References - Revision history

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Yevshin, I.; Sharipov, R.; Kolmykov, S.; Kondrakhin, Y.; Kolpakov, F. GTRD: a database on gene transcription regulation-2019 update. Nucleic Acids Res. 2019, 47, D100–D105, doi:10.1093/nar/gky1128.
2. Williams, G. P.; Marmion, D. J.; Schonhoff, A. M.; Jurkuvenaite, A.; Won, W.-J.; Standaert, D. G.; Kordower, J. H.; Harms, A. S. T cell infiltration in both human multiple system atrophy and a novel mouse model of the disease. Acta Neuropathol. 2020, 139, 855–874, doi:10.1007/s00401-020-02126-w.
3. Li, Y.; Li, J.; Zhu, J.; Sun, B.; Branca, M.; Tang, Y.; Foster, W.; Xiao, X.; Huard, J. Decorin gene transfer promotes muscle cell differentiation and muscle regeneration. Mol. Ther. 2007, 15, 1616–1622, doi:10.1038/sj.mt.6300250.
4. Li, S.; Moore, A. K.; Zhu, J.; Li, X.; Zhou, H.; Lin, J.; He, Y.; Xing, F.; Pan, Y.; Bohler, H. C.; Ding, J.; Cooney, A. J.; Lan, Z.; Lei, Z. Ggnbp2 is essential for pregnancy success via regulation of mouse trophoblast stem cell proliferation and differentiation. Biol. Reprod. 2016, 94, 41, doi:10.1095/biolreprod.115.136358.
5. Lin, I.-H.; Chang, J.-L.; Hua, K.; Huang, W.-C.; Hsu, M.-T.; Chen, Y.-F. Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression. BMC Genet. 2018, 19, 55, doi:10.1186/s12863-018-0660-5.
6. Fiuza-Luces, C.; Santos-Lozano, A.; Llavero, F.; Campo, R.; Nogales-Gadea, G.; Díez-Bermejo, J.; Baladrón, C.; González-Murillo, Á.; Arenas, J.; Martín, M. A.; Andreu, A. L.; Pinós, T.; Gálvez, B. G.; López, J. A.; Vázquez, J.; Zugaza, J. L.; Lucia, A. Muscle molecular adaptations to endurance exercise training are conditioned by glycogen availability: a proteomics-based analysis in the McArdle mouse model. J Physiol (Lond) 2018, 596, 1035–1061, doi:10.1113/JP275292.
7. Osisami, M.; Ali, W.; Frohman, M. A. A role for phospholipase D3 in myotube formation. PLoS ONE 2012, 7, e33341, doi:10.1371/journal.pone.0033341.
8. Fortuin, F. D.; Morisaki, T.; Holmes, E. W. Subunit composition of AMPD varies in response to changes in AMPD1 and AMPD3 gene expression in skeletal muscle. Proc. Assoc. Am. Physicians 1996, 108, 329–333.
9. Shiloh, R.; Gilad, Y.; Ber, Y.; Eisenstein, M.; Aweida, D.; Bialik, S.; Cohen, S.; Kimchi, A. Non-canonical activation of DAPK2 by AMPK constitutes a new pathway linking metabolic stress to autophagy. Nat. Commun. 2018, 9, 1759, doi:10.1038/s41467-018-03907-4.
10. Verma, M.; Shimizu-Motohashi, Y.; Asakura, Y.; Ennen, J. P.; Bosco, J.; Zhou, Z.; Fong, G.-H.; Josiah, S.; Keefe, D.; Asakura, A. Inhibition of FLT1 ameliorates muscular dystrophy phenotype by increased vasculature in a mouse model of Duchenne muscular dystrophy. PLoS Genet. 2019, 15, e1008468, doi:10.1371/journal.pgen.1008468.
11. Sellers, R. S.; Mahmood, S. R.; Perumal, G. S.; Macaluso, F. P.; Kurland, I. J. Phenotypic Modulation of Skeletal Muscle Fibers in LPIN1-Deficient Lipodystrophic ( fld) Mice. Vet. Pathol. 2019, 56, 322–331, doi:10.1177/0300985818809126.
12. Ghasemizadeh, A.; Christin, E.; Guiraud, A.; Couturier, N.; Risson, V.; Girard, E.; Soler, C.; Laddada, L.; Jagla, K.; Sanchez, C.; Jaque-Fernandez, F.-I.; Garcia, A.; Lanfranchi, M.; Jacquemond, V.; Gondin, J.; Courchet, J.; Schaeffer, L.; Gache, V. Muscle MACF1 maintains myonuclei and mitochondria localization through microtubules to control muscle functionalities. BioRxiv 2019, doi:10.1101/636464.
13. Laforêt, P.; Richard, P.; Said, M. A.; Romero, N. B.; Lacene, E.; Leroy, J.-P.; Baussan, C.; Hogrel, J.-Y.; Lavergne, T.; Wahbi, K.; Hainque, B.; Duboc, D. A new mutation in PRKAG2 gene causing hypertrophic cardiomyopathy with conduction system disease and muscular glycogenosis. Neuromuscul. Disord. 2006, 16, 178–182, doi:10.1016/j.nmd.2005.12.004.
14. Otten, C.; van der Ven, P. F.; Lewrenz, I.; Paul, S.; Steinhagen, A.; Busch-Nentwich, E.; Eichhorst, J.; Wiesner, B.; Stemple, D.; Strähle, U.; Fürst, D. O.; Abdelilah-Seyfried, S. Xirp proteins mark injured skeletal muscle in zebrafish. PLoS ONE 2012, 7, e31041, doi:10.1371/journal.pone.0031041.
15. Andersson, R.; Gebhard, C.; Miguel-Escalada, I.; Hoof, I.; Bornholdt, J.; Boyd, M.; Chen, Y.; Zhao, X.; Schmidl, C.; Suzuki, T.; Ntini, E.; Arner, E.; Valen, E.; Li, K.; Schwarzfischer, L.; Glatz, D.; Raithel, J.; Lilje, B.; Rapin, N.; Bagger, F. O.; Sandelin, A. An atlas of active enhancers across human cell types and tissues. Nature 2014, 507, 455–461, doi:10.1038/nature12787.
16. Nelson, B. R.; Wu, F.; Liu, Y.; Anderson, D. M.; McAnally, J.; Lin, W.; Cannon, S. C.; Bassel-Duby, R.; Olson, E. N. Skeletal muscle-specific T-tubule protein STAC3 mediates voltage-induced Ca2+ release and contractility. Proc Natl Acad Sci USA 2013, 110, 11881–11886, doi:10.1073/pnas.1310571110.
17. Glass, D. J. Skeletal muscle hypertrophy and atrophy signaling pathways. Int. J. Biochem. Cell Biol. 2005, 37, 1974–1984, doi:10.1016/j.biocel.2005.04.018.
18. Liu, Y.; Shen, H.; Greenbaum, J.; Liu, A.; Su, K.-J.; Zhang, L.-S.; Zhang, L.; Tian, Q.; Hu, H.-G.; He, J.-S.; Deng, H.-W. Gene Expression and RNA Splicing Imputation Identifies Novel Candidate Genes Associated with Osteoporosis. J. Clin. Endocrinol. Metab. 2020, 105, doi:10.1210/clinem/dgaa572.
19. Latimer, L. E.; Constantin, D.; Greening, N. J.; Calvert, L.; Menon, M. K.; Steiner, M. C.; Greenhaff, P. L. Impact of transcutaneous neuromuscular electrical stimulation or resistance exercise on skeletal muscle mRNA expression in COPD. Int. J. Chron. Obstruct. Pulmon. Dis. 2019, 14, 1355–1364, doi:10.2147/COPD.S189896.
20. Miyake, N.; Takahashi, H.; Nakamura, K.; Isidor, B.; Hiraki, Y.; Koshimizu, E.; Shiina, M.; Sasaki, K.; Suzuki, H.; Abe, R.; Kimura, Y.; Akiyama, T.; Tomizawa, S.-I.; Hirose, T.; Hamanaka, K.; Miyatake, S.; Mitsuhashi, S.; Mizuguchi, T.; Takata, A.; Obo, K.; Matsumoto, N. Gain-of-Function MN1 Truncation Variants Cause a Recognizable Syndrome with Craniofacial and Brain Abnormalities. Am. J. Hum. Genet. 2020, 106, 13–25, doi:10.1016/j.ajhg.2019.11.011.
21. Meester-Smoor, M. A.; Vermeij, M.; van Helmond, M. J. L.; Molijn, A. C.; van Wely, K. H. M.; Hekman, A. C. P.; Vermey-Keers, C.; Riegman, P. H. J.; Zwarthoff, E. C. Targeted disruption of the Mn1 oncogene results in severe defects in development of membranous bones of the cranial skeleton. Mol. Cell. Biol. 2005, 25, 4229–4236, doi:10.1128/MCB.25.10.4229-4236.2005.
22. Zhang, X.; Dowd, D. R.; Moore, M. C.; Kranenburg, T. A.; Meester-Smoor, M. A.; Zwarthoff, E. C.; MacDonald, P. N. Meningioma 1 is required for appropriate osteoblast proliferation, motility, differentiation, and function. J. Biol. Chem. 2009, 284, 18174–18183, doi:10.1074/jbc.M109.001354.
23. Kowanetz, K.; Crosetto, N.; Haglund, K.; Schmidt, M.; Heldin, C.-H.; Dikic, I. Suppressors of T-cell receptor signaling Sts-1 and Sts-2 bind to Cbl and inhibit endocytosis of receptor tyrosine kinases. J. Biol. Chem. 2004, 279, 32786–32795, doi:10.1074/jbc.M403759200.
24. Wang, Y. X.; Feige, P.; Brun, C. E.; Hekmatnejad, B.; Dumont, N. A.; Renaud, J.-M.; Faulkes, S.; Guindon, D. E.; Rudnicki, M. A. EGFR-Aurka Signaling Rescues Polarity and Regeneration Defects in Dystrophin-Deficient Muscle Stem Cells by Increasing Asymmetric Divisions. Cell Stem Cell 2019, 24, 419-432.e6, doi:10.1016/j.stem.2019.01.002.
25. Waymack, R.; Fletcher, A.; Enciso, G.; Wunderlich, Z. Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic. elife 2020, 9, doi:10.7554/eLife.59351.
26. Genin, A. M.; Il’in, A. E.; Kaplanskiĭ, A. S.; Kasatkina, T. B.; Kuznetsova, K. A.; Pestov, I. D.; Smirnova, T. A. [Bioethics of research on humans and animals in aviation, space and marine medicine]. Aviakosm. Ekolog. Med. 2001, 35, 14–20.

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-Yevshin, I.; Sharipov, R.; Kolmykov, S.; Kondrakhin, Y.; Kolpakov, F. GTRD: a database on gene transcription regulation-2019 update. Nucleic Acids Res. 2019, 47, D100–D105, doi:10.1093/nar/gky1128.
+.     Yevshin, I.; Sharipov, R.; Kolmykov, S.; Kondrakhin, Y.; Kolpakov, F. GTRD: a database on gene transcription regulation-2019 update. Nucleic Acids Res. 2019, 47, D100–D105, doi:10.1093/nar/gky1128.
 .     Williams, G. P.; Marmion, D. J.; Schonhoff, A. M.; Jurkuvenaite, A.; Won, W.-J.; Standaert, D. G.; Kordower, J. H.; Harms, A. S. T cell infiltration in both human multiple system atrophy and a novel mouse model of the disease. Acta Neuropathol. 2020, 139, 855–874, doi:10.1007/s00401-020-02126-w.
 .     Li, Y.; Li, J.; Zhu, J.; Sun, B.; Branca, M.; Tang, Y.; Foster, W.; Xiao, X.; Huard, J. Decorin gene transfer promotes muscle cell differentiation and muscle regeneration. Mol. Ther. 2007, 15, 1616–1622, doi:10.1038/sj.mt.6300250.
 .     Li, S.; Moore, A. K.; Zhu, J.; Li, X.; Zhou, H.; Lin, J.; He, Y.; Xing, F.; Pan, Y.; Bohler, H. C.; Ding, J.; Cooney, A. J.; Lan, Z.; Lei, Z. Ggnbp2 is essential for pregnancy success via regulation of mouse trophoblast stem cell proliferation and differentiation. Biol. Reprod. 2016, 94, 41, doi:10.1095/biolreprod.115.136358.
 .     Lin, I.-H.; Chang, J.-L.; Hua, K.; Huang, W.-C.; Hsu, M.-T.; Chen, Y.-F. Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression. BMC Genet. 2018, 19, 55, doi:10.1186/s12863-018-0660-5.
 .     Fiuza-Luces, C.; Santos-Lozano, A.; Llavero, F.; Campo, R.; Nogales-Gadea, G.; Díez-Bermejo, J.; Baladrón, C.; González-Murillo, Á.; Arenas, J.; Martín, M. A.; Andreu, A. L.; Pinós, T.; Gálvez, B. G.; López, J. A.; Vázquez, J.; Zugaza, J. L.; Lucia, A. Muscle molecular adaptations to endurance exercise training are conditioned by glycogen availability: a proteomics-based analysis in the McArdle mouse model. J Physiol (Lond) 2018, 596, 1035–1061, doi:10.1113/JP275292.
 .     Osisami, M.; Ali, W.; Frohman, M. A. A role for phospholipase D3 in myotube formation. PLoS ONE 2012, 7, e33341, doi:10.1371/journal.pone.0033341.
 .     Fortuin, F. D.; Morisaki, T.; Holmes, E. W. Subunit composition of AMPD varies in response to changes in AMPD1 and AMPD3 gene expression in skeletal muscle. Proc. Assoc. Am. Physicians 1996, 108, 329–333.
 .     Shiloh, R.; Gilad, Y.; Ber, Y.; Eisenstein, M.; Aweida, D.; Bialik, S.; Cohen, S.; Kimchi, A. Non-canonical activation of DAPK2 by AMPK constitutes a new pathway linking metabolic stress to autophagy. Nat. Commun. 2018, 9, 1759, doi:10.1038/s41467-018-03907-4.
 .     Verma, M.; Shimizu-Motohashi, Y.; Asakura, Y.; Ennen, J. P.; Bosco, J.; Zhou, Z.; Fong, G.-H.; Josiah, S.; Keefe, D.; Asakura, A. Inhibition of FLT1 ameliorates muscular dystrophy phenotype by increased vasculature in a mouse model of Duchenne muscular dystrophy. PLoS Genet. 2019, 15, e1008468, doi:10.1371/journal.pgen.1008468.
 .     Sellers, R. S.; Mahmood, S. R.; Perumal, G. S.; Macaluso, F. P.; Kurland, I. J. Phenotypic Modulation of Skeletal Muscle Fibers in LPIN1-Deficient Lipodystrophic ( fld) Mice. Vet. Pathol. 2019, 56, 322–331, doi:10.1177/0300985818809126.
 .     Ghasemizadeh, A.; Christin, E.; Guiraud, A.; Couturier, N.; Risson, V.; Girard, E.; Soler, C.; Laddada, L.; Jagla, K.; Sanchez, C.; Jaque-Fernandez, F.-I.; Garcia, A.; Lanfranchi, M.; Jacquemond, V.; Gondin, J.; Courchet, J.; Schaeffer, L.; Gache, V. Muscle MACF1 maintains myonuclei and mitochondria localization through microtubules to control muscle functionalities. BioRxiv 2019, doi:10.1101/636464.
 .     Laforêt, P.; Richard, P.; Said, M. A.; Romero, N. B.; Lacene, E.; Leroy, J.-P.; Baussan, C.; Hogrel, J.-Y.; Lavergne, T.; Wahbi, K.; Hainque, B.; Duboc, D. A new mutation in PRKAG2 gene causing hypertrophic cardiomyopathy with conduction system disease and muscular glycogenosis. Neuromuscul. Disord. 2006, 16, 178–182, doi:10.1016/j.nmd.2005.12.004.
 .     Otten, C.; van der Ven, P. F.; Lewrenz, I.; Paul, S.; Steinhagen, A.; Busch-Nentwich, E.; Eichhorst, J.; Wiesner, B.; Stemple, D.; Strähle, U.; Fürst, D. O.; Abdelilah-Seyfried, S. Xirp proteins mark injured skeletal muscle in zebrafish. PLoS ONE 2012, 7, e31041, doi:10.1371/journal.pone.0031041.
 .     Andersson, R.; Gebhard, C.; Miguel-Escalada, I.; Hoof, I.; Bornholdt, J.; Boyd, M.; Chen, Y.; Zhao, X.; Schmidl, C.; Suzuki, T.; Ntini, E.; Arner, E.; Valen, E.; Li, K.; Schwarzfischer, L.; Glatz, D.; Raithel, J.; Lilje, B.; Rapin, N.; Bagger, F. O.; Sandelin, A. An atlas of active enhancers across human cell types and tissues. Nature 2014, 507, 455–461, doi:10.1038/nature12787.
 .     Nelson, B. R.; Wu, F.; Liu, Y.; Anderson, D. M.; McAnally, J.; Lin, W.; Cannon, S. C.; Bassel-Duby, R.; Olson, E. N. Skeletal muscle-specific T-tubule protein STAC3 mediates voltage-induced Ca2+ release and contractility. Proc Natl Acad Sci USA 2013, 110, 11881–11886, doi:10.1073/pnas.1310571110.
 .     Glass, D. J. Skeletal muscle hypertrophy and atrophy signaling pathways. Int. J. Biochem. Cell Biol. 2005, 37, 1974–1984, doi:10.1016/j.biocel.2005.04.018.
 .     Liu, Y.; Shen, H.; Greenbaum, J.; Liu, A.; Su, K.-J.; Zhang, L.-S.; Zhang, L.; Tian, Q.; Hu, H.-G.; He, J.-S.; Deng, H.-W. Gene Expression and RNA Splicing Imputation Identifies Novel Candidate Genes Associated with Osteoporosis. J. Clin. Endocrinol. Metab. 2020, 105, doi:10.1210/clinem/dgaa572.
 .     Latimer, L. E.; Constantin, D.; Greening, N. J.; Calvert, L.; Menon, M. K.; Steiner, M. C.; Greenhaff, P. L. Impact of transcutaneous neuromuscular electrical stimulation or resistance exercise on skeletal muscle mRNA expression in COPD. Int. J. Chron. Obstruct. Pulmon. Dis. 2019, 14, 1355–1364, doi:10.2147/COPD.S189896.
 .     Miyake, N.; Takahashi, H.; Nakamura, K.; Isidor, B.; Hiraki, Y.; Koshimizu, E.; Shiina, M.; Sasaki, K.; Suzuki, H.; Abe, R.; Kimura, Y.; Akiyama, T.; Tomizawa, S.-I.; Hirose, T.; Hamanaka, K.; Miyatake, S.; Mitsuhashi, S.; Mizuguchi, T.; Takata, A.; Obo, K.; Matsumoto, N. Gain-of-Function MN1 Truncation Variants Cause a Recognizable Syndrome with Craniofacial and Brain Abnormalities. Am. J. Hum. Genet. 2020, 106, 13–25, doi:10.1016/j.ajhg.2019.11.011.
 .     Meester-Smoor, M. A.; Vermeij, M.; van Helmond, M. J. L.; Molijn, A. C.; van Wely, K. H. M.; Hekman, A. C. P.; Vermey-Keers, C.; Riegman, P. H. J.; Zwarthoff, E. C. Targeted disruption of the Mn1 oncogene results in severe defects in development of membranous bones of the cranial skeleton. Mol. Cell. Biol. 2005, 25, 4229–4236, doi:10.1128/MCB.25.10.4229-4236.2005.
 .     Zhang, X.; Dowd, D. R.; Moore, M. C.; Kranenburg, T. A.; Meester-Smoor, M. A.; Zwarthoff, E. C.; MacDonald, P. N. Meningioma 1 is required for appropriate osteoblast proliferation, motility, differentiation, and function. J. Biol. Chem. 2009, 284, 18174–18183, doi:10.1074/jbc.M109.001354.
 .     Kowanetz, K.; Crosetto, N.; Haglund, K.; Schmidt, M.; Heldin, C.-H.; Dikic, I. Suppressors of T-cell receptor signaling Sts-1 and Sts-2 bind to Cbl and inhibit endocytosis of receptor tyrosine kinases. J. Biol. Chem. 2004, 279, 32786–32795, doi:10.1074/jbc.M403759200.
 .     Wang, Y. X.; Feige, P.; Brun, C. E.; Hekmatnejad, B.; Dumont, N. A.; Renaud, J.-M.; Faulkes, S.; Guindon, D. E.; Rudnicki, M. A. EGFR-Aurka Signaling Rescues Polarity and Regeneration Defects in Dystrophin-Deficient Muscle Stem Cells by Increasing Asymmetric Divisions. Cell Stem Cell 2019, 24, 419-432.e6, doi:10.1016/j.stem.2019.01.002.
 .     Waymack, R.; Fletcher, A.; Enciso, G.; Wunderlich, Z. Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic. elife 2020, 9, doi:10.7554/eLife.59351.
 .     Genin, A. M.; Il’in, A. E.; Kaplanskiĭ, A. S.; Kasatkina, T. B.; Kuznetsova, K. A.; Pestov, I. D.; Smirnova, T. A. [Bioethics of research on humans and animals in aviation, space and marine medicine]. Aviakosm. Ekolog. Med. 2001, 35, 14–20.