Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.)

Krick, Madoka Vera; Desmarais, Erick; Samaras, Athanasios; Guéret, Elise; Dimitroglou, Arkadios; Pavlidis, Michalis; Tsigenopoulos, Costas; Guinand, Bruno

doi:10.1186/s12864-021-07420-9

Table 1 Differentially methylated cytosines (DMCs) found in this study between pre- and post-challenge sea bass

From: Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.)

D. labrax LG	Ensembl LG	q-value	methylation difference (%)	D. labrax Name	Gene ID	Gene Name	Location	References
LG1A	HG916837.1	0	-21,40	DLAgn_00094580	FOXJ3	forkhead box protein J3	gb	[37]
LG1A	HG916837.1	0	-21,67	–	–	–	gb	“
LG1A	HG916837.1	0	−15,51	–	–	–	gb	“
LG3	HG916843.1	1,54E-95	18,14	DLAgn_00141440	ABLIM2	actin binding LIM protein family -- member 2	gb	[37]
LG4	HG916844.1	1,08E-84	16,41	DLAgn_00145290	CELA3b	proproteinase E-like (elastase 2)
LG4	HG916844.1	0	21,38	DLAgn_00146200	NCBP2	nuclear cap-binding protein subunit 2	int.	[37, 38]
LG5	HG916845.1	3,67E-265	21,91	DLAgn_00159160	CILP1	cartilage intermediate layer protein 1	gb	[38]
LG5	HG916845.1	8,93E-89	16,64	DLAgn_00159900	GRPT1	growth hormone regulated TBC protein 1	gb
LG6	HG916846.1	6,44E-245	20,44	DLAgn_00164450	GLG1a	golgi glycoprotein 1	gb	[37, 39]
LG6	HG916846.1	0	−21,01	DLAgn_00166360	GDPGP1	gdp-d-glucose phosphorylase 1	exon
LG6	HG916846.1	0	−18,98	DLAgn_00172370	KBTBD13	kelch repeat and btb domain-containing protein 13-like	int.
LG6	HG916846.1	0	−18,18	–	–	–	int.
LG6	HG916846.1	0	−16,12	–	–	–	int.
LG8	HG916848.1	2,77E-247	22,52	DLAgn_00186250	BTPF	nucleosome-remodeling factor subunit bptf	gb
LG10	HG916827.1	2,44E-79	15,44	DLAgn_00005890	PBX1	pre-B-cell leukemia homeobox 1	gb	[37]
LG10	HG916827.1	6,98E-125	21,55	DLAgn_00006210	ADCY1	adenylate cyclase 1 (brain)	gb	[37, 39]
LG11	HG916828.1	0	27,70	DLAgn_00016970	MMNR2	multimerin 2a Precursor Elastin Microfibril Interface Located Elastin Microfibril Interfacer	gb
LG12	HG916829.1	0	22,32	DLAgn_00019700	FBXO33	F-box protein 33	int.
LG12	HG916829.1	1,23E-128	20,01	DLAgn_00025280	SASH1A	Sam and sh3 domain-containing protein 1-like	int.	[37, 39]
LG14	HG916831.1	1,48E-53	15,74	DLAgn_00037440	COL4A5	Collagen type IV alpha 5 chain	int.	[37, 39]
LG14	HG916831.1	0	42,05	DLAgn_00037440	COL4A5	“	gb	“
LG14	HG916831.1	0	22,46	DLAgn_00038760	ROBO3	Roundabout homolog 2-like	int.	[37, 39]
LG14	HG916831.1	5,22E-212	17,93	DLAgn_00044110	CLDN4	Claudin 4	gb	[37]
LG14	HG916831.1	1,25E−155	27,48	DLAgn_00046110	TMEM132E	Transmembrane protein 132e	gb
LG16	HG916833.1	2,78E-168	26,24	DLAgn_00063590	CSMD3a	CUB and Sushi multiple domains 3a	gb	[37]
LG16	HG916833.1	9,78E-92	17,12	DLAgn_00063770	TRMT11	tRNA methyltransferase 11 homolog	int.	[37]
LG16	HG916833.1	8,81E− 215	17,80	DLAgn_00064610	FURIN	Furin-like protease kpc-1	gb	[37, 38]
LG16	HG916833.1	0	17,76	DLAgn_00064820	SPIRE1b	Protein spire homolog 1-like	gb	[37]
LG17	HG916834.1	1,91E-82	18,84	DLAgn_00073160; DLAgn_00073170	PLG (sense); SLC22A2 (antisense)	Plasminogen (sense) / Solute carrier family 22 member 2-like (antisense)	gb / 3’UTR	[37]
LG17	HG916834.1	1,28E-231	19,86	DLAgn_00073770	RRM2	Ribonucleotide reductase regulatory subunit M2	gb	[37, 38]
LG20	HG916840.1	2,76E-207	15,01	DLAgn_00114460	TNKSb	Tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase b	gb	[37, 39]
LG20	HG916840.1	1,34E-115	15,35	DLAgn_00114810	LRRTM4L2	Leucine-rich repeat transmembrane neuronal protein 4-like	gb
LG20	HG916840.1	3,78E-68	15,32	DLAgn_00116160; DLAgn_00116150	FICD (sense); SART3 (antisense)	Adenosine monophosphate-protein transferase ficd-like (sense) / Spliceosome associated factor 3, U4/U6 recycling protein (antisense)	gb	[37]
LG20	HG916840.1	1,02E-88	18,04	DLAgn_00121270		Coding region of a truncated Non LTR Retrotransposable Element (RTE) RET-1_AFC	rr
LG20	HG916840.1	0	35,61	DLAgn_00122640	BMP3	Bone morphogenetic protein 3	gb	[37]
LG20	HG916840.1	0	15,40	DLAgn_00124110	ZMAT4	Zinc finger matrin-type 4b	gb	[37]
LG22–25	HG916841.1	7,62E-96	16,89	DLAgn_00125750	NOL4LB	Nucleolar protein 4-like b	gb	[39]
LG22–25	HG916841.1	3,26E-99	15,05	DLAgn_00132500	CCDC30	Coiled-coil domain containing protein 30 like	gb	[37]
LG24	HG916842.1	2,81E-43	-15,63	DLAgn_00136190	GLI2	Zinc finger protein gli2-like	gb	[37, 38]
LG24	HG916842.1	2,87E-112	16,47	DLAgn_00136980	LRRC3	Leucine rich repeat containing 3	int.
LG24	HG916842.1	0	30,68	DLAgn_00137190	UNC80	Protein unc-80 homolog isoform 2	gb	[37, 39]
LG24	HG916842.1	0	15,42	DLAgn_00137560	CHN1	N-chimerin	gb	[37]
LG24	HG916842.1	9,47E-204	17,08	DLAgn_00139980	PTGFRN	Prostaglandin f2 receptor negative regulator	gb	[37, 39]
LGx	HG916850.1	4,18E-251	19,94	DLAgn_00209310	MYF5	Myogenic factor 5	gb
LGx	HG916850.1	4,52E-204	23,46	DLAgn_00209760	CELF2	Cugbp elav-like family member 2	gb	[37, 38]
SB-UN	HG916851.1	1,61E-152	16,29	DLAgn_00218300	PRKCQ	Protein kinase c theta type	int.	[37]
SB-UN	HG916851.1	1,09E-120	16,34	DLAgn_00220000	PTPRB	Protein tyrosine phosphatase receptor type B	gb	[37]
SB-UN	HG916851.1	6,07E-154	18,95	DLAgn_00222790	NPAS3	Neuronal PAS domain-containing protein 3-like	gb	[37]
SB-UN	HG916851.1	0	-21,55	DLAgn_00227120	CRTC2	CREB regulated transcription coactivator 2	gb	[37]
SB-UN	HG916851.1	6,11E-56	15,79	–	–	–	gb	“
SB-UN	HG916851.1	4,15E-61	17,53	DLAgn_00227130	DENND4B	Denn domain-containing protein 4b	gb	[37]
SB-UN	HG916851.1	1,51E-46	15,84	DLAgn_00236500	GFRA2	GDNF family receptor alpha-2	gb	[37]
SB-UN	HG916851.1	0	46,39	DLAgn_00238280	DLG1	Disks large homolog 1-like	gb	[38,39,40]
SB-UN	HG916851.1	9,43E-157	26,15	DLAgn_00242570	BTR30	E3 ubiquitin-protein ligase TRIM39-like (bloodthirsty-related gene family, member 30)	gb
SB-UN	HG916851.1	6,99E-209	−17,71	–	–	–	gb
SB-UN	HG916851.1	2,11E-216	−27,49	DLAgn_00244380	GMPPB	GDP-mannose pyrophosphorylase B	exon	[37]
SB-UN	HG916851.1	5,09E-256	20,97	DLAgn_00245980	MATR3	Matrin-3	exon	[37]

Location on the European sea bass linkage groups (LGs) of the 57 differentially methylated cytosines (DMCs) found in this study between pre- and post-challenge individuals. For each DMC, the false-discovery rate adjusted q-values at the nominal q = 0.001 cut-off threshold are reported, together with their methylation difference. Gene names and gene symbols (IDs) of DMC-related genes (n = 51) are reported. The location of each DMC is given (gb: gene body, int.: intergenic, 3’UTR or rr: repeat region). We did not arbitrarily defined promoter regions in this study. The right column indicates high-throughput stress-related neurotranscriptomic studies in which some of these DMC-related genes were reported as differentially expressed. It does not mean that these DMC related genes are involved only in brain-derived studies of stress (see Discussion for few reports). LGs are labelled as in [19] (GenBank assembly: GCA_000689215.1). An extended version of this table reporting annotations and further useful information are offered in Additional File 3

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ISSN: 1471-2164

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