Chandel NS. Evolution of mitochondria as signaling organelles. Cell Metab. 2015;22(2):204–6.
Article
CAS
PubMed
Google Scholar
Spinelli JB, Haigis MC. The multifaceted contributions of mitochondria to cellular metabolism. Nat Cell Biol. 2018;20(7):745–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bulthuis EP, Adjobo-Hermans MJW, Willems P, Koopman WJH. Mitochondrial morphofunction in mammalian cells. Antioxid Redox Signal. 2019;30(18):2066–109.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eisner V, Picard M, Hajnóczky G. Mitochondrial dynamics in adaptive and maladaptive cellular stress responses. Nat Cell Biol. 2018;20(7):755–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olesen J, Kiilerich K, Pilegaard H. PGC-1alpha-mediated adaptations in skeletal muscle. Pflugers Arch. 2010;460(1):153–62.
Article
CAS
PubMed
Google Scholar
Puigserver P, Wu Z, Park CW, Graves R, Wright M, Spiegelman BM. A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis. Cell. 1998;92(6):829–39.
Article
CAS
PubMed
Google Scholar
Pilegaard H, Saltin B, Neufer PD. Exercise induces transient transcriptional activation of the PGC-1alpha gene in human skeletal muscle. J Physiol. 2003;546(Pt 3):851–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Handschin C, Rhee J, Lin J, Tarr PT, Spiegelman BM. An autoregulatory loop controls peroxisome proliferator-activated receptor gamma coactivator 1alpha expression in muscle. Proc Natl Acad Sci U S A. 2003;100(12):7111–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription? Sci Adv. 2017;3(9):eaao2110.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hombach S, Kretz M. Non-coding RNAs: classification, biology and functioning. Adv Exp Med Biol. 2016;937:3–17.
Article
CAS
PubMed
Google Scholar
Dong Y, Yoshitomi T, Hu JF, Cui J. Long noncoding RNAs coordinate functions between mitochondria and the nucleus. Epigenetics Chromatin. 2017;10(1):41.
Article
PubMed
PubMed Central
CAS
Google Scholar
Young TL, Matsuda T, Cepko CL. The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr Biol. 2005;15(6):501–12.
Article
CAS
PubMed
Google Scholar
Long J, Badal SS, Ye Z, Wang Y, Ayanga BA, Galvan DL, et al. Long noncoding RNA Tug1 regulates mitochondrial bioenergetics in diabetic nephropathy. J Clin Invest. 2016;126(11):4205–18.
Article
PubMed
PubMed Central
Google Scholar
Pillon NJ, Gabriel BM, Dollet L, Smith JAB, Sardón Puig L, Botella J, et al. Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity. Nat Commun. 2020;11(1):470.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trewin AJ, Parker L, Shaw CS, Hiam D, Garnham AP, Levinger I, et al. Acute HIIE elicits similar changes in human skeletal muscle mitochondrial H2O2 release, respiration and cell signaling as endurance exercise even with less work. Am J Phys Regul Integr Comp Phys. 2018;315(5):R1003–R16.
CAS
Google Scholar
Casas-Delucchi CS, Brero A, Rahn HP, Solovei I, Wutz A, Cremer T, et al. Histone acetylation controls the inactive X chromosome replication dynamics. Nat Commun. 2011;2:222.
Article
PubMed
CAS
Google Scholar
Yaffe D, Saxel O. Serial passaging and differentiation of myogenic cells isolated from dystrophic mouse muscle. Nature. 1977;270(5639):725–7.
Article
CAS
PubMed
Google Scholar
Blau HM, Chiu CP, Webster C. Cytoplasmic activation of human nuclear genes in stable heterocaryons. Cell. 1983;32(4):1171–80.
Article
CAS
PubMed
Google Scholar
Gagnon KT, Corey DR. Guidelines for experiments using antisense oligonucleotides and double-stranded RNAs. Nucleic Acid Ther. 2019;29(3):116–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moyes CD, Mathieu-Costello OA, Tsuchiya N, Filburn C, Hansford RG. Mitochondrial biogenesis during cellular differentiation. Am J Phys. 1997;272(4 Pt 1):C1345–51.
Article
CAS
Google Scholar
Rochard P, Rodier A, Casas F, Cassar-Malek I, Marchal-Victorion S, Daury L, et al. Mitochondrial activity is involved in the regulation of myoblast differentiation through myogenin expression and activity of myogenic factors. J Biol Chem. 2000;275(4):2733–44.
Article
CAS
PubMed
Google Scholar
Soriano FX, Liesa M, Bach D, Chan DC, Palacín M, Zorzano A. Evidence for a mitochondrial regulatory pathway defined by peroxisome proliferator-activated receptor-gamma coactivator-1 alpha, estrogen-related receptor-alpha, and mitofusin 2. Diabetes. 2006;55(6):1783–91.
Article
CAS
PubMed
Google Scholar
Trewin AJ, Berry BJ, Wojtovich AP. Exercise and mitochondrial dynamics: keeping in shape with ROS and AMPK. Antioxidants (Basel, Switzerland). 2018;7(1).
Trewin AJ, Silver J, Dillon HT, Della Gatta PA, Parker L, Hiam DS, et al. LncRNA TUG1 in skeletal muscle. Figshare. 2022. https://doi.org/10.6084/m9.figshare.20175770.
Schnuck JK, Gould LM, Parry HA, Johnson MA, Gannon NP, Sunderland KL, et al. Metabolic effects of physiological levels of caffeine in myotubes. J Physiol Biochem. 2018;74(1):35–45.
Article
CAS
PubMed
Google Scholar
Egawa T, Ohno Y, Goto A, Ikuta A, Suzuki M, Ohira T, et al. AICAR-induced activation of AMPK negatively regulates myotube hypertrophy through the HSP72-mediated pathway in C2C12 skeletal muscle cells. Am J Physiol Endocrinol Metab. 2014;306(3):E344–54.
Article
CAS
PubMed
Google Scholar
Tamura Y, Kouzaki K, Kotani T, Nakazato K. Electrically stimulated contractile activity-induced transcriptomic responses and metabolic remodeling in C(2)C(12) myotubes: twitch vs. tetanic contractions. Am J Physiol Cell Physiol. 2020;319(6):C1029–c44.
Article
CAS
PubMed
Google Scholar
Hoffman NJ, Parker BL, Chaudhuri R, Fisher-Wellman KH, Kleinert M, Humphrey SJ, et al. Global phosphoproteomic analysis of human skeletal muscle reveals a network of exercise-regulated kinases and AMPK substrates. Cell Metab. 2015;22(5):922–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Popov DV, Makhnovskii PA, Shagimardanova EI, Gazizova GR, Lysenko EA, Gusev OA, et al. Contractile activity-specific transcriptome response to acute endurance exercise and training in human skeletal muscle. Am J Physiol Endocrinol Metab. 2019;316(4):E605–e14.
Article
CAS
PubMed
Google Scholar
Pan X, Liu B, Chen S, Ding H, Yao X, Cheng Y, et al. Nr4a1 as a myogenic factor is upregulated in satellite cells/myoblast under proliferation and differentiation state. Biochem Biophys Res Commun. 2019;513(3):573–81.
Article
CAS
PubMed
Google Scholar
Feng X, Wang Z, Wang F, Lu T, Xu J, Ma X, et al. Dual function of VGLL4 in muscle regeneration. EMBO J. 2019;38(17):e101051.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hillen HS, Morozov YI, Sarfallah A, Temiakov D, Cramer P. Structural basis of mitochondrial transcription initiation. Cell. 2017;171(5):1072–81.e10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lewandowski JP, Dumbović G, Watson AR, Hwang T, Jacobs-Palmer E, Chang N, et al. The Tug1 lncRNA locus is essential for male fertility. Genome Biol. 2020;21(1):237.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sasaki T, Nakata R, Inoue H, Shimizu M, Inoue J, Sato R. Role of AMPK and PPARγ1 in exercise-induced lipoprotein lipase in skeletal muscle. Am J Physiol Endocrinol Metab. 2014;306(9):E1085–92.
Article
CAS
PubMed
Google Scholar
Hevener AL, He W, Barak Y, Le J, Bandyopadhyay G, Olson P, et al. Muscle-specific Pparg deletion causes insulin resistance. Nat Med. 2003;9(12):1491–7.
Article
CAS
PubMed
Google Scholar
Rangwala SM, Wang X, Calvo JA, Lindsley L, Zhang Y, Deyneko G, et al. Estrogen-related receptor gamma is a key regulator of muscle mitochondrial activity and oxidative capacity. J Biol Chem. 2010;285(29):22619–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Murray J, Auwerx J, Huss JM. Impaired myogenesis in estrogen-related receptor γ (ERRγ)-deficient skeletal myocytes due to oxidative stress. FASEB J. 2013;27(1):135–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eichner LJ, Giguère V. Estrogen related receptors (ERRs): a new dawn in transcriptional control of mitochondrial gene networks. Mitochondrion. 2011;11(4):544–52.
Article
CAS
PubMed
Google Scholar
Geng T, Li P, Okutsu M, Yin X, Kwek J, Zhang M, et al. PGC-1alpha plays a functional role in exercise-induced mitochondrial biogenesis and angiogenesis but not fiber-type transformation in mouse skeletal muscle. Am J Physiol Cell Physiol. 2010;298(3):C572–9.
Article
CAS
PubMed
Google Scholar
Leick L, Wojtaszewski JF, Johansen ST, Kiilerich K, Comes G, Hellsten Y, et al. PGC-1alpha is not mandatory for exercise- and training-induced adaptive gene responses in mouse skeletal muscle. Am J Physiol Endocrinol Metab. 2008;294(2):E463–74.
Article
CAS
PubMed
Google Scholar
Islam H, Hood DA, Gurd BJ. Looking beyond PGC-1α: emerging regulators of exercise-induced skeletal muscle mitochondrial biogenesis and their activation by dietary compounds. Appl Physiol Nutr Metab. 2020;45(1):11–23.
Article
PubMed
Google Scholar
Mortensen OH, Plomgaard P, Fischer CP, Hansen AK, Pilegaard H, Pedersen BK. PGC-1beta is downregulated by training in human skeletal muscle: no effect of training twice every second day vs. once daily on expression of the PGC-1 family. J Appl Physiol (1985). 2007;103(5):1536–42.
Article
CAS
Google Scholar
Shao D, Liu Y, Liu X, Zhu L, Cui Y, Cui A, et al. PGC-1 beta-regulated mitochondrial biogenesis and function in myotubes is mediated by NRF-1 and ERR alpha. Mitochondrion. 2010;10(5):516–27.
Article
CAS
PubMed
Google Scholar
Arany Z, Lebrasseur N, Morris C, Smith E, Yang W, Ma Y, et al. The transcriptional coactivator PGC-1beta drives the formation of oxidative type IIX fibers in skeletal muscle. Cell Metab. 2007;5(1):35–46.
Article
CAS
PubMed
Google Scholar
Wai T, García-Prieto J, Baker MJ, Merkwirth C, Benit P, Rustin P, et al. Imbalanced OPA1 processing and mitochondrial fragmentation cause heart failure in mice. Science. 2015;350(6265):aad0116.
Article
PubMed
CAS
Google Scholar
Rambold AS, Kostelecky B, Elia N, Lippincott-Schwartz J. Tubular network formation protects mitochondria from autophagosomal degradation during nutrient starvation. Proc Natl Acad Sci U S A. 2011;108(25):10190–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Klein MG, Simon BJ, Schneider MF. Effects of caffeine on calcium release from the sarcoplasmic reticulum in frog skeletal muscle fibres. J Physiol. 1990;425:599–626.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brookes PS, Yoon Y, Robotham JL, Anders MW, Sheu SS. Calcium, ATP, and ROS: a mitochondrial love-hate triangle. Am J Phys Cell Phys. 2004;287(4):C817–33.
CAS
Google Scholar
Chin ER, Olson EN, Richardson JA, Yang Q, Humphries C, Shelton JM, et al. A calcineurin-dependent transcriptional pathway controls skeletal muscle fiber type. Genes Dev. 1998;12(16):2499–509.
Article
CAS
PubMed
PubMed Central
Google Scholar
Silver J, Wadley G, Lamon S. Mitochondrial regulation in skeletal muscle: a role for non-coding RNAs? Exp Physiol. 2018;103(8):1132–44.
Article
CAS
PubMed
Google Scholar
Wadley GD, Lamon S, Alexander SE, McMullen JR, Bernardo BC. Non-coding RNAs regulating cardiac muscle mass. J Appl Physiol (1985). 2019;127(2):633–44.
Article
CAS
Google Scholar
Long J, Galvan DL, Mise K, Kanwar YS, Li L, Poungvarin N, et al. Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1. J Biol Chem. 2020. https://doi.org/10.1074/jbc.RA120.013228.
Saleem A, Hood DA. Acute exercise induces tumour suppressor protein p53 translocation to the mitochondria and promotes a p53-Tfam-mitochondrial DNA complex in skeletal muscle. J Physiol. 2013;591(14):3625–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Silver JL, Alexander SE, Dillon HT, Lamon S, Wadley GD. Extracellular vesicular miRNA expression is not a proxy for skeletal muscle miRNA expression in males and females following acute, moderate intensity exercise. Phys Rep. 2020;8(16):e14520.
CAS
Google Scholar
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England). 2018;34(17):i884–i90.
Article
CAS
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England). 2013;29(1):15–21.
Article
CAS
Google Scholar
Degust v4.1.1. Zenodo. [Internet]. 2019. https://doi.org/10.5281/zenodo.3501067.
Mi H, Ebert D, Muruganujan A, Mills C, Albou LP, Mushayamaha T, et al. PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 2021;49(D1):D394–d403.
Article
CAS
PubMed
Google Scholar
Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, et al. GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 2021;49(D1):D104–d11.
Article
CAS
PubMed
Google Scholar
Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, et al. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 2019;47(W1):W212–w24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen L, Icahn School of Medicine at Mount Sinai. (2022). GeneOverlap: test and visualize gene overlaps. R package version 1.32.0, http://shenlab-sinai.github.io/shenlab-sinai/.
Chey S, Claus C, Liebert UG. Improved method for simultaneous isolation of proteins and nucleic acids. Anal Biochem. 2011;411(1):164–6.
Article
CAS
PubMed
Google Scholar
Murphy RM, Lamb GD. Important considerations for protein analyses using antibody based techniques: down-sizing Western blotting up-sizes outcomes. J Physiol. 2013;591(23):5823–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trewin AJ, Levinger I, Parker L, Shaw CS, Serpiello FR, Anderson MJ, et al. Acute exercise alters skeletal muscle mitochondrial respiration and H2O2 emission in response to hyperinsulinemic-euglycemic clamp in middle-aged obese men. PLoS One. 2017;12(11):e0188421.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dagda RK, Cherra SJ 3rd, Kulich SM, Tandon A, Park D, Chu CT. Loss of PINK1 function promotes mitophagy through effects on oxidative stress and mitochondrial fission. J Biol Chem. 2009;284(20):13843–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trewin AJ, Silver J, Dillon HT, Della Gatta PA, Parker L, Hiam DS, et al. Long non-coding RNA Tug1 modulates mitochondrial and myogenic responses to exercise in skeletal muscle. Gene Expression Omnibus. 2022; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185530.