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Background  Environmental changes of biotic or abiotic nature during critical periods of early development may exert a profound influence on physiological functions later in life. This process, named developmental programming can also be driven through parental nutrition. At molecular level, epigenetic modifications are the most likely candidate for persistent modulation of genes expression in later life.    Results  In order to investigate epigenetic modifications induced by programming in rainbow trout, we focused on  bnip3  and  bnip3l  paralogous genes known to be sensitive to environmental changes but also regulated by epigenetic modifications. Two specific stimuli were used: (i) early acute hypoxia applied at embryo stage and (ii) broodstock and fry methionine deficient diet, considering methionine as one of the main methyl-group donor needed for DNA methylation. We observed a programming effect of hypoxia with an increase of  bnip3a  and the four paralogs of  bnip3l  expression level in fry. In addition, parental methionine nutrition was correlated to  bnip3a  and  bnip3lb1  expression showing evidence for early fry programming. We highlighted that both stimuli modified DNA methylation levels at some specific loci of  bnip3a  and  bnip3lb1 .    Conclusion  Overall, these data demonstrate that methionine level and hypoxia stimulus can be of critical importance in metabolic programming. Both stimuli affected DNA methylation of specific loci, among them, an interesting CpG site have been identified, namely − 884 bp site of  bnip3a , and may be positively related with mRNA levels.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5048-4) contains supplementary material, which is available to authorized users.

DNA methylation of the promoter region of bnip3 and bnip3l genes induced by metabolic programming