatory Role ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Embryonic Muscle ◽  
Embryonic Muscle Development

Abstract Background: The development of skeletal muscle during the embryonic stage in pigs is precisely regulated by transcriptional regulation, which depends on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq on skeletal muscle of pig embryos at 45, 70 and 100 days post coitus (dpc). Results: In total, 21638, 35447 and 60181 unique regions (or peaks) were found across 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100) embryos, respectively. More than 91% of peaks were annotated within -1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from 45 to 100 dpc embryos suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings of integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the peak intensities of ACRs could control the expression of associated genes. Finally, motif screening of stage-specific ACRs revealed some transcription factors that regulated muscle development-related genes, such as MyoD, Mef2c, Mef2d and Pax7. Several potential transcriptional repressors, including E2F6, GRHL2, OTX2 and CTCF, were identified among those genes that exhibited different change trends between the ATAC-seq and RNA-seq data. Conclusions: This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.

scholarly journals The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jingwei Yue ◽  
Xinhua Hou ◽  
Xin Liu ◽  
Ligang Wang ◽  
Hongmei Gao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factors ◽  
Embryonic Development ◽  
Muscle Development ◽  
Chromatin Accessibility ◽  
Regulatory Role ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Embryonic Muscle ◽  
Embryonic Muscle Development

Abstract Background The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc). Results In total, 21,638, 35,447 and 60,181 unique regions (or peaks) were found across the embryos at 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100), respectively. More than 91% of the peaks were annotated within − 1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes. Moreover, the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle development-related genes, such as MyoG, Mef2c, and Mef2d. Several potential transcriptional repressors, including E2F6, OTX2 and CTCF, were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data. Conclusions This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.

scholarly journals The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs

2021 ◽  
Author(s):  
Jingwei Yue ◽  
Xinhua Hou ◽  
Xin Liu ◽  
Ligang Wang ◽  
Hongmei Gao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factors ◽  
Embryonic Development ◽  
Muscle Development ◽  
Expression Patterns ◽  
Chromatin Accessibility ◽  
Rna Seq ◽  
Transcription Start Sites ◽  
Embryonic Muscle ◽  
Embryonic Muscle Development

Abstract Background: The development of skeletal muscle during the embryonic stage in pigs is precisely regulated by transcriptional mechanisms, which depends on chromatin accessibility. However, the landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq on skeletal muscle of pig embryos at 45, 70 and 100 days post coitus (dpc).Results: In total, 21638, 35447 and 60181 unique regions (or peaks) were found across 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100) embryos, respectively. More than 91% of peaks were annotated within -1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from 45 to 100 dpc embryos suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings of integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the peak intensities of ACRs could control the expression of associated genes. Finally, motif screening of stage-specific ACRs revealed some transcription factors that regulated muscle development-related genes, such as MyoD, Mef2c, and Mef2d. Motif screening of DPI of common peaks detected that a potential transcriptional repressor, namely CTCF, was identified among those genes that exhibited different change trends between the ATAC-seq and RNA-seq data.Conclusions: This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.

Integrated analysis of miRNA-mediated ceRNA networks in ovine skeletal muscle development

2020 ◽  
Author(s):  
Tianpei Shi ◽  
Xinyue WANG ◽  
Zhida ZHAO ◽  
Wenping HU ◽  
Li ZHANG
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factors ◽  
Muscle Development ◽  
Muscle Growth ◽  
Growth Potential ◽  
Regulatory Role ◽  
Integrated Analysis ◽  
Interaction Patterns ◽  
Rna Seq ◽  
Skeletal Muscle Development

Abstract Background: The embryo stage is a key period for sheep skeletal muscle growth and development. Proliferation, differentiation, and hypertrophy of fibers affect muscle growth potential directly. Analyzing transcriptome data is of great significance for revealing important time nodes of fetus muscle development and screening related regulation factors. Muscle development is a complex biological process, including a intricate network of multiple factor interactions. Among them, non-coding RNA, especially miRNA-mediated regulation, plays a fine regulatory role. The purpose of this study was to investigate the important genes and transcripts involved in the genetic mechanism of embryos skeletal muscle development in late pregnancy. Results: Herein we did a small RNA sequencing(RNA-Seq) of embryo at 85 days (D85N), 105 days (D105N) and 135 days(D135N), then performed bioinformatic analysis in order to identify the miRNA-mediated co-expression networks. Our findings identified 505 DE-miRNAs. Integrating the current miRNA data and the previously obtained lncRNA data, multiple networks were constructed, including miRNA-mRNA, miRNA-target gene(TG)-pathway, lncRNA-miRNA-mRNA, and miRNA-TG-transcription factor (TF) network. The results showed that the miRNA-mRNA network and lncRNA-miRNA-mRNA network identified three important lncRNAs (MSTRG.3533, MSTRG.4324, and MSTRG.1470) and three miRNAs(miR-493-3p, miR-3959-3p and miR-410-5p). The four genes ( TEAD1 , ZBTB34 , GSK3B, and POGLUT1 ) and three transcription factors (C / EBPbeta, TFIID, and PR B) play a key regulatory role in the miRNA-TG-TF network. Notably, a similar trend of gene expression was reported by RT-qPCR for RNA-seq data. Conclusions: This study identified three miRNAs, three lncRNAs, four genes, and three transcription factors, and revealed their crucial role in fetal fibrogenesis and lipid metabolism. It also shows that D105N is a pivotal turning point from myotube differentiation to fiber hypertrophy. These findings provide valuable references for network interaction patterns, which helps to evaluate the biological significance of skeletal muscle in the late development stage.

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 Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

2021 ◽  
Vol 8 ◽  
Author(s):  
Weiwei Miao ◽  
Zeqiang Ma ◽  
Zhanyang Tang ◽  
Lin Yu ◽  
Siqi Liu ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factors ◽  
Signaling Pathway ◽  
Growth And Development ◽  
Muscle Development ◽  
Muscle Fibers ◽  
Muscle Growth ◽  
Rna Seq ◽  
Accessible Chromatin

Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. There is a significant correlation between the quality of different breeds of pork and the characteristics of muscle fiber, which is an important factor affecting the quality of pork. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.

The Mef2c gene is a direct transcriptional target of myogenic bHLH and MEF2 proteins during skeletal muscle development

Development ◽  
2001 ◽  
Vol 128 (22) ◽  
pp. 4623-4633 ◽  
Author(s):  
Da-Zhi Wang ◽  
M. Renee Valdez ◽  
John McAnally ◽  
James Richardson ◽  
Eric N. Olson
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Transcription Factors ◽  
Binding Site ◽  
Control Region ◽  
Muscle Development ◽  
Regulatory Elements ◽  
Skeletal Muscle Development ◽  
Helix Loop Helix

Members of the MEF2 family of transcription factors are upregulated during skeletal muscle differentiation and cooperate with the MyoD family of myogenic basic helix-loop-helix (bHLH) transcription factors to control the expression of muscle-specific genes. To determine the mechanisms that regulate MEF2 gene expression during skeletal muscle development, we analyzed the mouse Mef2c gene for cis-regulatory elements that direct expression in the skeletal muscle lineage in vivo. We describe a skeletal muscle-specific control region for Mef2c that is sufficient to direct lacZ reporter gene expression in a pattern that recapitulates that of the endogenous Mef2c gene in skeletal muscle during pre- and postnatal development. This control region is a direct target for the binding of myogenic bHLH and MEF2 proteins. Mutagenesis of the Mef2c control region shows that a binding site for myogenic bHLH proteins is essential for expression at all stages of skeletal muscle development, whereas an adjacent MEF2 binding site is required for maintenance but not for initiation of Mef2c transcription. Our findings reveal the existence of a regulatory circuit between these two classes of transcription factors that induces, amplifies and maintains their expression during skeletal muscle development.

scholarly journals Overexpression of the Rybp Gene Inhibits Differentiation of Bovine Myoblasts into Myotubes

2018 ◽  
Vol 19 (7) ◽  
pp. 2082
Author(s):  
Xiaotong Su ◽  
Yanfang Zhao ◽  
Yaning Wang ◽  
Le Zhang ◽  
Linsen Zan ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Molecular Breeding ◽  
Theoretical Foundation ◽  
Negative Control ◽  
Myoblast Differentiation ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Morphological Differences ◽  
Bovine Skeletal Muscle

RING1 and YY1 binding protein (Rybp) genes inhibit myogenesis in mice, but there are no reports on the effects of these genes in cattle. The aim of this study is to investigate the roles of the Rybp gene on bovine skeletal muscle development and myoblast differentiation. In the present study, the Rybp gene was overexpressed in bovine myoblasts via adenovirus. RNA-seq was performed to screen differentially expressed genes (DEGs). The results showed that overexpressing the Rybp gene inhibits the formation of myotubes. The morphological differences in myoblasts began on the second day and were very significant 6 days after adenovirus induction. A total of 1311 (707 upregulated and 604 downregulated) DEGs were screened using RNA-seq between myoblasts with added negative control adenoviruses (AD-NC) and Rybp adenoviruses (AD-Rybp) after 6 days of induction. Gene ontology (GO) and KEGG analysis revealed that the downregulated DEGs were mainly involved in biological functions related to muscle, and, of the 32 pathways, those associated with muscle development were significantly enriched for the identified DEGs. This study can not only provide a theoretical basis for the regulation of skeletal muscle development in cattle by exploring the roles of the Rybp gene in myoblast differentiation, but it can also lay a theoretical foundation for molecular breeding of beef cattle.

scholarly journals Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Zheng ◽  
Cuiyun Zhu ◽  
Jing Jing ◽  
Yinghui Ling ◽  
Shuaiqi Qin ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Paraffin Section ◽  
Rabbit Skeletal Muscle ◽  
Differentially Expressed ◽  
Adult Rabbit ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Host Genes

Abstract Background The temporal expression pattern of circular RNAs (circRNAs) across developmental stages is essential for skeletal muscle growth and functional analysis. However, there are few analyses on the potential functions of circRNAs in rabbit skeletal muscle development. Results Initially, the paraffin sections showed extremely significant differences in the diameter, number, area and density of skeletal muscle fibers of the fetus, child, adult rabbit hind legs (P < 0.01). Then, RNA-seq libraries of these three stages were constructed. A total of 481 differentially expressed circRNAs (DE-circRNAs) and 5,658 differentially expressed genes (DEGs) were identified. Subsequently, DE-circRNAs, whose host genes were DEGs or non-DEGs, were analyzed by GO respectively. In the fetus vs. child group, up-regulated DE-circRNAs (whose host genes were DEGs) were related to muscle fiber structure, and down-regulated ones were related to mitosis. The up-regulated DE-circRNAs (whose host genes were non-DEGs) were involved in enzyme activity, methylation and glycosylation, and the down-regulated ones were involved in mitosis and catabolism. In the fetus vs. adult group, the up-regulated DE-circRNAs (whose host genes were DEGs) were related to skeletal muscle basic structure, and the down-regulated ones were also associated with cell proliferation. But the up-regulated DE-circRNAs (whose host genes were non-DEGs) were connected with regulation of histone ubiquitination, chromatin and organelles. The down-regulated DE-circRNAs were connected with the catabolism processes. In addition, novel_circ_0022663 and novel_circ_0005489, which might have coding potential, and novel_circ_0004210 and novel_circ_0001669, which might have miRNA sponge capability, were screened out. Conclusions In this study, hind leg muscles of fetus, child and adult rabbits were collected for paraffin section and RNA-seq to observe the structural changes of skeletal muscle and obtain circRNA expression profiles at different stages. These data provided a catalog of circRNAs related to muscle development in New Zealand rabbits, allowing us to better understand the functional transitions in mammalian muscle development.

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