Acharyya, S., M.E.R. Butchbach, Z. Sahenk, H. Wang, M. Saji, M. Carathers, M.D. Ringel, R.J.E. Skipworth, K.C.H. Fearon, M.A. Hollingsworth, et al. 2005. Dystrophin glycoprotein complex dysfunction: a regulatory link between muscular dystrophy and cancer cachexia. Cancer Cell. 8: 421–432. https://doi.org/10.1016/j.ccr.2005.10.004
Addicks, G.C., P. Marshall, B.J. Jasmin, J.-M. Renaud, H. Zhang, and K.J. Menzies. 2018. Critical assessment of the mdx mouse with ex vivo eccentric contraction of the diaphragm muscle. Curr. Protoc. Mouse Biol. 8: e49. https://doi.org/10.1002/cpmo.49
Ardite, E., E. Perdiguero, B. Vidal, S. Gutarra, A.L. Serrano, and P. Muñoz-Cánoves. 2012. PAI-1-regulated miR-21 defines a novel age-associated fibrogenic pathway in muscular dystrophy. J. Cell Biol. 196:163–175. https://doi.org/10.1083/jcb.201105013
Armstrong, R.B., R.W. Ogilvie, and J.A. Schwane. 1983. Eccentric exercise-induced injury to rat skeletal muscle. J. Appl. Physiol. 54:80–93. https://doi.org/10.1152/jappl.1983.54.1.80
Bachinski, L.L., M. Sirito, M. Böhme, K.A. Baggerly, B. Udd, and R. Krahe. 2010. Altered MEF2 isoforms in myotonic dystrophy and other neu-romuscular disorders. Muscle Nerve. 42:856–863. https://doi.org/10.1002/mus.21789
Bakay, M., Z. Wang, G. Melcon, L. Schiltz, J. Xuan, P. Zhao, V. Sartorelli, J. Seo, E. Pegoraro, C. Angelini, et al. 2006. Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb-MyoD pathways in muscle regeneration. Brain. 129:996–1013. https://doi.org/10.1093/brain/awl023
Barlev, N.A., L. Liu, N.H. Chehab, K. Mansfield, K.G. Harris, T.D. Halazonetis, and S.L. Berger. 2001. Acetylation of p53 activates transcription through recruitment of coactivators/histone acetyltransferases. Mol. Cell. 8:1243–1254. https://doi.org/10.1016/S1097-2765(01)00414-2
Bettica, P., S. Petrini, V. D’Oria, A. D’Amico, M. Catteruccia, M. Pane, S. Sivo, F. Magri, S. Brajkovic, S. Messina, et al. 2016. Histological effects of givinostat in boys with Duchenne muscular dystrophy. Neuromuscul. Disord. 26:643–649. https://doi.org/10.1016/j.nmd.2016.07.002
Bi, P., F. Yue, Y. Sato, S. Wirbisky, W. Liu, T. Shan, Y. Wen, D. Zhou, J. Freeman, and S. Kuang. 2016. Stage-specific effects of Notch activation during skeletal myogenesis. eLife. 5:e17355. https://doi.org/10.7554/eLife.17355
Bialek, P., C. Morris, J. Parkington, M. St Andre, J. Owens, P. Yaworsky, H. Seeherman, and S.A. Jelinsky. 2011. Distinct protein degradation profiles are induced by different disuse models of skeletal muscle atrophy. Physiol. Genomics. 43:1075–1086. https://doi.org/10.1152/physiolgenomics.00247.2010
Blättler, S.M., J.T. Cunningham, F. Verdeguer, H. Chim, W. Haas, H. Liu, K. Romanino, M.A. Rüegg, S.P. Gygi, Y. Shi, et al. 2012a. Yin Yang 1 defi-ciency in skeletal muscle protects against rapamycin-induced diabetic-like symptoms through activation of insulin/IGF signaling. Cell Metab. 15:505–517. https://doi.org/10.1016/j.cmet.2012.03.008
Blättler, S.M., F. Verdeguer, M. Liesa, J.T. Cunningham, R.O. Vogel, H. Chim, H. Liu, K. Romanino, O.S. Shirihai, F. Vazquez, et al. 2012b. Defective mitochondrial morphology and bioenergetic function in mice lacking the transcription factor Yin Yang 1 in skeletal muscle. Mol. Cell. Biol. 32: 3333–3346. https://doi.org/10.1128/MCB.00337-12
Breuer, K., A.K. Foroushani, M.R. Laird, C. Chen, A. Sribnaia, R. Lo, G.L. Winsor, R.E.W. Hancock, F.S.L. Brinkman, and D.J. Lynn. 2013. In-nateDB: systems biology of innate immunity and beyond—recent up-dates and continuing curation. Nucleic Acids Res. 41(D1):D1228–D1233. https://doi.org/10.1093/nar/gks1147
Bulfield, G., W.G. Siller, P.A. Wight, and K.J. Moore. 1984. X chromosome-linked muscular dystrophy (mdx) in the mouse. Proc. Natl. Acad. Sci. USA. 81:1189–1192. https://doi.org/10.1073/pnas.81.4.1189
Campbell, C., H.J. McMillan, J.K. Mah, M. Tarnopolsky, K. Selby, T. McClure, D.M. Wilson, M.L. Sherman, D. Escolar, and K.M. Attie. 2017. Myostatin inhibitor ACE-031 treatment of ambulatory boys with Duchenne muscular dystrophy: results of a randomized, placebo-controlled clinical trial. Muscle Nerve. 55:458–464. https://doi.org/10.1002/mus.25268
Champy, M.F., M. Selloum, L. Piard, V. Zeitler, C. Caradec, P. Chambon, and J. Auwerx. 2004. Mouse functional genomics requires standardization of mouse handling and housing conditions. Mamm. Genome. 15:768–783. https://doi.org/10.1007/s00335-004-2393-1
Champy, M.-F., M. Selloum, V. Zeitler, C. Caradec, B. Jung, S. Rousseau, L. Pouilly, T. Sorg, and J. Auwerx. 2008. Genetic background determines metabolic phenotypes in the mouse. Mamm. Genome. 19:318–331. https://doi.org/10.1007/s00335-008-9107-z
Chockalingam, P.S., R. Cholera, S.A. Oak, Y. Zheng, H.W. Jarrett, and D.B. Thomason. 2002. Dystrophin-glycoprotein complex and Ras and Rho GTPase signaling are altered in muscle atrophy. Am. J. Physiol. Cell Physiol. 283:C500–C511. https://doi.org/10.1152/ajpcell.00529.2001
Chua, J.P., S.L. Reddy, Z. Yu, E. Giorgetti, H.L. Montie, S. Mukherjee, J. Higgins, R.C. McEachin, D.M. Robins, D.E. Merry, et al. 2015. Disrupting SUMOylation enhances transcriptional function and ameliorates poly-glutamine androgen receptor-mediated disease. J. Clin. Invest. 125: 831–845. https://doi.org/10.1172/JCI73214
Church, J.E., J. Trieu, A. Chee, T. Naim, S.M. Gehrig, S. Lamon, C. Angelini, A.P. Russell, and G.S. Lynch. 2014. Alterations in Notch signalling in skeletal muscles from mdx and dko dystrophic mice and patients with Duchenne muscular dystrophy. Exp. Physiol. 99:675–687. https://doi.org/10.1113/expphysiol.2013.077255
Cohen, T.J., J.L. Guo, D.E. Hurtado, L.K. Kwong, I.P. Mills, J.Q. Trojanowski, and V.M.Y. Lee. 2011. The acetylation of tau inhibits its function and promotes pathological tau aggregation. Nat. Commun. 2:252. https://doi.org/10.1038/ncomms1255
Colussi, C., C. Mozzetta, A. Gurtner, B. Illi, J. Rosati, S. Straino, G. Ragone, M. Pescatori, G. Zaccagnini, A. Antonini, et al. 2008. HDAC2 blockade by nitric oxide and histone deacetylase inhibitors reveals a common target in Duchenne muscular dystrophy treatment. Proc. Natl. Acad. Sci. USA. 105:19183–19187. https://doi.org/10.1073/pnas.0805514105
Consalvi, S., V. Saccone, L. Giordani, G. Minetti, C. Mozzetta, and P.L. Puri. 2011. Histone deacetylase inhibitors in the treatment of muscular dys-trophies: epigenetic drugs for genetic diseases. Mol. Med. 17:457–465. https://doi.org/10.2119/molmed.2011.00049
Consalvi, S., C. Mozzetta, P. Bettica, M. Germani, F. Fiorentini, F. Del Bene, M. Rocchetti, F. Leoni, V. Monzani, P. Mascagni, et al. 2013. Preclinical studies in the mdx mouse model of Duchenne muscular dystrophy with the histone deacetylase inhibitor givinostat. Mol. Med. 19:79–87. https://doi.org/10.2119/molmed.2013.00011
Dent, J.R., V.F. Martins, K. Svensson, S.A. LaBarge, N.C. Schlenk, M.C. Es-parza, E.H. Buckner, G.A. Meyer, D.L. Hamilton, S. Schenk, et al. 2017. Muscle-specific knockout of general control of amino acid synthesis 5 (GCN5) does not enhance basal or endurance exercise-induced mito-chondrial adaptation. Mol. Metab. 6:1574–1584. https://doi.org/10.1016/j. molmet.2017.10.004
Donohoe, M.E., X. Zhang, L. McGinnis, J. Biggers, E. Li, and Y. Shi. 1999. Targeted disruption of mouse Yin Yang 1 transcription factor results in peri-implantation lethality. Mol. Cell. Biol. 19:7237–7244. https://doi.org/10.1128/MCB.19.10.7237
Dumonceaux, J., S. Marie, C. Beley, C. Trollet, A. Vignaud, A. Ferry, G. Butler-Browne, and L. Garcia. 2010. Combination of myostatin pathway in-terference and dystrophin rescue enhances tetanic and specific force in dystrophic mdx mice. Mol. Ther. 18:881–887. https://doi.org/10.1038/mt.2009.322
Ehmsen, J., E. Poon, and K. Davies. 2002. The dystrophin-associated protein complex. J. Cell Sci. 115:2801–2803. https://doi.org/10.1242/jcs.115.14.2801
Galvagni, F., E. Cartocci, and S. Oliviero. 1998. The dystrophin promoter is negatively regulated by YY1 in undifferentiated muscle cells. J. Biol. Chem. 273:33708–33713. https://doi.org/10.1074/jbc.273.50.33708
Gil, J., A. Ramírez-Torres, and S. Encarnación-Guevara. 2017. Lysine acety-lation and cancer: a proteomics perspective. J. Proteomics. 150:297–309. https://doi.org/10.1016/j.jprot.2016.10.003
Grant, P.A., L. Duggan, J. Côté, S.M. Roberts, J.E. Brownell, R. Candau, R. Ohba, T. Owen-Hughes, C.D. Allis, F. Winston, et al. 1997. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11:1640–1650. https://doi.org/10.1101/gad.11.13.1640
Hord, J.M., R. Botchlett, and J.M. Lawler. 2016. Age-related alterations in the sarcolemmal environment are attenuated by lifelong caloric restriction and voluntary exercise. Exp. Gerontol. 83:148–157. https://doi.org/10.1016/j.exger.2016.08.006
Houbaviy, H.B., A. Usheva, T. Shenk, and S.K. Burley. 1996. Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Proc. Natl. Acad. Sci. USA. 93:13577–13582. https://doi.org/10.1073/pnas.93.24.13577
Hughes, D.C., G.R. Marcotte, A.G. Marshall, D.W.D. West, L.M. Baehr, M.A. Wallace, P.M. Saleh, S.C. Bodine, and K. Baar. 2017. Age-related dif-ferences in dystrophin: impact on force transfer proteins, membrane integrity, and neuromuscular junction stability. J. Gerontol. A Biol. Sci. Med. Sci. 72:640–648. https://doi.org/10.1093/gerona/glw109
Jackman, R.W., C.-L. Wu, and S.C. Kandarian. 2012. The ChIP-seq-defined networks of Bcl-3 gene binding support its required role in skeletal muscle atrophy. PLoS One. 7:e51478. https://doi.org/10.1371/journal.pone.0051478
Johnson, N.M., G.H. Farr III, and L. Maves. 2013. The HDAC inhibitor TSA ameliorates a zebrafish model of Duchenne muscular dystrophy. PLoS Curr. 5:ecurrents.md.8273cf41db10e2d15dd3ab827cb4b027. https://doi.org/10.1371/currents.md.8273cf41db10e2d15dd3ab827cb4b027
Khairallah, R.J., G. Shi, F. Sbrana, B.L. Prosser, C. Borroto, M.J. Mazaitis, E.P. Hoffman, A. Mahurkar, F. Sachs, Y. Sun, et al. 2012. Microtubules un-derlie dysfunction in Duchenne muscular dystrophy. Sci. Signal. 5:ra56. https://doi.org/10.1126/scisignal.2002829
Kosek, D.J., and M.M. Bamman. 2008. Modulation of the dystrophin-associated protein complex in response to resistance training in young and older men. J Appl Physiol (1985). 104:1476–1484. https://doi.org/10.1152/japplphysiol.00708.2007
Kupershmidt, I., Q.J. Su, A. Grewal, S. Sundaresh, I. Halperin, J. Flynn, M. Shekar, H. Wang, J. Park, W. Cui, et al. 2010. Ontology-based meta-analysis of global collections of high-throughput public data. PLoS One. 5:e13066. https://doi.org/10.1371/journal.pone.0013066
Lerin, C., J.T. Rodgers, D.E. Kalume, S.H. Kim, A. Pandey, and P. Puigserver. 2006. GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1α. Cell Metab. 3:429–438. https://doi.org/10.1016/j.cmet.2006.04.013
Li, P., J. Ge, and H. Li. 2020. Lysine acetyltransferases and lysine deacetylases as targets for cardiovascular disease. Nat. Rev. Cardiol. 17:96–115. https://doi.org/10.1038/s41569-019-0235-9
Matys, V., O.V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, K. Hornischer, et al. 2006. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eu-karyotes. Nucleic Acids Res. 34(90001, Suppl 1):D108–D110. https://doi.org/10.1093/nar/gkj143
Mazzatti, D.J., M.A. Smith, R.C. Oita, F.-L. Lim, A.J. White, and M.B. Reid. 2008. Muscle unloading-induced metabolic remodeling is associated with acute alterations in PPARdelta and UCP-3 expression. Physiol. Genomics. 34: 149–161. https://doi.org/10.1152/physiolgenomics.00281.2007
McIntyre, R.L., E.G. Daniels, M. Molenaars, R.H. Houtkooper, and G.E. Janssens. 2019. From molecular promise to preclinical results: HDAC inhibitors in the race for healthy aging drugs. EMBO Mol. Med. 11:e9854. https://doi.org/10.15252/emmm.201809854
Meliala, I.T.S., R. Hosea, V. Kasim, and S. Wu. 2020. The biological implications of Yin Yang 1 in the hallmarks of cancer. Theranostics. 10: 4183–4200. https://doi.org/10.7150/thno.43481
Migliavacca, E., S.K.H. Tay, H.P. Patel, T. Sonntag, G. Civiletto, C. McFarlane, T. Forrester, S.J. Barton, M.K. Leow, E. Antoun, et al. 2019. Mitochon-drial oxidative capacity and NAD+ biosynthesis are reduced in human sarcopenia across ethnicities. Nat. Commun. 10:5808. https://doi.org/10.1038/s41467-019-13694-1
Minetti, G.C., C. Colussi, R. Adami, C. Serra, C. Mozzetta, V. Parente, S. Fortuni, S. Straino, M. Sampaolesi, M. Di Padova, et al. 2006. Functional and morphological recovery of dystrophic muscles in mice treated with deacetylase inhibitors. Nat. Med. 12:1147–1150. https://doi.org/10.1038/nm1479
Miniou, P., D. Tiziano, T. Frugier, N. Roblot, M. Le Meur, and J. Melki. 1999. Gene targeting restricted to mouse striated muscle lineage. Nucleic Acids Res. 27:e27–e30. https://doi.org/10.1093/nar/27.19.e27
Narita, T., B.T. Weinert, and C. Choudhary. 2019. Functions and mechanisms of non-histone protein acetylation. Nat. Rev. Mol. Cell Biol. 20:156–174. https://doi.org/10.1038/s41580-018-0081-3
Nouet, J., E. Himelman, K.C. Lahey, Q. Zhao, and D. Fraidenraich. 2020. Connexin-43 reduction prevents muscle defects in a mouse model of manifesting Duchenne muscular dystrophy female carriers. Sci. Rep. 10: 5683. https://doi.org/10.1038/s41598-020-62844-9
Pambianco, S., M. Giovarelli, C. Perrotta, S. Zecchini, D. Cervia, I. Di Renzo, C. Moscheni, M. Ripolone, R. Violano, M. Moggio, et al. 2016. Reversal of defective mitochondrial biogenesis in limb-girdle muscular dystrophy 2D by independent modulation of histone and PGC-1α acetylation. Cell Rep. 17:3010–3023. https://doi.org/10.1016/j.celrep.2016.11.044
Patel, J.H., Y. Du, P.G. Ard, C. Phillips, B. Carella, C.-J. Chen, C. Rakowski, C. Chatterjee, P.M. Lieberman, W.S. Lane, et al. 2004. The c-MYC onco-protein is a substrate of the acetyltransferases hGCN5/PCAF and TIP60. Mol. Cell. Biol. 24:10826–10834. https://doi.org/10.1128/MCB.24.24.10826-10834.2004
Peñuelas-Urquides, K., C. Becerril-Esquivel, L.C. Mendoza-de-León, B. Silva-Ramírez, J. Dávila-Velderrain, B. Cisneros, and M.B. de León. 2016. Transcription factors YY1, Sp1 and Sp3 modulate dystrophin Dp71 gene expression in hepatic cells. Biochem. J. 473:1967–1976. https://doi.org/10.1042/BCJ20160163
Petrof, B.J., J.B. Shrager, H.H. Stedman, A.M. Kelly, and H.L. Sweeney. 1993. Dystrophin protects the sarcolemma from stresses developed during muscle contraction. Proc. Natl. Acad. Sci. USA. 90:3710–3714. https://doi.org/10.1073/pnas.90.8.3710
Pusch, M. 2002. Myotonia caused by mutations in the muscle chloride channel gene CLCN1. Hum. Mutat. 19:423–434. https://doi.org/10.1002/humu.10063
Rahimov, F., O.D. King, L.C. Warsing, R.E. Powell, C.P. Emerson Jr., L.M. Kunkel, and K.R. Wagner. 2011. Gene expression profiling of skeletal muscles treated with a soluble activin type IIB receptor. Physiol. Genomics. 43: 398–407. https://doi.org/10.1152/physiolgenomics.00223.2010
Risson, V., L. Mazelin, M. Roceri, H. Sanchez, V. Moncollin, C. Corneloup, H. Richard-Bulteau, A. Vignaud, D. Baas, A. Defour, et al. 2009. Muscle inactivation of mTOR causes metabolic and dystrophin defects leading to severe myopathy. J. Cell Biol. 187:859–874. https://doi.org/10.1083/jcb.200903131
Schmalbruch, H. 1975. Segmental fibre breakdown and defects of the plas-malemma in diseased human muscles. Acta Neuropathol. 33:129–141. https://doi.org/10.1007/BF00687539
Shi, Y., J.-S. Lee, and K.M. Galvin. 1997. Everything you have ever wanted to know about Yin Yang 1…. Biochim. Biophys. Acta. 1332:F49–F66. https://doi.org/10.1016/S0304-419X(96)00044-3
Smith, L.R., D.W. Hammers, H.L. Sweeney, and E.R. Barton. 2016. Increased collagen cross-linking is a signature of dystrophin-deficient muscle. Muscle Nerve. 54:71–78. https://doi.org/10.1002/mus.24998
Stedman, H.H., H.L. Sweeney, J.B. Shrager, H.C. Maguire, R.A. Panettieri, B. Petrof, M. Narusawa, J.M. Leferovich, J.T. Sladky, and A.M. Kelly. 1991. The mdx mouse diaphragm reproduces the degenerative changes of Duchenne muscular dystrophy. Nature. 352:536–539. https://doi.org/10.1038/352536a0
Svensson, K., S. Tahvilian, V.F. Martins, J.R. Dent, A. Lemanek, N. Barooni, K. Greyslak, C.E. McCurdy, and S. Schenk. 2020. Combined over-expression of SIRT1 and knockout of GCN5 in adult skeletal muscle does not affect glucose homeostasis or exercise performance in mice. Am. J. Physiol. Endocrinol. Metab. 318:E145–E151. https://doi.org/10.1152/ajpendo.00370.2019
Swiderski, K., C.J. Brock, J. Trieu, A. Chee, S.S. Thakur, D.M. Baum, P. Gre-gorevic, K.T. Murphy, and G.S. Lynch. 2021. Phosphorylation of ERK and dystrophin S3059 protects against inflammation-associated C2C12 myotube atrophy. Am. J. Physiol. Cell Physiol. 320:C956–C965. https://doi.org/10.1152/ajpcell.00513.2020
Thomas, M.J., and E. Seto. 1999. Unlocking the mechanisms of transcription factor YY1: are chromatin modifying enzymes the key? Gene. 236: 197–208. https://doi.org/10.1016/S0378-1119(99)00261-9
Townsend, D., M. Daly, J.S. Chamberlain, and J.M. Metzger. 2011. Age-dependent dystrophin loss and genetic reconstitution establish a molecular link between dystrophin and heart performance during aging. Mol. Ther. 19:1821–1825. https://doi.org/10.1038/mt.2011.120
Vieira, N.M., I. Elvers, M.S. Alexander, Y.B. Moreira, A. Eran, J.P. Gomes, J.L. Marshall, E.K. Karlsson, S. Verjovski-Almeida, K. Lindblad-Toh, et al. 2015. Jagged 1 rescues the Duchenne muscular dystrophy phenotype. Cell. 163:1204–1213. https://doi.org/10.1016/j.cell.2015.10.049
Wooddell, C.I., G. Zhang, J.B. Griffin, J.O. Hegge, T. Huss, and J.A. Wolff. 2010. Use of Evans blue dye to compare limb muscles in exercised young and old mdx mice. Muscle Nerve. 41:487–499. https://doi.org/10.1002/mus.21527
Yang, X., J.E. Koltes, C.A. Park, D. Chen, and J.M. Reecy. 2015. Gene co-expression network analysis provides novel insights into myostatin regulation at three different mouse developmental timepoints. PLoS One. 10:e0117607. https://doi.org/10.1371/journal.pone.0117607
Yao, Y.-L., W.-M. Yang, and E. Seto. 2001. Regulation of transcription factor YY1 by acetylation and deacetylation. Mol. Cell. Biol. 21:5979–5991. https://doi.org/10.1128/MCB.21.17.5979-5991.2001
Zanotti, S., S. Gibertini, M. Curcio, P. Savadori, B. Pasanisi, L. Morandi, F. Cornelio, R. Mantegazza, and M. Mora. 2015. Opposing roles of miR-21 and miR-29 in the progression of fibrosis in Duchenne muscular dys-trophy. Biochim. Biophys. Acta. 1852:1451–1464. https://doi.org/10.1016/j.bbadis.2015.04.013
Zhang, Z., D.L. Gasser, E.F. Rappaport, and M.J. Falk. 2010. Cross-platform expression microarray performance in a mouse model of mitochondrial disease therapy. Mol. Genet. Metab. 99:309–318. https://doi.org/10.1016/j.ymgme.2009.10.179
