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Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle

Ashley J Waardenberg, Antonio Reverter, Christine A Wells, Brian P Dalrymple
2008 BMC Systems Biology  
differentiation using a new 3D visualisation tool: the Virtual Muscle 3D (VMus3D).  ...  To gain further insight into the orchestration of these structural changes we have overlaid the spatial organisation of the protein components of a muscle cell with their gene expression changes during  ...  We have developed the virtual muscle (VMus3D), an animated 3D computer graphics model to visualise the relative locations of the products of muscle gene expression which characterises striated muscle structure  ... 
doi:10.1186/1752-0509-2-88 pmid:18945372 pmcid:PMC2596796 fatcat:2dcoteyavbaopbafacskkz4r3u

Repositioning of Muscle-specific Genes Relative to the Periphery of SC-35 Domains during Skeletal Myogenesis

Phillip T. Moen, Carol Villnave Johnson, Meg Byron, Lindsay S. Shopland, Ivana L. de la Serna, Anthony N. Imbalzano, Jeanne Bentley Lawrence
2004 Molecular Biology of the Cell  
., "Repositioning of muscle-specific genes relative to the periphery of SC-35 domains during skeletal myogenesis" (2003).  ...  This gene relocation adjacent to a prominent SC-35 domain was recapitulated in mouse 3T3 cells induced into myogenesis by introduction of MyoD.  ...  This work was further supported by fellowships to I.L.D. from the National Institutes of Health and the Charles A.  ... 
doi:10.1091/mbc.e03-06-0388 pmid:14617810 pmcid:PMC307540 fatcat:dgnkxu2mzfddneqmjkpwpii5km

Tbx6, Mesp-b and Ripply1 regulate the onset of skeletal myogenesis in zebrafish

S. E. Windner, R. A. Doris, C. M. Ferguson, A. C. Nelson, G. Valentin, H. Tan, A. C. Oates, F. C. Wardle, S. H. Devoto
2015 Development  
to skeletal myogenesis in zebrafish.  ...  Persistent Tbx6 expression in Ripply1 knockdown embryos correlates with a deficit in dermomyotome and myotome marker gene expression, suggesting that Ripply1 promotes myogenesis by terminating Tbx6-dependent  ...  We propose a model that explains how the readout of genes associated with segmentation leads to the spatially restricted specification of myogenic progenitors within the somites, and to the temporal coordination  ... 
doi:10.1242/dev.113431 pmid:25725067 pmcid:PMC4360180 fatcat:kfvfiyhowja3todbd3ewbvulbq

Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology

Nan Zhang, Julen Mendieta-Esteban, Alessandro Magli, Karin C. Lilja, Rita C. R. Perlingeiro, Marc A. Marti-Renom, Aristotelis Tsirigos, Brian David Dynlacht
2020 Nature Communications  
Our studies lay the groundwork for understanding the role of Pax7 in orchestrating changes in the three-dimensional chromatin conformation in muscle progenitors.  ...  AbstractUsing Hi-C, promoter-capture Hi-C (pCHi-C), and other genome-wide approaches in skeletal muscle progenitors that inducibly express a master transcription factor, Pax7, we systematically characterize  ...  Acknowledgements We are most grateful to S. Schoenfelder and P. Fraser for their generous assistance in setting up pCHi-C in our laboratory, and M. Schober and J. Skok and A.  ... 
doi:10.1038/s41467-020-19999-w pmid:33277476 pmcid:PMC7718254 fatcat:4uaeejp3zzaqpbfajpburk7tem

Expression profiles of muscle disease-associated genes and their isoforms during differentiation of cultured human skeletal muscle cells

Saba Abdul-Hussein, Peter F M van der Ven, Homa Tajsharghi
2012 BMC Musculoskeletal Disorders  
The expression of several disease-associated proteins indicates that they might be a useful model system for studying the pathogenesis of muscle diseases caused by defects in specific sarcomeric constituents  ...  It is likely that elucidation of the expression patterns of muscle-specific sarcomeric proteins is important to understand muscle disorders originating from defects in contractile sarcomeric proteins.  ...  Acknowledgements The study was supported by a grant from the Swedish Research Council (Project No 073018 to HT), Åke Wiberg's Foundation to HT.  ... 
doi:10.1186/1471-2474-13-262 pmid:23273262 pmcid:PMC3549291 fatcat:g3yswht6lrfszpy5g2i3h5i23u

Abstracts of the XII Annual Meeting of the Interuniversity Institute of Myology | Reggio Emilia, Italy, October 1-4, 2015

The Editors
2016 European Journal of Translational Myology  
derived vesicles) as mediators of the functional interactions between mononuclear cell types that contribute to muscle regeneration  ...  Given the importance of the cross-talk between FAPs and MuSCs in DMD progression, we are currently deciphering the role of FAP-released extracellular vesicles (and in particular the exosomes -endosome  ...  A transcriptome analysis performed during in vitro murine muscle differentiation allowed us to identify a subset of new lncRNAs differentially expressed during myogenesis (1).  ... 
doi:10.4081/ejtm.2016.5830 pmid:27054019 pmcid:PMC4821221 fatcat:73jfhcmru5ccjediduk4pqkcmm

Regulation of myosin expression during myotome formation

L. D. Sacks
2003 Development  
Each of the slow MyHC genes showed the same initial pattern of spatial mRNA location and each underwent the same developmental change in location of the transcripts as the somites matured (data not shown  ...  No detailed study has examined the expression of the various MyHC isoforms during myogenesis in the somites.  ... 
doi:10.1242/dev.00541 pmid:12810587 fatcat:muyahky6hbakhg4pgru7ym4jz4

Report and Abstracts of the 17th Meeting of IIM, the Interuniversity Institute of Myology:Virtual meeting, October 16-18, 2020

Guglielmo Sorci, Davide Gabellini
2021 European Journal of Translational Myology  
The course, on a virtual platform, showcased lectures on muscle development and regulation of muscle gene expression by international speakers, and roundtables discussions on "Single cell analysis of skeletal  ...  In 2020, due to the COVID-19 pandemic, the annual meeting of the Interuniversity Institute of Myology (IIM), took place on a virtual platform.  ...  Acknowledgements None Funding This typescript was partially sponsored by PAGEpress, Pavia, Italy and the A&C M-C Foundation for Translational Myology, Padova, Italy.  ... 
doi:10.4081/ejtm.2020.9485 pmid:33520148 pmcid:PMC7844406 fatcat:pxzzfexzlzbnran4tnnvaqjeza

A single cdk inhibitor, p27Xic1, functions beyond cell cycle regulation to promote muscle differentiation in Xenopus

A. E. Vernon
2003 Development  
We have investigated the role of the cyclin-dependent kinase inhibitor p27 Xic1 in the co-ordination of cell cycle exit and differentiation during early myogenesis in vivo using Xenopus embryos.  ...  In this report, we demonstrate that p27 Xic1 is highly expressed in the developing myotome, that ablation of p27 Xic1 protein prevents muscle differentiation and that p27 Xic1 synergizes with the transcription  ...  Therefore, p27 Xic1 is appropriately temporally and spatially expressed to function during myogenesis and could be regulated by MyoD later in development.  ... 
doi:10.1242/dev.00180 pmid:12441292 fatcat:bdmatrpmbbcszjpxewl52hh4ci

Report and Abstracts of the 18th Meeting of the Interuniversity Institute of Myology: Virtual meeting, October 21-24, 2021

Francesca Grassi, Sestina Falcone
2021 European Journal of Translational Myology  
In 2021, as the situation due to COVID-19 pandemic was still uncertain, the 18 th annual meeting of the Interuniversity Institute of Myology (IIM), took place on a virtual platform, following the same  ...  All participants shared the wish to continue and implement IIM meeting with new insights on muscle biology, perspectives in the understanding of the muscle-related diseases and in novel therapeutic approaches  ...  Psat1, produces alpha-ketoglutarate (aKG), which is used as a cofactor for histone and DNA demethylase enzymes. This led us to investigate if Psat1 could link metabolism and gene expression in MuSCs.  ... 
doi:10.4081/ejtm.2021.10270 pmid:34850623 pmcid:PMC8758965 fatcat:mink26a3jzhifizcz6xshxmvda

Abstracts of the XI Annual Meeting of the Interuniversity Institute of Myology | Borgo San Luigi Monteriggioni (Siena), Italy, October 2-5, 2014

The Editors
2014 European Journal of Translational Myology  
Unlike the majority of genetic diseases, FSHD is not caused by mutation in a protein-coding gene, but it is linked to decrease in copy number of a 3.3-Kb tandem repeated macrosatellite (D4Z4), located  ...  Moreover, the use of twodimensional spatial sampling allowed also to get a reliable estimate of the muscle fiber conduction velocity.  ... 
doi:10.4081/ejtm.2014.4848 fatcat:bmpq5fond5d2lb2shhkkwlrl74

Abstracts of the XI Annual Meeting of the Interuniversity Institute of Myology | Borgo San Luigi Monteriggioni (Siena), Italy, October 2-5, 2014

The Editors
2014 European Journal of Translational Myology  
Unlike the majority of genetic diseases, FSHD is not caused by mutation in a protein-coding gene, but it is linked to decrease in copy number of a 3.3-Kb tandem repeated macrosatellite (D4Z4), located  ...  Moreover, the use of twodimensional spatial sampling allowed also to get a reliable estimate of the muscle fiber conduction velocity.  ... 
doi:10.4081/bam.2014.4.229 fatcat:scu5722af5h5vg24spu2nfw2ja

Human muscle stem cells are refractory to aging

James S. Novak, Davi A. G. Mázala, Marie Nearing, Ravi Hindupur, Prech Uapinyoying, Nayab F. Habib, Tessa Dickson, Olga B. Ioffe, Brent T. Harris, Marie N. Fidelia‐Lambert, Christopher T. Rossi, D. Ashely Hill (+3 others)
2021 Aging Cell  
In the present study, we used our established model of human muscle xenografting to test whether muscle samples taken from cadavers, of a range of ages, maintained their myogenic potential after being  ...  We conclude that the loss of muscle mass with increasing age is not attributable to any intrinsic loss of myogenicity and is most likely a reflection of progressive and detrimental changes in the muscle  ...  Normalized gene expression fold-change was calculated using the formula, 2 −(ΔΔCt) .  ... 
doi:10.1111/acel.13411 pmid:34089289 pmcid:PMC8282247 fatcat:zfkil6tu35c2blqdipc2n5xaei

The Msx1 Homeoprotein Recruits Polycomb to the Nuclear Periphery during Development

Jingqiang Wang, Roshan M. Kumar, Vanessa J. Biggs, Hansol Lee, Yun Chen, Michael H. Kagey, Richard A. Young, Cory Abate-Shen
2011 Developmental Cell  
ACKNOWLEDGMENTS We are indebted to Drs. Danny Reinberg and Raphael Margueron for providing reagents and many helpful discussions, Dr. Murty Vundavalli for assistance with FISH, and Dr.  ...  Our findings highlight a hitherto unappreciated role of spatial context of chromatin marks as a key factor in regulating gene expression during development.  ...  INTRODUCTION Appropriate spatial and temporal control of gene expression during development involves a coordinated network of chromatin-modifying complexes and sequence-specific DNA binding proteins, which  ... 
doi:10.1016/j.devcel.2011.07.003 pmid:21852201 pmcid:PMC3673563 fatcat:dneneclzmjfg7nytfeopn5alda

Shox2 function couples neural, muscular and skeletal development in the proximal forelimb

Lori Vickerman, Stanley Neufeld, John Cobb
2011 Developmental Biology  
In order to understand in more detail the development of the proximal limb, we searched for Shox2dependent gene expression patterns using Affymetrix microarrays.  ...  Strikingly, several of the identified genes were predicted to have functions in tissues other than the skeleton, including nerves and muscle precursors, prompting us to analyze neural and muscular patterning  ...  This work was supported in Geneva by funds from the Canton de Genève and the Swiss National Research Fund and in Calgary by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the  ... 
doi:10.1016/j.ydbio.2010.11.031 pmid:21156168 fatcat:g7thw4jds5gqvf74riqyp6ttzq
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