Review 1 65 2 Exercise-associated DNA methylation change in 66 3 67 4 skeletal muscle and the importance of imprinted 68 5 69 Q16 genes: a bioinformatics meta-analysis 70 Q2¶7 71 Q3¶8 William M Brown 72 ¶9 73 10 74 ▸ Additional material is 11 ABSTRACT processes of development, with an emphasis on 75 published online only. To view Background Epigenetics is the study of processes— interactions among genes and between genes and 12 please visit the journal online 76 — the environment. In contrast, Nanney3 used ‘epi- 13 (http://dx.doi.org/10.1136/ beyond DNA sequence alteration producing heritable 77 fi ’ 14 bjsports-2014-094073). characteristics. For example, DNA methylation modi es genetic in 1958 to describe a system of cellular 78 gene expression without altering the nucleotide heredity that was not based on DNA sequence. 15 Correspondence to 79 16 Dr William M Brown, sequence. A well-studied DNA methylation-based Most molecular biologists use the term epigen- 80 17 Department of Sport Science phenomenon is genomic imprinting (ie, genotype- etic to mean the study of heritable changes in gene 81 and Physical Activity, Faculty of 18 independent parent-of-origin effects). expression or cellular phenotype caused by 82 Education and Sport, Health Objective We aimed to elucidate: (1) the effect of mechanisms other than changes in the underlying 19 Epigenetics and Ageing 83 DNA sequence—hence the name epi- (Greek for 20 Laboratory (HEAL), Institute of exercise on DNA methylation and (2) the role of 84 Sport and Physical Activity imprinted genes in skeletal muscle gene networks ‘over’, ‘above’ or ‘outer’) -genetics. Examples of Q7 21 fi 85 22 Research, University of (ie, gene group functional pro ling analyses). such changes are DNA methylation and histone 86 Bedfordshire, Polhill Avenue, fi fi 23 Design Gene ontology (ie, gene product elucidation)/ modi cations ( gure 1), both of which can regulate Q887 Bedford, Bedfordshire, MK41 meta-analysis. gene expression without altering the underlying 24 9EA, UK; 88 Q425 [email protected] Data sources 26 skeletal muscle and 86 imprinted DNA sequence. One well-studied epigenetic phe- 89 fi ¶26 genes were subjected to g:Pro ler ontology analysis. nomenon based on DNA methylation in mammals 90 Accepted 18 February 2015 4 27 Meta-analysis assessed exercise-associated DNA (and notably humans) is genomic imprinting. One 91 28 methylation change. purpose of this review is to introduce this term to 92 Data extraction g:Profiler found four muscle gene the sports and exercise medicine/physiotherapy 29 fi 93 30 networks with imprinted loci. Meta-analysis identi ed 16 community and explain its importance. 94 31 articles (387 genes/1580 individuals) associated with 95 32 exercise. Age, method, sample size, sex and tissue Genomic imprinting 96 33 variation could elevate effect size bias. Genomic imprinting is defined as genotype-independ- 97 34 Data synthesis Skeletal muscle gene networks ent parent-of-origin gene expression. Specifically, for 98 Q635 including imprinted genes reported. Exercise-associated most genes we inherit two working parental copies. 99 36 effect sizes were calculated by gene. Age, method, However, in the case of imprinted genes, an epigen- 100 37 sample size, sex and tissue variation were moderators. etic tag (via DNA methylation) is placed on either the 101 38 Results Six imprinted loci (RB1, MEG3, UBE3A, maternal or paternal copy rendering the other 102 PLAGL1, SGCE, INS) were important for muscle gene 39 fi inactive. Such parent-of-origin gene expression is 103 40 networks, while meta-analysis uncovered ve exercise- mediated by epigenetic modifications which differ 104 41 associated imprinted loci (KCNQ1, MEG3, GRB10, between the two parentally derived chromosomes.5 105 42 L3MBTL1, PLAGL1). DNA methylation decreased with Approximately 1% of the human genome is 106 43 exercise (60% of loci). Exercise-associated DNA imprinted.67Despite their rarity, imprinted genes are 107 44 methylation change was stronger among older people of great medical importance. Studies of metabolic 108 45 (ie, age accounted for 30% of the variation). Among growth and neurodevelopmental disorders have 109 46 older people, genes exhibiting DNA methylation shown that imprinted genes are absolutely essential 110 – 47 decreases were part of a microRNA-regulated gene for healthy development.8 13 Furthermore, epigenetic 111 48 network functioning to suppress cancer. — 112 fi dysregulation in imprinted genes which often have 49 Conclusions Imprinted genes were identi ed in growth-enhancing and tumour suppressor functions 113 50 skeletal muscle gene networks and exercise-associated —predict disease and cancer outcomes. 114 51 DNA methylation change. Exercise-associated DNA Once epigenetic mechanisms emerged during 115 fi ‘ 52 methylation modi cation could rewind the epigenetic mammalian evolution (eg, genomic imprinting), a 116 ’ 53 clock as we age. source of environmental information (ie, 117 54 Trial registration number CRD42014009800. parent-of-origin of a gene) was transmitted transge- 118 55 nerationally. Imprinting machinery (eg, DNA 119 56 methylation, see figure 1—a type of silencer at a 120 57 INTRODUCTION gene’s promoter—places marks on a gene when the 121 58 British developmental biologist Sir Conrad H gametes are produced) allowed for biased gene 122 59 Waddington introduced the term ‘epigenetics’ as a expression in the subsequent generation (ie, mono- 123 60 science of development from genotype to pheno- allelic gene expression). 124 To cite: Brown WM. Br J 1 61 Sports Med Published Online type. However, the term ‘epigenetics’ had an inde- The realisation that the environment has pro- 125 62 First: [please include Day pendent origin and meaning, which led to a found influences on the epigenome has led to a 126 63 Month Year] doi:10.1136/ conflation of terms.2 Recall Waddington’s use of strong hypothesis that exercise can also affect DNA 127 64 bjsports-2014-094073 the term ‘epigenetics’ to refer to the causal methylation and have long-term health outcomes. 128 Brown WM. Br J Sports Med 2015;0:1–18. doi:10.1136/bjsports-2014-094073 1 Review 129 193 130 194 131 195 132 196 133 197 134 198 135 199 136 200 137 201 138 202 139 203 140 204 141 205 142 206 143 207 144 208 145 209 146 210 147 211 148 212 149 213 150 214 151 215 152 216 153 217 154 218 155 219 156 220 157 221 158 222 159 223 160 224 161 Figure 1 DNA methylation: DNA methylation occurs when methyl groups ‘tag’ DNA and activate or repress gene expression. DNA methyltransferase 225 162 is a catalyst, which transfers methyl groups to DNA. Silencing of a gene activity can occur if the hydrogen (H) molecule of cytosine (C) is replaced by a 226 163 methyl (Me) group at a gene’s promoter. Histones: Histones are proteins around which DNA can wind for compaction and histone modification can 227 fi 164 regulate gene activity. Both epigenetic processes (ie, DNA methylation and histone modi cations) affect health resulting in cancer, autoimmune 228 fi 165 disease, neurological disorders or diabetes. Image modi ed from the National Institutes of Health, Benjamin I. Laufer and Forluvoft. 229 166 230 167 Specifically, we propose that the same mechanism that controls methylation outside the promoter region (eg, gene body) is 231 168 genomic imprinting in mammals (ie, DNA methylation) allows sometimes associated with increased gene expression. In the 232 169 for phenotypic modification and the possibility of multiple case of genomic imprinting, hypermethylation of one of the 233 170 sources of environmental information (eg, exercise, nutrition) to two parental alleles leads to monoallelic expression (conceptu- 234 171 be transmitted to the next generation. Muscle and nerve cells ally similar to gene-dosage reduction in X-inactivation, see 235 172 share the property of responding to electrochemical/environ- figure 2). DNA methylation has been implicated in cancer, neu- 236 15 173 mental stimuli and thus are ideal epigenetic interfaces for trans- rodevelopmental disorders and autoimmune diseases. Thus, if 237 174 generational phenotypic modification, which may explain in exercise can influence DNA methylation, it may be the mechan- 238 175 part why imprinted genes are particularly involved in neural ism that underpins the lower cancer rate in those who are phys- 239 176 development. ically active. 240 177 241 178 DNA methylation DNA methylation, health and diverse disease states 242 179 DNA methylation refers to the adding of a methyl group on a Cancer cells are characterised by a global loss of DNA methyla- 243 180 cytosine base. It occurs primarily in the context of CpG dinu- tion among growth enhancers; and the coordinated acquisition 244 181 cleotides, which cluster in regions called CpG islands.14 ‘CpG’ of hypermethylation at the CpG islands of tumour suppressor 245 182 refers to regions of DNA where a cytosine nucleotide appears genes. Global hypomethylation occurs primarily at parasitic 246 183 next to guanine nucleotide interconnected by phosphate. When DNA regions of the genome. For example, the LINE family 247 184 cytosines in CpG dinucleotides are methylated to form member L1 is hypomethylated in a variety of cancers, such as 248 185 5-methylcytosine, a gene can be turned off. CpG dinucleotides those of the breast and colon.16 249 186 are rare in mammals (∼1%), but ∼50% of gene promoters are Neurological disorders are also associated with epigenetic dys- 250 187 linked to CpG islands which are often unmethylated in healthy regulation (ie, reversed patterns of a normal DNA methylation 251 188 cells. Cells become methylated in a tissue-specific and age- profile). Specifically, dysregulation of DNA methylation occurs 252 189 specific manner during development. Where DNA methylation in several neurological diseases, giving rise to hypermethylated 253 190 occurs can be critical for its effect.