Adolescent sleep timing and dietary patterns in relation to DNA methylation of core circadian genes: a pilot study of Mexican youth

Figures & data

Table 1. Characteristics of the 142 Mexican adolescents

Sociodemographic and lifestyle characteristics	Midpoint <4 AM, mean (SD)	Midpoint ≥4 AM, mean (SD)	P value
N	87	55
Age	13.6 (1.9)	14.5 (1.9)	0.006
Sex (%)			0.35
Male	65.2	34.8
Female	57.5	42.5
BMI for age z score	0.51 (1.20)	0.57 (1.36)	0.76
Mother’s education (years)	11.0 (2.9)	11.1 (2.9)	0.80
Physical activity, moderate/vigorous minutes/day	84.1 (27.2)	82.4 (32.1)	0.73
Total energy intake (kcals)	2514 (1062)	2279 (873)	0.17
Dietary pattern scores
Diet pattern 1: Plant-based and lean proteins	0.21 (1.28)	0.07 (1.33)	0.54
Diet pattern 2: Meat & starchy foods	0.06 (1.08)	0.03 (0.87)	0.88
Diet pattern 3: Eggs, milk & refined grain	0.14 (0.72)	−0.07 (0.98)	0.14
Weekday sleep duration (min)	497 (59)	542 (59)	<0.0001

Table 2. Associations between sleep and dietary patterns and DNA methylation of circadian genes in Mexican adolescents, P < 0.05

Probe	Chromosome	Position	Gene	Relation to island	Gene region feature category	Beta values^1	P value
Sleep Midpoint (median of bed and wake time)
cg15603424	chr11	13300592	BMAL1	Island	5ʹUTR	0.000820	0.00300*
cg11591729	chr4	56411904	CLOCK	N_Shore	1stExon	0.000857	0.0318
cg14618246	chr11	45888058	CRY2	OpenSea	Body	0.00169	0.0253
cg25904177	chr11	45884565	CRY2	OpenSea	Body	−0.00178	0.0307
cg25736892	chr11	45888911	CRY2	OpenSea	Body	−0.00147	0.0450
cg13476336	chr17	38255694	NR1D1	Island	Body	0.00112	0.00564
cg06474323	chr17	38257020	NR1D1	Island	TSS200	0.000217	0.0185
cg02923856	chr3	23989124	NR1D2	S_Shore	5ʹUTR	0.00383	0.0302
cg10669351	chr3	24007477	NR1D2	OpenSea	Body	0.00301	0.0305
cg03301481	chr17	8052075	PER1	N_Shelf	Body	−0.00291	0.00360*
cg13433366	chr17	8057058	PER1	S_Shore	TSS1500	0.00292	0.0263
cg25250717	chr15	61144420	RORA	OpenSea	Body	−0.00207	0.0150
cg23965982	chr15	61055848	RORA	OpenSea	Body	0.00286	0.0154
cg18136062	chr15	61520931	RORA	Island	Body	0.000990	0.0156
cg09859112	chr15	61520370	RORA	N_Shore	Body	0.00170	0.0217
cg07701191	chr15	61520424	RORA	Island	Body	0.000502	0.0223
cg12061096	chr15	61028241	RORA	OpenSea	Body	0.00320	0.0260
cg02775377	chr15	61476554	RORA	OpenSea	Body	0.00232	0.0272
cg22536351	chr15	61044565	RORA	OpenSea	Body	0.00246	0.0388
cg20525725	chr15	61497556	RORA	OpenSea	Body	−0.00145	0.0488
cg13301933	chr15	61521439	RORA	Island	5ʹUTR	0.000819	0.0126
cg26087678	chr15	60884119	RORA	Island	Body	0.00328	0.0309
cg08700690	chr15	60884630	RORA	Island	Body	0.000523	0.0455
cg14170313	chr9	77112896	RORB	Island	1stExon	0.00109	0.00116*
Diet pattern 1: Plant-based and lean proteins
cg06116839	chr11	13376988	BMAL1	OpenSea	Body	−0.00125	0.0340
cg19429538	chr4	56303887	CLOCK	OpenSea	Body	−0.00184	0.0400
cg02359589	chr17	8045663	PER1	OpenSea	Body	−0.00225	0.0495
cg07719617	chr2	239169696	PER2	OpenSea	Body	−0.00209	0.0102
cg21462970	chr2	239161488	PER2	OpenSea	Body	−0.00118	0.0148
cg06246651	chr2	239187798	PER2	OpenSea	5ʹUTR	−0.00325	0.0390
cg13469320	chr2	239162122	PER2	OpenSea	Body	−0.000987	0.0474
cg04917262	chr1	7868469	PER3	OpenSea	Body	−0.00414	0.000601*
cg11641053	chr1	7844184	PER3	Island	TSS1500	−0.000426	0.0293
cg13146107	chr15	61122353	RORA	OpenSea	Body	−0.00115	0.0286
cg05912053	chr15	60919520	RORA	OpenSea	Body	−0.00191	0.0265
cg20667664	chr17	38254448	NR1D1	N_Shore	Body	−0.00323	0.0207
Diet pattern 2: Meat & starchy foods
cg16259330	chr11	13299070	BMAL1	Island	TSS1500	0.00109	0.00395*
cg21078679	chr11	13377829	BMAL1	OpenSea	Body	−0.00216	0.0237
cg03327818	chr11	13370408	BMAL1	OpenSea	5ʹUTR	0.00219	0.0271
cg27298069	chr4	56412099	CLOCK	Island	TSS200	−0.000441	0.0145
cg16345521	chr12	107486801	CRY1	Island	1stExon	0.000713	0.00535
cg26125082	chr11	45868418	CRY2	N_Shore	TSS1500	0.00942	0.0229
cg20855344	chr3	2398090	NR1D2	N_Shore	TSS1500	−0.00301	0.0332
cg08506046	chr3	23987101	NR1D2	Island	TSS1500	0.00105	0.0369
cg21093368	chr17	8055834	PER1	Island	TSS200	−0.00144	0.0459
cg03067929	chr15	61191921	RORA	OpenSea	Body	0.00607	0.0253
cg26065596	chr15	61448727	RORA	OpenSea	Body	−0.00198	0.0351
cg03461216	chr15	61197849	RORA	OpenSea	Body	−0.00278	0.0380
cg04324336	chr15	60941269	RORA	OpenSea	Body	0.00218	0.0431
cg19170589	chr15	60883569	RORA	Island	Body	0.00189	0.000658*
cg14331163	chr9	77111663	RORB	N_Shore	TSS1500	0.00321	0.0471
Diet pattern 3: Eggs, milk & refined grain
cg22322535	chr11	13299888	BMAL1	Island	5ʹUTR	−0.00118	0.0184
cg13250711	chr11	13298675	BMAL1	N_Shore	TSS1500	−0.00139	0.0211
cg07032258	chr11	13357037	BMAL1	OpenSea	5ʹUTR	−0.00448	0.0328
cg08367205	chr11	13298296	BMAL1	N_Shore	TSS1500	−0.00102	0.0356
cg18579796	chr11	13371358	BMAL1	OpenSea	5ʹUTR	0.00285	0.00229*
cg14666553	chr11	13374140	BMAL1	OpenSea	5ʹUTR	0.00198	0.0125
cg16839955	chr11	13298683	BMAL1	N_Shore	TSS1500	−0.00119	0.0164
cg21860398	chr11	13379485	BMAL1	OpenSea	Body	−0.00271	0.0212
cg16340122	chr11	13377690	BMAL1	OpenSea	Body	0.00389	0.0447
cg02683371	chr4	56298893	CLOCK	OpenSea	3ʹUTR	0.00204	0.0441
cg24000108	chr4	56376331	CLOCK	OpenSea	5ʹUTR	0.00373	0.0174
cg12893431	chr4	56315641	CLOCK	OpenSea	Body	0.00450	0.0196
cg24004414	chr4	56369919	CLOCK	OpenSea	5ʹUTR	0.00674	0.0232
cg15048607	chr4	56310021	CLOCK	OpenSea	Body	0.00526	0.0262
cg19429538	chr4	56303887	CLOCK	OpenSea	Body	0.00288	0.0394
cg08407670	chr4	56303880	CLOCK	OpenSea	Body	0.00273	0.0442
cg26520722	chr12	107486229	CRY1	N_Shore	Body	−0.00240	0.00536
cg08756366	chr12	107444216	CRY1	OpenSea	Body	0.00308	0.00749
cg20879606	chr11	45868932	CRY2	Island	Body	−0.00181	0.00831
cg07524456	chr11	45868501	CRY2	N_Shore	TSS1500	−0.00941	0.0321
cg14858951	chr17	38257028	NR1D1	Island	TSS200	−0.000435	0.0134
cg01059731	chr17	38255663	NR1D1	Island	Body	−0.00230	0.0152
cg13476336	chr17	38255694	NR1D1	Island	Body	−0.00130	0.0205
cg20667664	chr17	38254448	NR1D1	N_Shore	Body	0.00471	0.0303
cg04534726	chr3	23987467	NR1D2	Island	TSS200	−0.000452	0.00999
cg17680792	chr3	23986459	NR1D2	N_Shore	TSS1500	−0.000750	0.0282
cg19399789	chr3	23987441	NR1D2	Island	TSS200	−0.000492	0.00869
cg06103301	chr3	23987730	NR1D2	Island	5ʹUTR	−0.000306	0.00991
cg10028884	chr17	8054829	PER1	Island	5ʹUTR	−0.00111	0.0166
cg03301481	chr17	8052075	PER1	N_Shelf	Body	0.00303	0.0299
cg20503576	chr17	8055884	PER1	S_Shore	TSS200	−0.00199	0.0440
cg13469320	chr2	239162122	PER2	OpenSea	Body	0.00233	0.00234*
cg12308675	chr2	239169537	PER2	OpenSea	Body	−0.00298	0.00290
cg02976543	chr2	239197607	PER2	Island	TSS1500	−0.00616	0.0138
cg06174546	chr2	239171720	PER2	OpenSea	Body	0.00152	0.0247
cg00811891	chr1	7904830	PER3	OpenSea	3ʹUTR	0.00204	0.0409
cg11129701	chr1	7862851	PER3	OpenSea	5ʹUTR	−0.00203	0.0449
cg22148904	chr1	7862234	PER3	OpenSea	5ʹUTR	0.00392	0.0498
cg27391826	chr15	61395262	RORA	OpenSea	Body	0.00616	0.00516
cg08574592	chr15	61520873	RORA	Island	Body	−0.00199	0.0112
cg18760360	chr15	60953215	RORA	OpenSea	Body	0.00409	0.0121
cg02076826	chr15	61477299	RORA	OpenSea	Body	−0.00395	0.0174
cg20822028	chr15	61038077	RORA	OpenSea	Body	−0.00256	0.0182
cg27024408	chr15	61327619	RORA	OpenSea	Body	0.00285	0.0184
cg18730873	chr15	61462794	RORA	OpenSea	Body	0.00276	0.0232
cg27077827	chr15	60943536	RORA	OpenSea	Body	−0.00272	0.0311
cg13146553	chr15	61343563	RORA	OpenSea	Body	−0.00444	0.0320
cg12061096	chr15	61028241	RORA	OpenSea	Body	−0.00416	0.0367
cg05673940	chr15	61334658	RORA	OpenSea	Body	−0.00241	0.0390
cg12643950	chr15	61210235	RORA	OpenSea	Body	−0.00273	0.0401
cg00237177	chr15	61233587	RORA	OpenSea	Body	0.00134	0.0444
cg21756476	chr15	61182765	RORA	OpenSea	Body	0.00716	0.0491
cg11227596	chr15	61029537	RORA	OpenSea	Body	−0.00269	0.0495
cg01691639	chr15	61521458	RORA	Island	5ʹUTR	−0.00204	0.00293*
cg05334993	chr15	60888221	RORA	S_Shelf	Body	0.00246	0.0158
cg19170589	chr15	60883569	RORA	Island	Body	−0.00165	0.0142
cg18064474	chr15	60885021	RORA	Island	Body	−0.000368	0.0499
cg04600961	chr15	60787182	RORA	OpenSea	3ʹUTR	0.00681	0.0381
cg14736496	chr15	60920638	RORA	OpenSea	TSS1500	0.00668	0.00822
cg09094797	chr9	77230369	RORB	OpenSea	Body	−0.00658	0.0469
cg09363447	chr1	151787446	RORC	OpenSea	Body	0.00528	0.00180*
cg25206113	chr1	151788262	RORC	OpenSea	Body	0.00679	0.0404

¹Adjusted for sex, age, and % monocyte.

*Meets Bonferroni-corrected P value threshold (P < 0.004).

Table 3. Associations between sleep and dietary patterns and DNA methylation of circadian genes in Mexican adolescents, overall description

	Number of probes in gene	Proportion of probes with association P < 0.05	Number of probes in islands	Proportion of island probes with P < 0.05	Direction of island probe association (majority)
Sleep Midpoint (median of bed and wake time)
BMAL	64	0.016	9	0.11	+
CLOCK	43	0.023	13	0
CRY1	28	0	11	0
CRY2	32	0.094	8	0
NR1D1	22	0.091	12	0.17	+
NR1D2	26	0.077	10	0
PER1	19	0.11	5	0
PER2	39	0	6	0
PER3	34	0	15	0
RORA	192	0.063	28	0.18	+
RORB	26	0.038	4	0.25	+
RORC	23	0	0	0
Diet pattern 1: Plant-based and lean proteins
BMAL1	64	0.016	9	0
CRY1	28	0	11	0
CRY2	32	0	8	0
CLOCK	43	0.023	13	0
NR1D1	21	0.048	11	0
NR1D2	26	0	10	0
PER1	19	0.053	5	0.2	-
PER2	39	0.103	6	0
PER3	34	0.059	15	0.07	-
RORA	192	0.010	28	0.04	-
RORB	26	0	4	0
RORC	23	0	0	0
Diet pattern 2: Meat & starchy foods
BMAL1	64	0.047	9	0.11	+
CLOCK	43	0.023	13	0.08	-
CRY1	28	0.036	11	0.09	+
CRY2	32	0.031	8	0
NR1D1	21	0	11	0
NR1D2	26	0.077	10	0.1	+
PER1	19	0.053	5	0.2	-
PER2	39	0	6	0
PER3	34	0	15	0
RORA	192	0.026	28	0.04	+
RORB	19	0.053	4	0
RORC	23	0	0	0
Diet pattern 3: Eggs, milk & refined grain
CLOCK	43	0.163	13	0
BMAL1	64	0.141	9	0.11	-
CRY1	28	0.071	11	0
CRY2	32	0.063	8	0.13	-
NR1D1	21	0.190	11	0.27	-
NR1D2	26	0.154	10	0.3	-
PER1	19	0.158	5	0.2	-
PER2	39	0.103	7	0.17	-
PER3	34	0.088	15	0
RORA	192	0.005	28	0.14	-
RORB	26	0.038	4	0
RORC	23	0.087	0	0

Table 4. Associations between sleep and dietary patterns and DNA methylation of circadian gene CpG islands in adolescents

	All		Boys		Girls
	Beta coefficient^1	P value	Beta coefficient^2	P value	Beta coefficient^2	P value
Sleep Midpoint (median of bed and wake time)
PER1	.0140337	0.240	−.0102469	0.550	.0345147	0.042
PER2	.0040428	0.615	−.0017354	0.893	.0081995	0.421
PER3 island 1	−.0081581	0.664	−.0257108	0.286	.0083659	0.773
PER3 island 2	−.001583	0.848	.0043872	0.734	−.0082874	0.445
PER3 island 3	.0774699	0.096	.0523266	0.464	.1028792	0.099
CRY2	.0029527	0.711	.0088452	0.400	−.0039388	0.742
BMAL1	.0117632	0.140	.0107429	0.327	.0114565	0.331
CLOCK	.0069998	0.298	.0026318	0.766	.0101371	0.320
RORA island 1	.0095559	0.204	.0031786	0.754	.0131733	0.233
RORA island 2	.0074266	0.442	−.0092649	0.503	.0215126	0.119
RORA island 3	.0175065	0.045	.0039397	0.768	.0281399	0.014
RORB	.0353199	0.003	.0372594	0.050	.0330129	0.030
NR1D1 island 1	.0127016	0.244	.0116515	0.471	.0151853	0.317
NR1D1 island 2	.0080007	0.360	.0180043	0.134	−.0024247	0.846
NR1D2	.0110481	0.104	.0072648	0.448	.0134684	0.172
Diet pattern 1: Plant-based and lean proteins
PER1	.0008977	0.023	.00123	0.007	.0002354	0.751
PER2	.0000904	0.791	−.0000792	0.857	.0005708	0.305
PER3 island 1	.0004076	0.408	.0003283	0.517	.0006691	0.498
PER3 island 2	.0000113	0.978	−.0001049	0.830	.0001876	0.807
PER3 island 3	−.0002882	0.939	−.002409	0.649	.0035876	0.520
CRY2	.0000126	0.935	.0001874	0.296	−.0003008	0.281
BMAL1	−.0001708	0.330	.0001164	0.562	−.0007621	0.019
CLOCK	.0000122	0.893	.000103	0.314	−.0001479	0.386
RORA island 1	−.0000955	0.693	.0000768	0.783	−.0003675	0.400
RORA island 2	−.0001234	0.339	.0000478	0.760	−.0004734	0.039
RORA island 3	.0000297	0.864	.0002662	0.216	−.0003976	0.176
RORB	−.0003219	0.282	−.000339	0.387	−.0003028	0.544
NR1D1 island 1	.0002256	0.509	.0006367	0.127	−.0006509	0.281
NR1D1 island 2	−.00004	0.766	.0000442	0.779	−.0001438	0.542
NR1D2	.0000639	0.514	.0000652	0.547	.0000771	0.681
Diet pattern 2: Meat & starchy foods
PER1	.0001683	0.745	.0007263	0.373	−.0001832	0.792
PER2	−.0004792	0.277	−.0003113	0.686	−.0007297	0.161
PER3 island 1	.000674	0.291	.0011211	0.203	.0003541	0.703
PER3 island 2	−.0005741	0.285	−.0008578	0.314	−.0003475	0.629
PER3 island 3	−.0002193	0.964	−.0025248	0.785	.0015882	0.762
CRY2	−.0000955	0.632	.0001579	0.616	−.0003013	0.250
BMAL1	.000112	0.623	.0003808	0.277	−.0000548	0.860
CLOCK	.0000891	0.450	.0003705	0.036	−.0001049	0.513
RORA island 1	.0002087	0.506	.0003642	0.455	4.67e-06	0.991
RORA island 2	.0000125	0.940	.0003688	0.175	−.0002097	0.336
RORA island 3	−.0000466	0.836	.0002262	0.550	−.0002784	0.314
RORB	.0003113	0.422	−.0002669	0.698	.0006562	0.158
NR1D1 island 1	−.0001372	0.757	.0001722	0.815	−.0002654	0.641
NR1D1 island 2	−.0000136	0.938	.0002066	0.452	−.0002197	0.320
NR1D2	.0000413	0.745	.0001992	0.291	−.0000729	0.679
Diet pattern 3: Eggs, milk & refined grain
PER1	−.0010701	0.083	−.0013847	0.082	−.0006233	0.533
PER2	−.0012047	0.022	−.0004974	0.511	−.0019366	0.008
PER3 island 1	−.0002299	0.764	.0001473	0.866	−.0007279	0.585
PER3 island 2	−.0006967	0.280	−.001359	0.102	3.43e-07	1.000
PER3 island 3	−.0031526	0.588	−.0033161	0.716	−.0035995	0.632
CRY2	−.0005672	0.017	−.0006632	0.029	−.0003686	0.328
BMAL1	−.0005028	0.064	−.0006093	0.075	−.000339	0.447
CLOCK	−.0001487	0.293	−.0001681	0.340	−.000082	0.722
RORA island 1	−.0009331	0.012	−.0006093	0.202	−.0011282	0.053
RORA island 2	−.0002716	0.175	−.0006511	0.013	.0002449	0.435
RORA island 3	−.0006814	0.010	−.000516	0.163	−.0007874	0.045
RORB	−.0004259	0.360	−.0003936	0.560	−.000444	0.509
NR1D1 island 1	−.0010925	0.038	−.0017573	0.013	−.0004323	0.597
NR1D1 island 2	−.0003233	0.120	−.000532	0.046	.0000399	0.900
NR1D2	−.0002782	0.066	−.0002651	0.152	−.0002584	0.305

¹Adjusted for sex, age, and % monocytes.

²Adjusted for age and % monocytes.