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Int J Mol Sci
2022 Dec 16;2324:. doi: 10.3390/ijms232416037.
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Muscle Regeneration in Holothurians without the Upregulation of Muscle Genes.
Nizhnichenko VA
,
Boyko AV
,
Ginanova TT
,
Dolmatov IY
.
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The holothurian Eupentacta fraudatrix is capable of fully restoring its muscles after transverse dissection. Although the regeneration of these structures is well studied at the cellular level, the molecular basis of the process remains poorly understood. To identify genes that may be involved in the regulation of muscle regeneration, the transcriptome of the longitudinal muscle band of E. fraudatrix has been sequenced at different time periods post-injury. An analysis of the map of biological processes and pathways has shown that most genes associated with myogenesis decrease their expression during the regeneration. The only exception is the genes united by the GO term "heart valve development". This may indicate the antiquity of mechanisms of mesodermal structure transformation, which was co-opted into various morphogeneses in deuterostomes. Two groups of genes that play a key role in the regeneration have been analyzed: transcription factors and matrix metalloproteinases. A total of six transcription factor genes (Ef-HOX5, Ef-ZEB2, Ef-RARB, Ef-RUNX1, Ef-SOX17, and Ef-ZNF318) and seven matrix metalloproteinase genes (Ef-MMP11, Ef-MMP13, Ef-MMP13-1, Ef-MMP16-2, Ef-MMP16-3, Ef-MMP24, and Ef-MMP24-1) showing differential expression during myogenesis have been revealed. The identified genes are assumed to be involved in the muscle regeneration in holothurians.
Alonso-Martin,
SOXF factors regulate murine satellite cell self-renewal and function through inhibition of β-catenin activity.
2018, Pubmed
Alonso-Martin,
SOXF factors regulate murine satellite cell self-renewal and function through inhibition of β-catenin activity.
2018,
Pubmed
Bankevich,
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
2012,
Pubmed
Beffagna,
Zebrafish as a Smart Model to Understand Regeneration After Heart Injury: How Fish Could Help Humans.
2019,
Pubmed
Bolger,
Trimmomatic: a flexible trimmer for Illumina sequence data.
2014,
Pubmed
Boyko,
The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation.
2020,
Pubmed
,
Echinobase
Boyko,
Reference assembly and gene expression analysis of Apostichopus japonicus larval development.
2019,
Pubmed
,
Echinobase
Brabletz,
The ZEB/miR-200 feedback loop--a motor of cellular plasticity in development and cancer?
2010,
Pubmed
Brockes,
Amphibian limb regeneration: rebuilding a complex structure.
1997,
Pubmed
Bürglin,
Homeodomain proteins: an update.
2016,
Pubmed
Carlson,
Muscle regeneration in amphibians and mammals: passing the torch.
2003,
Pubmed
Castresana,
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
2000,
Pubmed
Chen,
Role of matrix metalloproteinases in skeletal muscle: migration, differentiation, regeneration and fibrosis.
2009,
Pubmed
Chuang,
The Multiple Interactions of RUNX with the Hippo-YAP Pathway.
2021,
Pubmed
Coffman,
Evaluation of developmental phenotypes produced by morpholino antisense targeting of a sea urchin Runx gene.
2004,
Pubmed
,
Echinobase
Di Filippo,
Zeb2 Regulates Myogenic Differentiation in Pluripotent Stem Cells.
2020,
Pubmed
Dickey-Sims,
Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo.
2005,
Pubmed
,
Echinobase
Dolmatov,
Muscle regeneration in holothurians.
2001,
Pubmed
,
Echinobase
Dolmatov,
Muscle regeneration in the holothurian Stichopus japonicus.
1996,
Pubmed
,
Echinobase
Dolmatov,
Metalloproteinase inhibitor GM6001 delays regeneration in holothurians.
2019,
Pubmed
,
Echinobase
Dolmatov,
Expression of Piwi, MMP, TIMP, and Sox during Gut Regeneration in Holothurian Eupentacta fraudatrix (Holothuroidea, Dendrochirotida).
2021,
Pubmed
,
Echinobase
Dolmatov,
Matrix Metalloproteinases and Tissue Inhibitors of Metalloproteinases in Echinoderms: Structure and Possible Functions.
2021,
Pubmed
,
Echinobase
Dolmatov,
Molecular mechanisms of fission in echinoderms: Transcriptome analysis.
2018,
Pubmed
,
Echinobase
Dolmatov,
Molecular Aspects of Regeneration Mechanisms in Holothurians.
2021,
Pubmed
,
Echinobase
Fanjul-Fernández,
Matrix metalloproteinases: evolution, gene regulation and functional analysis in mouse models.
2010,
Pubmed
Galliot,
Regeneration and tissue repair: themes and variations.
2008,
Pubmed
García-Arrarás,
Echinoderms: potential model systems for studies on muscle regeneration.
2010,
Pubmed
,
Echinobase
Gheldof,
Evolutionary functional analysis and molecular regulation of the ZEB transcription factors.
2012,
Pubmed
Ghyselinck,
Retinoic acid signaling pathways.
2019,
Pubmed
Guindon,
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
2010,
Pubmed
Hajirnis,
Homeotic Genes: Clustering, Modularity, and Diversity.
2021,
Pubmed
Hall,
RUNX represses Pmp22 to drive neurofibromagenesis.
2019,
Pubmed
Hombría,
Beyond homeosis--HOX function in morphogenesis and organogenesis.
2003,
Pubmed
Jopling,
Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation.
2010,
Pubmed
Kagoshima,
RUNX regulates stem cell proliferation and differentiation: insights from studies of C. elegans.
2007,
Pubmed
Kam,
Roles of Hoxb5 in the development of vagal and trunk neural crest cells.
2015,
Pubmed
Kudtarkar,
Echinobase: an expanding resource for echinoderm genomic information.
2017,
Pubmed
Lanfear,
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.
2017,
Pubmed
Langmead,
Fast gapped-read alignment with Bowtie 2.
2012,
Pubmed
Leclère,
Diversity of Cnidarian Muscles: Function, Anatomy, Development and Regeneration.
2016,
Pubmed
Lei,
Matrix metalloproteinase 13 is a new contributor to skeletal muscle regeneration and critical for myoblast migration.
2013,
Pubmed
Li,
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
2011,
Pubmed
Lin,
Wound healing in jellyfish striated muscle involves rapid switching between two modes of cell motility and a change in the source of regulatory calcium.
2000,
Pubmed
Love,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
2014,
Pubmed
Merico,
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.
2010,
Pubmed
Nagase,
Structure and function of matrix metalloproteinases and TIMPs.
2006,
Pubmed
Nakano,
The developmental origins and lineage contributions of endocardial endothelium.
2016,
Pubmed
Nishimura,
DeltaEF1 mediates TGF-beta signaling in vascular smooth muscle cell differentiation.
2006,
Pubmed
O'Donnell,
Mechanisms of heart valve development and disease.
2020,
Pubmed
Ortiz-Pineda,
Gene expression profiling of intestinal regeneration in the sea cucumber.
2009,
Pubmed
,
Echinobase
Osato,
Point mutations in the RUNX1/AML1 gene: another actor in RUNX leukemia.
2004,
Pubmed
Poliacikova,
Hox Proteins in the Regulation of Muscle Development.
2021,
Pubmed
Quispe-Parra,
Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima.
2021,
Pubmed
,
Echinobase
Robertson,
CBFbeta is a facultative Runx partner in the sea urchin embryo.
2006,
Pubmed
,
Echinobase
Robertson,
Runx expression is mitogenic and mutually linked to Wnt activity in blastula-stage sea urchin embryos.
2008,
Pubmed
,
Echinobase
Rux,
Hox genes in the adult skeleton: Novel functions beyond embryonic development.
2017,
Pubmed
Seo,
The Roles of RUNX Family Proteins in Development of Immune Cells.
2020,
Pubmed
Shannon,
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
2003,
Pubmed
She,
SOX family transcription factors involved in diverse cellular events during development.
2015,
Pubmed
Siles,
ZEB1 protects skeletal muscle from damage and is required for its regeneration.
2019,
Pubmed
Simão,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
2015,
Pubmed
Smith,
Matrix Metalloproteinase 13 from Satellite Cells is Required for Efficient Muscle Growth and Regeneration.
2020,
Pubmed
Subramanian,
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
2005,
Pubmed
Sullivan,
The evolutionary origin of the Runx/CBFbeta transcription factors--studies of the most basal metazoans.
2008,
Pubmed
Tamura,
MEGA11: Molecular Evolutionary Genetics Analysis Version 11.
2021,
Pubmed
Thomas,
Terminal osteoblast differentiation, mediated by runx2 and p27KIP1, is disrupted in osteosarcoma.
2004,
Pubmed
Thorndyke,
Molecular approach to echinoderm regeneration.
2001,
Pubmed
,
Echinobase
Vandewalle,
SIP1/ZEB2 induces EMT by repressing genes of different epithelial cell-cell junctions.
2005,
Pubmed
Viera-Vera,
Retinoic Acid Signaling Is Associated with Cell Proliferation, Muscle Cell Dedifferentiation, and Overall Rudiment Size during Intestinal Regeneration in the Sea Cucumber, Holothuria glaberrima.
2019,
Pubmed
,
Echinobase
Wallace,
Large- and small-scale phenol extractions.
1987,
Pubmed
Wu,
HoxB5 is an upstream transcriptional switch for differentiation of the vascular endothelium from precursor cells.
2003,
Pubmed
Zerbino,
Ensembl 2018.
2018,
Pubmed
Zhao,
Retinoic acid signalling in fibro/adipogenic progenitors robustly enhances muscle regeneration.
2020,
Pubmed
Zullo,
The Diversity of Muscles and Their Regenerative Potential across Animals.
2020,
Pubmed
