Epigenetic changes in healthy human skeletal muscle following exercise– a systematic review

Figures & data

Figure 1. Epigenetic modifications after environmental stimuli (e.g. exercise).

Figure 2. Identification and selection summary for systematic review and meta-analyses.

Table 1. Summary of DNA methylation study’s findings.

Author	Year	Age	BMI	Sex	Sample size	Type of intervention	Length of intervention	Biopsy time	Technique	Results
Acute Exercise
Candidate Gene Approach
Bajpeyi et al.	2017	24.6 ± 1 years	23.2 ± 0.5	Males	11	Cycling until 650 Kcal	1 session (acute)	Before and immediately after	Pyrosequencing	Repositioning of −1N within the PGC1a promoter, which in turn increased fold change of PGC1a gene expression after acute exercise (1.05 ± 0.08 to 1.29 ± 0.11 fold change).
Barrès et al.	2012	NA	NA	M/F	14	Endurance exercise	1 session (acute)	Before, immediately after and +3 h	Pyrosequencing	HIIT reduced DNA methylation of PGC-1a, TFAM, MEF2A, and PDK4 immediately after exercise, whereas PPAR-d methylation was decreased 3 hr after exercise. Decreases in DNA methylation were associated with increase in gene expression at the same or following time point.
EWAS
Seaborne et al.	2018	27.6 ± 2.4	<30	Males	8	Resistance exercise	1 session (acute) + 7 week	Before, immediately after and post 7 week	Illumina EPIC array GEO: GSE114763	17,365 CpG sites were significantly (P < 0.05) differentially epigenetically modified following 7 week resistance training compared to baseline, with a larger number being hypomethylated (9,153) compared to hypermethylated (8,212). Following a period of 7 week without training, another 7 week of resistance exercise was conducted and it was observed an increase in the number of epigenetically modified sites (27,155) and an enhanced number of hypomethylated DNA sites (18,816). Hypermethylation remained stable during second 7 week of training (8,339) versus untraining period (8,638) and initial 7 week (8,212).
Chronic Exercise
Candidate Gene Approach
Alibegovic et al.	2010	25 ± 1	24.1 ± 2.3	Males	20	Endurance training	4 weeks	Before and After intervention	Sequenced with the ABI 3130xl genetic analyser.	General increased DNA methylation of PPARGC1A gene after bed rest (only one site of 3 being significant −816 p = 0.04), tending to reversibility after retraining but not achieving same levels as before.
EWAS
Lindholm et al.	2014	27 ± 0.8	24 ± 0.8	12M/11F	23	One-legged knee extension	3 months	Rest, before and after training	Illumina Infinium HumanMethylation450 array GEO: GSE60655	Endurance training induced significant changes in 4919 sites across the genome of the trained leg. The corresponding transcriptional analyses resulted in 4076 differentially expressed genes.
Nitert et al.	2012	37.5 ± 5.2	27.85 ± 3.0	Males	28	Endurance exercise	6 months	Before and after intervention	MeDIP-Chip GEO: Not Available	134 individual genes changed amount of methylation after exercise (115 hypomethylation and 19 hypermethylation). See supplementary data – has complete data set.
Robinson et al.	2017	23–26	24.6–25.6	M/F	34	HIIT	3 months	Before and After intervention	Infinium 450 K array (Illumina). GEO: GSE97084	Relatively small changes (<10%) in DNA methylation in comparison to a more substantial increase in gene expression following exercise training.
Seaborne et al.	2018	27.6 ± 2.4	<30	Males	8	Resistance exercise	1 session (acute) + 7 week	Before, immediately after and post 7 week	Illumina EPIC array GEO: GSE114763	17,365 CpG sites were significantly (P < 0.05) differentially epigenetically modified following 7 week resistance training compared to baseline, with a larger number being hypomethylated (9,153) compared to hypermethylated (8,212). Following a period of 7 week without training, another 7 week of resistance exercise was conducted and it was observed an increase in the number of epigenetically modified sites (27,155) and an enhanced number of hypomethylated DNA sites (18,816). Hypermethylation remained stable during second 7 week of training (8,339) versus untraining period (8,638) and initial 7 week (8,212).

Table 2. Summary of miRNAs study’s findings.

Author	Year	Age	BMI	Sex	Sample size	Type of intervention	Length of intervention	Biopsy time	Technique	Results
Acute Exercise
Candidate Gene Approach
D’Souza et al.	2017	24.6 ± 4.9	28.1 ± 3.3	Males	9	Resistance Training	1 session (acute)	Baseline, 2 h and 4 h	TaqMan RT-PCR (10 ng of total RNA)	30 miRNAs were analysed, of which 6 were significantly altered by exercise (miRNA −24a, −133a, −146a, −206, −378b and 486) p = <0.05.
Fyfe et al.	2016	27 ± 4	26.5 ± 2.8	Males	8	Concurrent Training	1 session (acute)	Baseline, 1 h and 3 h	TaqMan RT-PCR (20 ng of total RNA)	4 miRNAs were analysed, of which miRNA −133a decreased in expression after RE and after HIIT+RE. In addition differences between types of training (HIIT+RE vs RE) and miRNA expression for miRNA −133a, −378 and −486 were also observed. miRNA −1 didn’t show any changes.
Rivas et al.	2014	22 ± 1	NA	Males	8	Resistance Training	1 session (acute)	Baseline and 6 hrs after exercise	miRNA PCR array from Qiagen (total RNA amount not described)	Of the 60 miRNAs analysed 17 were significantly altered by resistance exercise in young men. Only one miRNA was increased in expression both in young and old subjects after exercise (miR-423-5p)
Russell et al.	2013	23 ± 5		Males	9	Endurance training + HIIT	1 session (acute) + 10 days of training	Acute: 0 h, 3 h	TaqMan RT-PCR (10 ng of total RNA)	Of the 12 miRNAs analysed miR-1, −133a, 133b, −181 were significantly increased after acute endurance exercise (60%, 35%, 40% and 35% respectively). miR-9, −23a, −23b, and −31 reduced after exercise (50%, 24%, 27% and 28%). Short term training increased miR-29b by 210% and decreased miR-31 by 35%.
Nielsen et al.	2010	30.5 ± 5.5	<30	Males	10	Endurance training	1 session (acute) + 12 weeks	Baseline, +1 hr, +3 h. Before and After intervention	TaqMan RT-PCR (10 ng of total RNA)	After the acute exercise miR-1 and −133a increased in expression(p < 0.05). After chronic exercise all miRNAs showed a decrease in expression. (mir-1 (32%, P < 0.05), mir-133a (23%, P < 0.01), mir-133b (19%, P < 0.05) and mir-206 (49%, P < 0.01)). Such levels returned to baseline after 2 weeks.
Ringholm et al.	2011	26.2 ± 5.3	22.8 ± 2.7	Males	12	Endurance	1 session (acute)	Baseline, immediately after, +3 h	TaqMan RT-PCR (total RNA amount not described)	Only miR-23a had a decrease of 27% (p < 0.05) in response to exercise. miR-1, −29b, −133a did not change in response to exercise.
EWAS
Russell et al.	2017	24.2 ± 0.9	23.3 ± 0.9	Males	10	Resistance training	1 session (acute)	NA	TaqMan Array Human MicroRNA A + B Cards version Set v3.0 (total RNA amount not described) GEO:NA	26 miRNAs expression were significantly changed by age, exercise or a combination of both.
Ogasawara et al.	2016	21.4 ± 1.1	22.4 ± 1	Males	6	Resistance training	12 week	Baseline, +3 hr, after 12 weeks	Digital multiplex Nano string nCounter human miRNA expression assay (10–30 ng of total RNA) GEO: NA	Analysed patterns of 800 miRNAs before and after acute exercise and 12 week exercise. Expression levels of 85 and 102 miRNAs were altered after acute and chronic exercise respectively (p < 0.05).
Zacharewicz et al.	2014	24.2 ± 0.9	23.3 ± 0.9	Males	10	Resistance training	1 session (acute)	NA	TaqMan Array Human MicroRNA A + B Cards version Set v3.0 (350 ng of total RNA) GEO: NA	26 miRNAs were regulated by age or exercise. Of those 7 were differentially regulated by age and exercise, and other 7 miRNAs were regulated by exercise in either young or older subjects.
McLean et al.	2015	33 ± 2	27.2 ± 0.8	9M/5F	6	Aerobic exercise (cycling)	1 session (acute)	Baseline, 30 min post exercise	microRNA sequencing – Illumina HiSeq 2000 (total RNA amount not described) GEO: GSE66334	13 miRNAs increased in expression after exercise. Only 2 miRNAs decreased expression after exercise miRNA −144-5p and −144-3p but such decrease was not statistically significant.
Chronic Exercise
Candidate Gene Approach
Russell et al.	2013	23 ± 5		Males	9	Endurance training + HIIT	1 session (acute) + 10 days of training	Acute: 0 h, 3 h	TaqMan RT-PCR (10 ng of total RNA)	Of the 12 miRNAs analysed miR-1, −133a, 133b, −181 were significantly increased after acute endurance exercise (60%, 35%, 40% and 35% respectively). miR-9, −23a, −23b, and −31 reduced after exercise (50%, 24%, 27% and 28%). Short term training increased miR-29b by 210% and decreased miR-31 by 35%.
Keller et al.	2010	29 ± 6		Males	8	Endurance training	6 weeks	Before and after intervention	TaqMan RT-PCR (10 ng of total RNA)	21 miRNAs were investigated. There was a trend for reduced in miRNA expression after exercise (14 miRNAs vs 7 miRNAs respectively) >1.5FC, FDR <15%.
Nielsen et al.	2010	30.5 ± 5.5	<30	Males	10	Endurance training	1 session (acute) + 12 weeks	Baseline, +1 hr, +3 h. Before and After intervention	TaqMan RT-PCR (10 ng of total RNA)	After the acute exercise miR-1 and −133a increased in expression(p < 0.05). After chronic exercise all miRNAs showed a decrease in expression. (mir-1 (32%, P < 0.05), mir-133a (23%, P < 0.01), mir-133b (19%, P < 0.05) and mir-206 (49%, P < 0.01)). Such levels returned to baseline after 2 weeks.
Zhang et al.	2015	70.5 ± 2.5		3M/4F	7	Resistance training	5 months	Before and after intervention	TaqMan RT-PCR (total RNA amount not described)	After RE all miRNAs tended to decrease, however the only significant one was miR-133b (−26.5 ± 27.5%; p = 0.043; ES = −1.46).
Mueller et al.	2011	80.1 ± 3.7		14M/14F	28	Resistance training	12 weeks	Before and after intervention	Taqman MicroRNA assays (total RNA amount not described)	miRNA 1 expression was decreased after training.
D’ Souza et al.	2017	25.1 ± 5.8		Males	28	Powerlifters	Powerlifting athletes (resistance training) vs controls	Biopsy in athletes and controls	TaqMan RT-PCR (10 ng of total RNA)	17miRs species were analysed. 12 were differently expressed (p < 0.05) between groups with 7 being more abundant in powerlifters and five having lower expression. The unique miR expression profiles between groups allow for categorization of individuals as either powerlifter or healthy controls based on a five miR signature (miR-126, −23b, −16, −23a, −15a).
EWAS
Ogasawara et al.	2016	21.4 ± 1.1	22.4 ± 1	Males	18	Resistance training	12 week	Baseline, +3 hr, after 12 weeks	Digital multiplex Nano string nCounter human miRNA expression assay (10–30 ng of total RNA) GEO: NA	Analysed patterns of 800 miRNAs before and after acute exercise and 12 week exercise. Expression levels of 85 and 102 miRNAs were altered after acute and chronic exercise respectively (p < 0.05).

Table 3. Summary of miRNAs that were up- or down-regulated after exercise.

ACUTE EXERCISE – Candidate Genes
Author	Type of exercise	Number of participants	miRNAs upregulated	miRNAs downregulated
D’Souza, 2017	Resistance	9	miR-133a, miR-206, miR-486, miR-146a	miR-378, miR-23a
Fyfe, 2016	Concurrent	11	NA	miR-133a
Rivas, 2014	Resistance	8	miR-423-5p	miR-16-5p, miR-23b-3p, miR-24-3p, miR-26a-5p, miR-26b-5p, miR-27a-3p, miR-27b-3p, miR-29a-3p, miR-29c-3p, miR-30a-5p, miR-30d-5p, miR-95-3p, miR-107, miR-126-3p, miR-133b, miR-140-3p, miR-181a-5p, miR-324-3p, miR-378a-5p
Russell, 2013	Endurance	9	miR-1, miR-133a, miR-133b, miR-181a	miR-9, miR-23a, miR-23b, miR-31
Nielsen, 2010	Endurance	10	miR-1, miR-133a	NA
Ringholm, 2011	Endurance	12	NA	miR-23a
ACUTE EXERCISE – High-throughput
Russell, 2017 & Zacharewicz, 2014	Resistance	10	miR-486-3p, miR-518b	miR-1201, miR-149, miR-520g, miR-99b
Ogasawara, 2016	Resistance	6	miR-29a-3p, miR-146a-5p	let-7b-5p, miR-18a-5p, miR-95, miR-99a-5p, miR-139-5p, miR-146b-3p, miR-147b, miR-188-5p, miR-192-5p, miR-219–1-3p, miR-298, miR-320a, miR-323a-3p, miR-323a-5p, miR-326, miR-330-3p, miR-338-5p, miR-362-5p, miR-369-3p, miR-369-5p, miR-378b, miR-380-3p, miR-382-5p, miR-429, miR-429a, miR-486-3p, miR-491-5p, miR-494, miR-506-3p, miR-520a-3p, miR-524-3p, miR-539-5p, miR-548ad, miR-548ag, miR-548ah-5p, miR-548k, miR-548x-3p, miR-550b-3p, miR-553, miR-556-3p, miR-559, miR-561-3p, miR-566, miR-577, miR-582-3p, miR-584-5p, miR-585, miR-587, miR-590-3p, miR-602, miR-627, miR-653, miR-664a-3p, miR-744-5p, miR-759, miR-802, miR-875-3p, miR-888-5p, miR-943, miR-1179, miR-1204, miR-1233, miR-1251, miR-1265, miR-1267, miR-1269a, miR-1275, miR-1284, miR-1285-3p, miR-1290, miR-1291, miR-1301, miR-1321, miR-1322, miR-1323, miR-1324, miR-1468, miR-2113, miR-2278, miR-3180, miR-3190-5p, miR-3934, miR-4792
McLean, 2015	Endurance	6	miR-10a-5p, miR-30a-5p, miR-30d-5p, miR-22-3p, miR-128, miR-378a-3p, miR-378a-5p, miR-378f, miR-378g, miR-378i, miR-422a, miR-532-5p	NA
CHRONIC EXERCISE – Candidate Genes
Russell, 2013	Endurance training	9	miR-29b, miR-1, miR-133b	miR-31
Keller, 2010	Endurance training	8	miR-125a, miR-183, miR-189, miR-432, miR-575, miR-616, miR-637	miR-101, miR-133, miR-144, miR-15b, miR-26b, miR-28, miR-29b, miR-338, miR-455, miR-92, miR-98, miR-451, miR-589, miR-1
Nielsen, 2010	Endurance training	10	NA	miR-1, miR-133a, miR-133b, miR-206
Zhang, 2015	Resistance training	7	NA	miR-133b
Mueller, 2011	Resistance training	28	NA	miR-1
D’Souza, 2017	Powerlifting	28	miR-206, miR-15a, miR-16, miR-451a, miR-23a, miR-23b, miR-30b	miR-486, miR-499a, miR-133a, miR-1, miR-126
CHRONIC EXERCISE – High-throughput
Ogasawara, 2016	Resistance	6	miR-19b-3p, miR-21-5p, miR-126-3p, miR-136-5p, miR-376a-3p, miR-663b	miR-7-5p, let-7b-5p, let-7c, miR-22-3p, miR-30d-5p, miR-99a-5p, miR-141-3p, miR-146b-3p, miR-147b, miR-192-5p, miR-198, miR-222-3p, miR-297, miR-323a-5p, miR-325, miR-338-5p, miR-361-5p, miR-362-5p, miR-369-3p, miR-369-5p, miR-371a-5p, miR-378d, miR-380-3p, miR-422a, miR-424-5p, miR-429, miR-449a, miR-450b-3p, miR-483-5p, miR-485-5p, miR-496, miR-499a-3p, miR-502-3p, miR-502-5p, miR-512-5p, miR-526b-5p, miR-548ag, miR-548an, miR-548x-3p, miR-549, miR-550a-5p, miR-551b-3p, miR-552, miR-555, miR-559, miR-574-3p, miR-577, miR-581, miR-582-3p, miR-583, miR-584-5p, miR-596, miR-603, miR-627, miR-628-3p, miR-637, miR-640, miR-653, miR-664-3p, miR-744-5p, miR-802, miR-875-5p, miR-877-5p, miR-888-5p, miR-891a, miR-920, miR-937, miR-1185-5p, miR-1202, miR-1206, miR-1233, miR-1247-5p, miR-1251, miR-1267, miR-1269a, miR-1272, miR-1273f, miR-1275, miR-1283, miR-1284, miR-1285-3p, miR-1290, miR-1291, miR-1301, miR-1827, miR-1908, miR-1915-3p, miR-2053, miR-3123, miR-3151, miR-3168, miR-3182, miR-3190-5p, miR-3934, miR-4458, miR-4532