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Background  The identification of DNA methyltransferases (Dnmt) expression patterns during development and their regulation is important to understand the epigenetic mechanisms that modulate larval plasticity in marine fish. In this study,  dnmt1  and  dnmt3  paralogs were identified in the flatfish  Solea senegalensis  and expression patterns in early developmental stages and juveniles were determined. Additionally, the regulation of Dnmt transcription by a specific inhibitor (5-aza-2′-deoxycytidine) and temperature was evaluated.    Results  Five paralog genes of  dnmt3 , namely  dnmt3aa ,  dnmt3ab, dnmt3ba ,  dnmt3bb.1  and  dnmt3bb. 2 and one gene for  dnmt1  were identified. Phylogenetic analysis revealed that the  dnmt  gene family was highly conserved in teleosts and three fish-specific genes,  dnmt3aa ,  dnmt3ba  and  dnmt3bb.2  have evolved .  The spatio-temporal expression patterns of four  dnmts  ( dnmt1 ,  dnmt3aa ,  dnmt3ab  and  dnmt3bb.1 ) were different in early larval stages although all of them reduced expression with the age and were detected in neural organs and  dnmt3aa  appeared specific to somites. In juveniles, the four  dnmt  genes were expressed in brain and hematopoietic tissues such as kidney, spleen and gills. Treatment of sole embryos with 5-aza-2′-deoxycytidine down-regulated  dntm1  and up-regulated  dntm3aa . Moreover, in lecithotrophic larval stages,  dnmt3aa  and  dnmt3ab  were temperature sensitive and their expression was higher in larvae incubated at 16 °C relative to 20 °C.    Conclusion  Five  dnmt3  and one  dnmt1  paralog were identified in sole and their distinct developmental and tissue-specific expression patterns indicate that they may have different roles during development. The inhibitor 5-aza-2′-deoxycytidine modified the transcript abundance of  dntm1  and  dntm3aa  in embryos, which suggests that a regulatory feedback mechanism exists for these genes. The impact of thermal regime on expression levels of  dnmt3aa  and  dnmt3ab  in lecithotrophic larval stages suggests that these paralogs might be involved in thermal programing.    Electronic supplementary material  The online version of this article (doi:10.1186/s12861-017-0154-0) contains supplementary material, which is available to authorized users.

Phylogeny, expression patterns and regulation of DNA Methyltransferases in early development of the flatfish, Solea senegalensis