Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle. 2021

Renqiang Yuan, and Jiaman Zhang, and Yujie Wang, and Xingxing Zhu, and Silu Hu, and Jianhua Zeng, and Feng Liang, and Qianzi Tang, and Yaosheng Chen, and Luxi Chen, and Wei Zhu, and Mingzhou Li, and Delin Mo
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.

Myofibres (primary and secondary myofibre) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibres to secondary myofibres in pigs, we conducted an integrative three-dimensional structure of genome and transcriptomic characterization of longissimus dorsi muscle of pig from primary myofibre formation stage [embryonic Day 35 (E35)] to secondary myofibre formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains are changed intradomain interactions (D-scores) and 2,730 genes with differential promoter-enhancer interactions and (or) enhancer activity from E35 to E80. The alterations of genome architecture were found to correlate with expression of genes that play significant roles in neuromuscular junction, embryonic morphogenesis, skeletal muscle development or metabolism, typically, NEFL, MuSK, SLN, Mef2D and GCK. Significantly, Sox6 and MATN2 play important roles in the process of primary to secondary myofibres formation and increase the regulatory potential score and genes expression in it. In brief, we reveal the genomic reorganization from E35 to E80 and construct genome-wide high-resolution interaction maps that provide a resource for studying long-range control of gene expression from E35 to E80.

UI MeSH Term Description Entries
D002843 Chromatin The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell. Chromatins
D004622 Embryo, Mammalian The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS. Embryonic Structures, Mammalian,Mammalian Embryo,Mammalian Embryo Structures,Mammalian Embryonic Structures,Embryo Structure, Mammalian,Embryo Structures, Mammalian,Embryonic Structure, Mammalian,Embryos, Mammalian,Mammalian Embryo Structure,Mammalian Embryonic Structure,Mammalian Embryos,Structure, Mammalian Embryo,Structure, Mammalian Embryonic,Structures, Mammalian Embryo,Structures, Mammalian Embryonic
D005260 Female Females
D000081204 Chromatin Immunoprecipitation Sequencing A technique for identifying the BINDING SITES on nucleic acid sequences that are associated with binding proteins. ATAC-Seq,Assay for Transposase-Accessible Chromatin Using Sequencing,CLIP-Seq,ChIA-PET,ChIP Sequencing,ChIP-Chip,ChIP-Exo,ChIP-Exonuclease,ChIP-PET,ChIP-Seq,Chromatin Immuno-Precipitation Paired-End Tag,Chromatin Immuno-precipitation Sequencing,Chromatin Immunoprecipitation Paired-End Tag,Chromatin Immunoprecipitation Sequencing-Chip,Cross-Linking and Immunoprecipitation Followed by Deep Sequencing,HITS-CLIP,High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation,Assay for Transposase Accessible Chromatin Using Sequencing,ChIP Exonuclease,Chromatin Immuno Precipitation Paired End Tag,Chromatin Immuno precipitation Sequencing,Chromatin Immunoprecipitation Paired End Tag,Chromatin Immunoprecipitation Sequencing Chip,Chromatin Immunoprecipitation Sequencing-Chips,Cross Linking and Immunoprecipitation Followed by Deep Sequencing,High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation,Sequencing, ChIP,Sequencing, Chromatin Immuno-precipitation,Sequencing, Chromatin Immunoprecipitation
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D017423 Sequence Analysis, RNA A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE. RNA Sequence Analysis,Sequence Determination, RNA,Analysis, RNA Sequence,Determination, RNA Sequence,Determinations, RNA Sequence,RNA Sequence Determination,RNA Sequence Determinations,RNA Sequencing,Sequence Determinations, RNA,Analyses, RNA Sequence,RNA Sequence Analyses,Sequence Analyses, RNA,Sequencing, RNA
D042002 Chromatin Assembly and Disassembly The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA. Chromatin Remodeling,Chromatin Assembly,Chromatin Disassembly,Chromatin Modeling,Chromatin Disassemblies,Disassembly, Chromatin,Remodeling, Chromatin
D047108 Embryonic Development Morphological and physiological development of EMBRYOS. Embryo Development,Embryogenesis,Postimplantation Embryo Development,Preimplantation Embryo Development,Embryonic Programming,Post-implantation Embryo Development,Postnidation Embryo Development,Postnidation Embryo Development, Animal,Pre-implantation Embryo Development,Prenidation Embryo Development, Animal,Development, Embryo,Development, Embryonic,Development, Postnidation Embryo,Embryo Development, Post-implantation,Embryo Development, Postimplantation,Embryo Development, Postnidation,Embryo Development, Pre-implantation,Embryo Development, Preimplantation,Embryonic Developments,Embryonic Programmings,Post implantation Embryo Development,Pre implantation Embryo Development
D059467 Transcriptome The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells. Transcriptomes,Gene Expression Profiles,Gene Expression Signatures,Transcriptome Profiles,Expression Profile, Gene,Expression Profiles, Gene,Expression Signature, Gene,Expression Signatures, Gene,Gene Expression Profile,Gene Expression Signature,Profile, Gene Expression,Profile, Transcriptome,Profiles, Gene Expression,Profiles, Transcriptome,Signature, Gene Expression,Signatures, Gene Expression,Transcriptome Profile
D018482 Muscle, Skeletal A subtype of striated muscle, attached by TENDONS to the SKELETON. Skeletal muscles are innervated and their movement can be consciously controlled. They are also called voluntary muscles. Anterior Tibial Muscle,Gastrocnemius Muscle,Muscle, Voluntary,Plantaris Muscle,Skeletal Muscle,Soleus Muscle,Muscle, Anterior Tibial,Muscle, Gastrocnemius,Muscle, Plantaris,Muscle, Soleus,Muscles, Skeletal,Muscles, Voluntary,Skeletal Muscles,Tibial Muscle, Anterior,Voluntary Muscle,Voluntary Muscles

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