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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]
  1. 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