Contrasting DNA methylation responses of inbred fish lines to different rearing environments

Figures & data

Figure 1. Heat map illustrating percentage of methylation for all differentially methylated cytosines (DMCs) identified (a) between genotypes, (b) between environments, (c) between environments for DAN strain, and (d) between environments for R strain (logistic regression q < 0.01 and |ΔM|>20%, and t.test p < 0.01) using unsupervised hierarchical clustering. Rows represent a unique CpG site and columns individual fish.

Table 1. Methylation differences averaged (percentage) for differentially methylated cytosines (DMCs) between environments (poor, enriched), shared between genotypes (DAN, R) which overlap annotated genes (reference genome ASM164957v1, GCA_00164975.1). Epiallele classification (pure or facilitated) followed [9]. Positive and negative values represent increased and decreased methylation in enriched and poor environments, respectively. Q-value is the p-value adjusted by false discovery rate (FDR = 0.05).

Gene symbol	Entrez gene name	Epiallele classification	Meth diff DAN	Q-value	Meth diff R	Q-value
acvr2a	Activin A receptor type 2A	P	34.37	0.007	29.17	<0.001
col25a1	Collagen type XXV alpha 1 chain	F	43.61	0.005	−21.63	0.005
dmap1	DNA methyltransferase 1 associated protein 1	F	26.99	<0.001	−21.69	<0.001
foxp4	Forkhead box P4	F	22.50	<0.001	−37.56	<0.001
gpc5	Glypican 5	F	31.82	0.01	−32.06	<0.001
mipol1	Mirror-image polydactyly 1	F	35.85	<0.001	−30.59	<0.001
necab2	N-terminal EF-hand calcium binding protein 2	F	20.25	0.01	−23.56	<0.001
neo1	Neogenin 1	F	20.25	<0.001	−31.24	<0.001
nudcd1	NudC domain containing 1	F	39.76	<0.001	−21.05	<0.001
ramp3	Receptor activity-modifying protein 3-like	P	−27.12	0.037	−29.15	<0.001
ryr3	Ryanodine receptor 3	P	−30.48	0.003	−25.4	<0.001
sorcs2	Sortilin-related VPS10 domain containing receptor 2	F	36.81	0.008	−33.20	<0.001
trit1	tRNA isopentenyltransferase 1	F	20.38	<0.001	−29.70	<0.001
trmt44	tRNA methyltransferase 44	F	23.98	<0.001	−28.21	<0.001
ubald1	UBA like domain containing 1	F	36.76	0.019	−31.02	0.004
zeb2	Zinc finger E-box binding homeobox 2	F	31.83	<0.001	−28.35	<0.001
znf516	Zinc finger protein 516	F	31.51	<0.001	−31.60	<0.001
zranb3	Zinc finger RANBP2-type containing 3	F	41.41	<0.001	−33.79	<0.001
LOC108234847	Adhesion G protein-coupled receptor L3-like	F	48.57	<0.001	−39.35	<0.001
LOC108240988	Non-muscle caldesmon-like	F	32.49	0.005	−32.78	<0.001
LOC108243470	Protein-methionine sulfoxide oxidase mical2b-like	F	33.35	<0.001	−25.70	<0.001
LOC108243852	Receptor-type tyrosine-protein phosphatase N2-like	F	37.97	0.014	−30.28	<0.001
LOC108245430	Uncharacterized protein	F	42.94	<0.001	−41.49	<0.001
LOC108247402	Spectrin beta chain, non-erythrocytic 1-like	F	40.73	0.006	−27.58	<0.001
LOC108251479	Transcriptional regulator Myc-B-like	F	30.49	0.010	−25.13	<0.001

Table 2. Linear model of principal component scores for mangrove killifish epialleles shared between genotypes (R, DAN) and environments (poor, enriched).

	t-values	Prop. of variance (%)	df	p-value
(a) Facilitated epialleles
PC1 scores
Genotype	1.63	0.06	1	0.80
Environment	1.58	12.41	1	0.003
Genotype x Environment	−11.25	68.08	1	<0.001
PC2 scores
Genotype	−1.64	91.35	1	<0.001
Environment	8.28	0.21	1	0.49
Genotype x Environment	10.29	0.35	1	0.38
(b) Pure epialleles
PC1 scores
Genotype	2.28	13.18	1	0.008
Environment	−2.81	59.28	1	<0.001
Genotype x Environment	0.98	0.09	1	0.80
PC2 scores			1
Genotype	0.29	37.96	1	0.003
Environment	−1.82	1.14	1	0.56
Genotype x Environment	−2.97	0.67	1	0.65

Figure 2. Principal component analysis (PCA) and reaction norms of epialleles across genotypes and environments. PCAs were based on individual scores of methylation across either (a) facilitated or (b) pure annotated DMCs. Dark yellow for DAN individuals on enriched environments; light yellow for DAN genotype on poor environments; dark green for R individuals on enriched environments; light green for R genotype on poor environments. Each reaction norm represents the change on averaged methylation scores (in percentage) for (c) facilitated and (d) pure epialelles annotated DMCs across environments. Different colours represent the genotypes (yellow for DAN; green for R). Different shapes (d) represent different annotated DMCs. Epialelles were classified according to Richards (2006). Detailed information for each annotated DMCs methylation score across genotypes is available in Table 1.

Richards EJ. Inherited epigenetic variation – revisiting soft inheritance. Nat Rev Genet. 2006;7:395.

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