Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2022-05-03

AUTHORS

Qiuxia Lei, Xin Hu, Haixia Han, Jie Wang, Wei Liu, Yan Zhou, Dingguo Cao, Fuwei Li, Jie Liu

ABSTRACT

BackgroundThe growth and development of skeletal muscle are regulated by protein-coding genes and non-coding RNA. Circular RNA (circRNA) is a type of non-coding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. To better understand the regulatory mechanism of circRNAs during the development of muscle in chicken, we performed RNA-seq with linear RNA depletion for chicken breast muscle in 12 (E 12) and17 (E 17) day embryos, and 1 (D 1), 14 (D 14), 56 (D 56), and 98 (D 98) days post-hatch.ResultsWe identified 5755 differentially expressed (DE)-circRNAs during muscle development. We profiled the expression of DE-circRNAs and mRNAs (identified in our previous study) at up to six time points during chicken muscle development and uncovered a significant profile (profile 16) for circRNA upregulation during aging in muscle tissues. To investigate competing endogenous RNA (ceRNA) regulation in muscle and identify muscle-related circRNAs, we constructed a circRNA-miRNA-mRNA regulatory network using the circRNAs and mRNAs from profile 16 and miRNAs identified in our previous study, which included 361 miRNAs, 68 circRNAs, 599 mRNAs, and 31,063 interacting pairs. Functional annotation showed that upregulated circRNAs might contribute to glycolysis/gluconeogenesis, biosynthesis of amino acids, pyruvate metabolism, carbon metabolism, glycogen and sucrose metabolism through the ceRNA network, and thus affected postnatal muscle development by regulating muscle protein deposition. Of them, circRNA225 and circRNA226 from the same host gene might be key circRNAs that could regulate muscle development by interacting with seven common miRNAs and 207 mRNAs. Our experiments also demonstrated that there were interactions among circRNA225, gga-miR-1306-5p, and heat shock protein alpha 8 (HSPA8).ConclusionsOur results suggest that adequate supply of nutrients such as energy and protein after hatching may be a key factor in ensuring chicken yield, and provide several candidate circRNAs for future studies concerning ceRNA regulation during chicken muscle development. More... »

PAGES

342

References to SciGraph publications

  • 2011-05-23. Transcriptional mechanisms regulating skeletal muscle differentiation, growth and homeostasis in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2007-03-01. Target genes of myostatin loss-of-function in muscles of late bovine fetuses in BMC GENOMICS
  • 2012-03-27. Identification and characterization of genes related to the development of breast muscles in Pekin duck in MOLECULAR BIOLOGY REPORTS
  • 2021-01-19. Deciphering the miRNA transcriptome of breast muscle from the embryonic to post-hatching periods in chickens in BMC GENOMICS
  • 2013-04-25. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions in GENOME BIOLOGY
  • 2007-03-13. Birth size, adult body composition and muscle strength in later life in INTERNATIONAL JOURNAL OF OBESITY
  • 2017-10-23. Uncovering the embryonic development-related proteome and metabolome signatures in breast muscle and intramuscular fat of fast-and slow-growing chickens in BMC GENOMICS
  • 2017-10-09. Dynamic transcriptomic analysis in hircine longissimus dorsi muscle from fetal to neonatal development stages in FUNCTIONAL & INTEGRATIVE GENOMICS
  • 2009-02-10. MicroRNA transcriptome profiles during swine skeletal muscle development in BMC GENOMICS
  • 2011-08-11. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts in GENOME BIOLOGY
  • 2015-08-09. The role of leucine and its metabolites in protein and energy metabolism in AMINO ACIDS
  • 2006-04-05. STEM: a tool for the analysis of short time series gene expression data in BMC BIOINFORMATICS
  • 2012-03-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s12864-022-08525-5

    DOI

    http://dx.doi.org/10.1186/s12864-022-08525-5

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1147539595

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/35505302


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biochemistry and Cell Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Animals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chickens", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "MicroRNAs", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Muscle Development", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Circular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Messenger", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Poultry Breeding Engineering Technology Center of Shandong Province, 250023, Ji\u2019nan, China", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
                "Poultry Breeding Engineering Technology Center of Shandong Province, 250023, Ji\u2019nan, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lei", 
            "givenName": "Qiuxia", 
            "id": "sg:person.013304734357.25", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013304734357.25"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Li\u00e8ge, 5030, Gembloux, Belgium", 
              "id": "http://www.grid.ac/institutes/grid.410510.1", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
                "Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193, Beijing, China", 
                "Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Li\u00e8ge, 5030, Gembloux, Belgium"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hu", 
            "givenName": "Xin", 
            "id": "sg:person.013601164623.16", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013601164623.16"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Han", 
            "givenName": "Haixia", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wang", 
            "givenName": "Jie", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Liu", 
            "givenName": "Wei", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zhou", 
            "givenName": "Yan", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Cao", 
            "givenName": "Dingguo", 
            "id": "sg:person.07746265657.47", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07746265657.47"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Li", 
            "givenName": "Fuwei", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Poultry Breeding Engineering Technology Center of Shandong Province, 250023, Ji\u2019nan, China", 
              "id": "http://www.grid.ac/institutes/None", 
              "name": [
                "Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji\u2019nan, China", 
                "Poultry Breeding Engineering Technology Center of Shandong Province, 250023, Ji\u2019nan, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Liu", 
            "givenName": "Jie", 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/s10142-017-0573-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092133134", 
              "https://doi.org/10.1007/s10142-017-0573-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/sj.ijo.0803612", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039854557", 
              "https://doi.org/10.1038/sj.ijo.0803612"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00726-015-2067-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041340932", 
              "https://doi.org/10.1007/s00726-015-2067-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12864-021-07374-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1134708972", 
              "https://doi.org/10.1186/s12864-021-07374-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm3118", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032683516", 
              "https://doi.org/10.1038/nrm3118"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11033-012-1599-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030205582", 
              "https://doi.org/10.1007/s11033-012-1599-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1923", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006541515", 
              "https://doi.org/10.1038/nmeth.1923"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12864-017-4150-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092310832", 
              "https://doi.org/10.1186/s12864-017-4150-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2013-14-4-r36", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015459845", 
              "https://doi.org/10.1186/gb-2013-14-4-r36"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-7-191", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023286996", 
              "https://doi.org/10.1186/1471-2105-7-191"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-10-77", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042080527", 
              "https://doi.org/10.1186/1471-2164-10-77"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2011-12-8-r72", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006381787", 
              "https://doi.org/10.1186/gb-2011-12-8-r72"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-8-63", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053657340", 
              "https://doi.org/10.1186/1471-2164-8-63"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2022-05-03", 
        "datePublishedReg": "2022-05-03", 
        "description": "BackgroundThe growth and development of skeletal muscle are regulated by protein-coding genes and non-coding RNA. Circular RNA (circRNA) is a type of non-coding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. To better understand the regulatory mechanism of circRNAs during the development of muscle in chicken, we performed RNA-seq with linear RNA depletion for chicken breast muscle in 12 (E 12) and17 (E 17) day embryos, and 1 (D 1), 14 (D 14), 56 (D 56), and 98 (D 98) days post-hatch.ResultsWe identified 5755 differentially expressed (DE)-circRNAs during muscle development. We profiled the expression of DE-circRNAs and mRNAs (identified in our previous study) at up to six time points during chicken muscle development and uncovered a significant profile (profile 16) for circRNA upregulation during aging in muscle tissues. To investigate competing endogenous RNA (ceRNA) regulation in muscle and identify muscle-related circRNAs, we constructed a circRNA-miRNA-mRNA regulatory network using the circRNAs and mRNAs from profile 16 and miRNAs identified in our previous study, which included 361 miRNAs, 68 circRNAs, 599 mRNAs, and 31,063 interacting pairs. Functional annotation showed that upregulated circRNAs might contribute to glycolysis/gluconeogenesis, biosynthesis of amino acids, pyruvate metabolism, carbon metabolism, glycogen and sucrose metabolism through the ceRNA network, and thus affected postnatal muscle development by regulating muscle protein deposition. Of them, circRNA225 and circRNA226 from the same host gene might be key circRNAs that could regulate muscle development by interacting with seven common miRNAs and 207 mRNAs. Our experiments also demonstrated that there were interactions among circRNA225, gga-miR-1306-5p, and heat shock protein alpha 8 (HSPA8).ConclusionsOur results suggest that adequate supply of nutrients such as energy and protein after hatching may be a key factor in ensuring chicken yield, and provide several candidate circRNAs for future studies concerning ceRNA regulation during chicken muscle development.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s12864-022-08525-5", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1023790", 
            "issn": [
              "1471-2164"
            ], 
            "name": "BMC Genomics", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "23"
          }
        ], 
        "keywords": [
          "chicken muscle development", 
          "non-coding RNAs", 
          "muscle development", 
          "ceRNA regulation", 
          "protein-coding genes", 
          "post-transcriptional regulation", 
          "endogenous RNA regulation", 
          "same host gene", 
          "glycolysis/gluconeogenesis", 
          "mRNA regulatory network", 
          "DE circRNAs", 
          "RNA regulation", 
          "functional annotation", 
          "circRNA-miRNA", 
          "carbon metabolism", 
          "key circRNAs", 
          "regulatory networks", 
          "circular RNAs", 
          "RNA-seq", 
          "host genes", 
          "ceRNA network", 
          "upregulated circRNAs", 
          "muscle protein deposition", 
          "regulatory mechanisms", 
          "RNA depletion", 
          "circRNAs", 
          "development of muscle", 
          "postnatal muscle development", 
          "candidate circRNAs", 
          "biological processes", 
          "integrative analysis", 
          "alpha 8", 
          "pyruvate metabolism", 
          "common miRNAs", 
          "amino acids", 
          "miRNAs", 
          "RNA", 
          "post-hatch period", 
          "mRNA", 
          "regulation", 
          "genes", 
          "skeletal muscle", 
          "day embryos", 
          "chicken breast muscle", 
          "muscle tissue", 
          "metabolism", 
          "protein deposition", 
          "biosynthesis", 
          "miRNA", 
          "embryonic", 
          "embryos", 
          "protein", 
          "ConclusionsOur results", 
          "hatching", 
          "adequate supply", 
          "annotation", 
          "breast muscle", 
          "significant profiles", 
          "nutrients", 
          "expression", 
          "upregulation", 
          "gluconeogenesis", 
          "muscle", 
          "previous studies", 
          "future studies", 
          "development", 
          "glycogen", 
          "growth", 
          "chickens", 
          "depletion", 
          "tissue", 
          "acid", 
          "key factors", 
          "mechanism", 
          "interaction", 
          "time points", 
          "variety", 
          "pairs", 
          "yield", 
          "study", 
          "profile", 
          "factors", 
          "analysis", 
          "types", 
          "ResultsWe", 
          "supply", 
          "process", 
          "experiments", 
          "network", 
          "results", 
          "days", 
          "period", 
          "deposition", 
          "point", 
          "energy"
        ], 
        "name": "Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods", 
        "pagination": "342", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1147539595"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s12864-022-08525-5"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "35505302"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s12864-022-08525-5", 
          "https://app.dimensions.ai/details/publication/pub.1147539595"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-06-01T22:25", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220601/entities/gbq_results/article/article_926.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s12864-022-08525-5"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s12864-022-08525-5'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s12864-022-08525-5'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12864-022-08525-5'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12864-022-08525-5'


     

    This table displays all metadata directly associated to this object as RDF triples.

    293 TRIPLES      22 PREDICATES      141 URIs      119 LITERALS      13 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s12864-022-08525-5 schema:about N33a168c3a91e47998fd4c75e38d4c2e8
    2 N670e00d2b0954df89f9aa03f2631a52c
    3 N6dd3322315f24fc185dbad7ae5d3d7d5
    4 N990b6a86dfe447db9a1a49b0a8bc4e40
    5 Na3e4ff7a513c4a1a8d994cb57057289b
    6 Ne87e21ab2f774932bc53cc5e74161524
    7 anzsrc-for:06
    8 anzsrc-for:0601
    9 anzsrc-for:0604
    10 schema:author N32fcc81f67074ae690c93306467f62b2
    11 schema:citation sg:pub.10.1007/s00726-015-2067-1
    12 sg:pub.10.1007/s10142-017-0573-9
    13 sg:pub.10.1007/s11033-012-1599-7
    14 sg:pub.10.1038/nmeth.1923
    15 sg:pub.10.1038/nrm3118
    16 sg:pub.10.1038/sj.ijo.0803612
    17 sg:pub.10.1186/1471-2105-7-191
    18 sg:pub.10.1186/1471-2164-10-77
    19 sg:pub.10.1186/1471-2164-8-63
    20 sg:pub.10.1186/gb-2011-12-8-r72
    21 sg:pub.10.1186/gb-2013-14-4-r36
    22 sg:pub.10.1186/s12864-017-4150-3
    23 sg:pub.10.1186/s12864-021-07374-y
    24 schema:datePublished 2022-05-03
    25 schema:datePublishedReg 2022-05-03
    26 schema:description BackgroundThe growth and development of skeletal muscle are regulated by protein-coding genes and non-coding RNA. Circular RNA (circRNA) is a type of non-coding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. To better understand the regulatory mechanism of circRNAs during the development of muscle in chicken, we performed RNA-seq with linear RNA depletion for chicken breast muscle in 12 (E 12) and17 (E 17) day embryos, and 1 (D 1), 14 (D 14), 56 (D 56), and 98 (D 98) days post-hatch.ResultsWe identified 5755 differentially expressed (DE)-circRNAs during muscle development. We profiled the expression of DE-circRNAs and mRNAs (identified in our previous study) at up to six time points during chicken muscle development and uncovered a significant profile (profile 16) for circRNA upregulation during aging in muscle tissues. To investigate competing endogenous RNA (ceRNA) regulation in muscle and identify muscle-related circRNAs, we constructed a circRNA-miRNA-mRNA regulatory network using the circRNAs and mRNAs from profile 16 and miRNAs identified in our previous study, which included 361 miRNAs, 68 circRNAs, 599 mRNAs, and 31,063 interacting pairs. Functional annotation showed that upregulated circRNAs might contribute to glycolysis/gluconeogenesis, biosynthesis of amino acids, pyruvate metabolism, carbon metabolism, glycogen and sucrose metabolism through the ceRNA network, and thus affected postnatal muscle development by regulating muscle protein deposition. Of them, circRNA225 and circRNA226 from the same host gene might be key circRNAs that could regulate muscle development by interacting with seven common miRNAs and 207 mRNAs. Our experiments also demonstrated that there were interactions among circRNA225, gga-miR-1306-5p, and heat shock protein alpha 8 (HSPA8).ConclusionsOur results suggest that adequate supply of nutrients such as energy and protein after hatching may be a key factor in ensuring chicken yield, and provide several candidate circRNAs for future studies concerning ceRNA regulation during chicken muscle development.
    27 schema:genre article
    28 schema:inLanguage en
    29 schema:isAccessibleForFree true
    30 schema:isPartOf N95489bd38a564bb885b235fc199b8fcc
    31 Ne271a6b115a740e1bf633bcc6fe3c4f5
    32 sg:journal.1023790
    33 schema:keywords ConclusionsOur results
    34 DE circRNAs
    35 RNA
    36 RNA depletion
    37 RNA regulation
    38 RNA-seq
    39 ResultsWe
    40 acid
    41 adequate supply
    42 alpha 8
    43 amino acids
    44 analysis
    45 annotation
    46 biological processes
    47 biosynthesis
    48 breast muscle
    49 candidate circRNAs
    50 carbon metabolism
    51 ceRNA network
    52 ceRNA regulation
    53 chicken breast muscle
    54 chicken muscle development
    55 chickens
    56 circRNA-miRNA
    57 circRNAs
    58 circular RNAs
    59 common miRNAs
    60 day embryos
    61 days
    62 depletion
    63 deposition
    64 development
    65 development of muscle
    66 embryonic
    67 embryos
    68 endogenous RNA regulation
    69 energy
    70 experiments
    71 expression
    72 factors
    73 functional annotation
    74 future studies
    75 genes
    76 gluconeogenesis
    77 glycogen
    78 glycolysis/gluconeogenesis
    79 growth
    80 hatching
    81 host genes
    82 integrative analysis
    83 interaction
    84 key circRNAs
    85 key factors
    86 mRNA
    87 mRNA regulatory network
    88 mechanism
    89 metabolism
    90 miRNA
    91 miRNAs
    92 muscle
    93 muscle development
    94 muscle protein deposition
    95 muscle tissue
    96 network
    97 non-coding RNAs
    98 nutrients
    99 pairs
    100 period
    101 point
    102 post-hatch period
    103 post-transcriptional regulation
    104 postnatal muscle development
    105 previous studies
    106 process
    107 profile
    108 protein
    109 protein deposition
    110 protein-coding genes
    111 pyruvate metabolism
    112 regulation
    113 regulatory mechanisms
    114 regulatory networks
    115 results
    116 same host gene
    117 significant profiles
    118 skeletal muscle
    119 study
    120 supply
    121 time points
    122 tissue
    123 types
    124 upregulated circRNAs
    125 upregulation
    126 variety
    127 yield
    128 schema:name Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods
    129 schema:pagination 342
    130 schema:productId N6d70ff5f34b74064b6b64b978573fcc0
    131 N7265b779a13f4274bf79804669d1c3a1
    132 Nd2e282da6515458b82afe6220275d3bf
    133 schema:sameAs https://app.dimensions.ai/details/publication/pub.1147539595
    134 https://doi.org/10.1186/s12864-022-08525-5
    135 schema:sdDatePublished 2022-06-01T22:25
    136 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    137 schema:sdPublisher N1fe0d5737f4a4581a8714060bc0a7237
    138 schema:url https://doi.org/10.1186/s12864-022-08525-5
    139 sgo:license sg:explorer/license/
    140 sgo:sdDataset articles
    141 rdf:type schema:ScholarlyArticle
    142 N085a2708a5d34af783fed69c899c7e85 rdf:first N531076f83e34409badbaac873ee8adf1
    143 rdf:rest N8b472eeff2b64e96af7b0bf028651e3f
    144 N0941e906d4ee4569a293a8e8d760828d rdf:first sg:person.013601164623.16
    145 rdf:rest N28612aca576a4eaca99d6edb96608ef6
    146 N0f6f3cca1bed4950a1c1138ea14bce6a schema:affiliation grid-institutes:None
    147 schema:familyName Liu
    148 schema:givenName Wei
    149 rdf:type schema:Person
    150 N1fe0d5737f4a4581a8714060bc0a7237 schema:name Springer Nature - SN SciGraph project
    151 rdf:type schema:Organization
    152 N28612aca576a4eaca99d6edb96608ef6 rdf:first N461b6891e3bb46afaa07f78dce4ed7e7
    153 rdf:rest N56a11fa7e35447d09a59740fe2aab48e
    154 N32fcc81f67074ae690c93306467f62b2 rdf:first sg:person.013304734357.25
    155 rdf:rest N0941e906d4ee4569a293a8e8d760828d
    156 N33a168c3a91e47998fd4c75e38d4c2e8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    157 schema:name RNA, Circular
    158 rdf:type schema:DefinedTerm
    159 N3b3ee43e347f4d20bcc159d8c60ab9e9 schema:affiliation grid-institutes:None
    160 schema:familyName Liu
    161 schema:givenName Jie
    162 rdf:type schema:Person
    163 N461b6891e3bb46afaa07f78dce4ed7e7 schema:affiliation grid-institutes:None
    164 schema:familyName Han
    165 schema:givenName Haixia
    166 rdf:type schema:Person
    167 N4b5203b985e9408cad3e2ad68cbf77cc rdf:first Nbb7f7ad6ac3b49ada722048b314bb9d6
    168 rdf:rest N7b4bb2b750a64000931eab7457a0fbef
    169 N531076f83e34409badbaac873ee8adf1 schema:affiliation grid-institutes:None
    170 schema:familyName Zhou
    171 schema:givenName Yan
    172 rdf:type schema:Person
    173 N56a11fa7e35447d09a59740fe2aab48e rdf:first N7b7f9ce5540e4ee3862be8b41adfbcc1
    174 rdf:rest Nbb2fdad0dd744f7099861ec59733cc49
    175 N670e00d2b0954df89f9aa03f2631a52c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    176 schema:name RNA, Messenger
    177 rdf:type schema:DefinedTerm
    178 N6d70ff5f34b74064b6b64b978573fcc0 schema:name dimensions_id
    179 schema:value pub.1147539595
    180 rdf:type schema:PropertyValue
    181 N6dd3322315f24fc185dbad7ae5d3d7d5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    182 schema:name MicroRNAs
    183 rdf:type schema:DefinedTerm
    184 N7265b779a13f4274bf79804669d1c3a1 schema:name pubmed_id
    185 schema:value 35505302
    186 rdf:type schema:PropertyValue
    187 N7b4bb2b750a64000931eab7457a0fbef rdf:first N3b3ee43e347f4d20bcc159d8c60ab9e9
    188 rdf:rest rdf:nil
    189 N7b7f9ce5540e4ee3862be8b41adfbcc1 schema:affiliation grid-institutes:None
    190 schema:familyName Wang
    191 schema:givenName Jie
    192 rdf:type schema:Person
    193 N8b472eeff2b64e96af7b0bf028651e3f rdf:first sg:person.07746265657.47
    194 rdf:rest N4b5203b985e9408cad3e2ad68cbf77cc
    195 N95489bd38a564bb885b235fc199b8fcc schema:volumeNumber 23
    196 rdf:type schema:PublicationVolume
    197 N990b6a86dfe447db9a1a49b0a8bc4e40 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    198 schema:name Animals
    199 rdf:type schema:DefinedTerm
    200 Na3e4ff7a513c4a1a8d994cb57057289b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    201 schema:name Muscle Development
    202 rdf:type schema:DefinedTerm
    203 Nbb2fdad0dd744f7099861ec59733cc49 rdf:first N0f6f3cca1bed4950a1c1138ea14bce6a
    204 rdf:rest N085a2708a5d34af783fed69c899c7e85
    205 Nbb7f7ad6ac3b49ada722048b314bb9d6 schema:affiliation grid-institutes:None
    206 schema:familyName Li
    207 schema:givenName Fuwei
    208 rdf:type schema:Person
    209 Nd2e282da6515458b82afe6220275d3bf schema:name doi
    210 schema:value 10.1186/s12864-022-08525-5
    211 rdf:type schema:PropertyValue
    212 Ne271a6b115a740e1bf633bcc6fe3c4f5 schema:issueNumber 1
    213 rdf:type schema:PublicationIssue
    214 Ne87e21ab2f774932bc53cc5e74161524 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    215 schema:name Chickens
    216 rdf:type schema:DefinedTerm
    217 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    218 schema:name Biological Sciences
    219 rdf:type schema:DefinedTerm
    220 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    221 schema:name Biochemistry and Cell Biology
    222 rdf:type schema:DefinedTerm
    223 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    224 schema:name Genetics
    225 rdf:type schema:DefinedTerm
    226 sg:journal.1023790 schema:issn 1471-2164
    227 schema:name BMC Genomics
    228 schema:publisher Springer Nature
    229 rdf:type schema:Periodical
    230 sg:person.013304734357.25 schema:affiliation grid-institutes:None
    231 schema:familyName Lei
    232 schema:givenName Qiuxia
    233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013304734357.25
    234 rdf:type schema:Person
    235 sg:person.013601164623.16 schema:affiliation grid-institutes:grid.410510.1
    236 schema:familyName Hu
    237 schema:givenName Xin
    238 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013601164623.16
    239 rdf:type schema:Person
    240 sg:person.07746265657.47 schema:affiliation grid-institutes:None
    241 schema:familyName Cao
    242 schema:givenName Dingguo
    243 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07746265657.47
    244 rdf:type schema:Person
    245 sg:pub.10.1007/s00726-015-2067-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041340932
    246 https://doi.org/10.1007/s00726-015-2067-1
    247 rdf:type schema:CreativeWork
    248 sg:pub.10.1007/s10142-017-0573-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092133134
    249 https://doi.org/10.1007/s10142-017-0573-9
    250 rdf:type schema:CreativeWork
    251 sg:pub.10.1007/s11033-012-1599-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030205582
    252 https://doi.org/10.1007/s11033-012-1599-7
    253 rdf:type schema:CreativeWork
    254 sg:pub.10.1038/nmeth.1923 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006541515
    255 https://doi.org/10.1038/nmeth.1923
    256 rdf:type schema:CreativeWork
    257 sg:pub.10.1038/nrm3118 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032683516
    258 https://doi.org/10.1038/nrm3118
    259 rdf:type schema:CreativeWork
    260 sg:pub.10.1038/sj.ijo.0803612 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039854557
    261 https://doi.org/10.1038/sj.ijo.0803612
    262 rdf:type schema:CreativeWork
    263 sg:pub.10.1186/1471-2105-7-191 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023286996
    264 https://doi.org/10.1186/1471-2105-7-191
    265 rdf:type schema:CreativeWork
    266 sg:pub.10.1186/1471-2164-10-77 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042080527
    267 https://doi.org/10.1186/1471-2164-10-77
    268 rdf:type schema:CreativeWork
    269 sg:pub.10.1186/1471-2164-8-63 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053657340
    270 https://doi.org/10.1186/1471-2164-8-63
    271 rdf:type schema:CreativeWork
    272 sg:pub.10.1186/gb-2011-12-8-r72 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006381787
    273 https://doi.org/10.1186/gb-2011-12-8-r72
    274 rdf:type schema:CreativeWork
    275 sg:pub.10.1186/gb-2013-14-4-r36 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015459845
    276 https://doi.org/10.1186/gb-2013-14-4-r36
    277 rdf:type schema:CreativeWork
    278 sg:pub.10.1186/s12864-017-4150-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092310832
    279 https://doi.org/10.1186/s12864-017-4150-3
    280 rdf:type schema:CreativeWork
    281 sg:pub.10.1186/s12864-021-07374-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1134708972
    282 https://doi.org/10.1186/s12864-021-07374-y
    283 rdf:type schema:CreativeWork
    284 grid-institutes:None schema:alternateName Poultry Breeding Engineering Technology Center of Shandong Province, 250023, Ji’nan, China
    285 Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji’nan, China
    286 schema:name Poultry Breeding Engineering Technology Center of Shandong Province, 250023, Ji’nan, China
    287 Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji’nan, China
    288 rdf:type schema:Organization
    289 grid-institutes:grid.410510.1 schema:alternateName Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
    290 schema:name Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
    291 Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
    292 Poultry Institute, Shandong Academy of Agricultural Sciences, 250023, Ji’nan, China
    293 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...