Epigenetic changes in pyloric caeca of Atlantic salmon fed diets containing increasing levels of lipids and choline

Figures & data

Table 1. Global cytosine methylation levels detected in CpG, CHG and CHH contexts.

	Total number (million) of		% of methylated C’s
Diet group	Cytosines (C’s)analyzed	Methylated C’s (% of total C’s)	CpG context	CHG context	CHH context
L16	151 ± 12	26.6 (17.6%)	84.6	0.9	0.8
L25	157 ± 7	27.1 (17.3%)	84.2	1.0	0.8
L28	166 ± 17	29.3 (17.6%)	84.5	1.0	0.8

Total number of cytosines analysed ± SEM from n = 6 per diet group.

Table 2. General statistics on significantly differentially methylated cytosines in CpG context.

	Differentially methylated CpGs (>10%, q < 0.1)
Comparisons	Total	Hypermethylation*	Hypomethylation*
L25 vs L16	195	92 (47.2%)	103 (52.8%)
L28 vs L25	360	190 (52.8%)	170 (47.2%)

*The percentages of hypermethylation and hypomethylation are shown in parentheses.

Figure 1. Bar plots showing the percentage of hyper- and hypomethylated CpGs per chromosome over all the covered CpGs in a given chromosome. (a) Comparison of L25 vs L16 diet groups and (b) L28 vs L25 diet groups. CpGs with q < 0.1 and methylation differences > 10% were considered as hyper- and hypomethylated.

Figure 2. Genomic feature analysis of differentially methylated cytosines in each of the comparisons between diet groups.

Table 3. The total number of genes associated with DMCs in each pairwise comparison of diet groups.

Comparisons	Total no. of genes	Genes assigned with symbol/name*	Genes not assigned with symbol/name*
L25 vs L16	167	89 (53.3%)	78 (46.7%)
L28 vs L25	290	143 (49.3%)	147 (50.7%)

*Percentages of assigned and not assigned genes are presented in parentheses.

Table 4. Selected genes associated with DMCs in the pyloric caeca genome of Atlantic salmon fed diets with increasing lipid or choline content.

Gene symbol	Gene Name	L25 vs L16*	L28 vs L25*
Promoter
tjap1	tight junction associated protein 1	4(4)	4(0)
slc22a15	solute carrier family 22-member 15	0	3(0)
LOC106597856	acyl-CoA desaturase-like (scd)	0	1(0)
LOC106564195	ARF GTPase-activating protein Git2 (git2)	1(1)	0
LOC106610877	kelch-like protein 28 (klhl28)	3(0)	0
sstr2a	somatostatin receptor 2a	0	2(2)
TTS
LOC106580941	major facilitator superfamily domain-containing protein 1-like (mfsd1)	0	3(0)
Exon
LOC123728301	potassium voltage-gated channel subfamily A member 1-like (kcna1)	2(0)	3(3)
Intron
ssa-mir-212a-2	ssa-mir-212a-2	1(1)	0
irf4a	interferon regulatory factor 4a	0	3(0)
LOC106594380	arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 (acap3)	0	4(4)
agap3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	0	2(2)
gabrb2	gamma-aminobutyric acid type A receptor subunit beta2	0	4(0)

*Total number of DMCs are presented with the number of hypermethylated cytosines in parentheses.

Figure 3. Increased dietary choline levels induced epigenetic regulation of several genes involved in fatty acid (FA) transport and metabolism. Peripheral tight junction protein tjap1, solute carrier, slc22a15, and scd involved in fatty acid biosynthesis showed hypomethylation in promoter region and major facilitator superfamily transporter mfsd1 showed hypomethylation in TTS with increased dietary choline levels. Cd36 - cluster of differentiation 36, CptI and CptII - carnitine palmitoyltransferase I and II. Figure created with Biorender.com.

Data availability statement

The sequence data were deposited in the NCBI Sequence Read Archive (SRA) with reference number (PRJNA992799).