Characterizing the expression, binding and function properties of Methyl-CpG-binding Domain (MBDs) genes in tomato [DAP-Seq]

Genomic DNA methylation is an epigenetic mark, which plays important roles in plant growth and development, and gene stability. In Arabidopsis thaliana, studies have demonstrated that the methyl-CpG-binding domain (MBD) proteins AtMBD5, AtMBD6 and AtMBD7 can specifically bind methylated CpG dinucleotides and AtMBD7 is involved in active DNA demethylation to limit DNA hypermethylation and gene silencing. Yet, the features of MBDs in tomato are not well known. In tomato, 17 putative MBD proteins were identified. Here, we found that 9 MBDs are constitute expressed in different tissues and only SlMBD2, SlMBD10, SlMBD10L3 are highly expressed in tomato fruit. In addition, we detected that SlMBD5 and SlMBD7 can bind specifically on symmetrically mCG sites. While, SlMBD13L can bind in different cytosine contexts depending on the 5 different MBD domains in this protein. To gain insight into MBDs binding capacity in vivo, ChIP-sequencing was performed on MBD5, it showed that SlMBD5 preferentially binds to regions that are enriched with mCG and are close to genes. Knockout of MBD5 reduces seeds germinated speed via increase the expression of GA depredated genes, SlGAox4, resulting the faster metabolism of bioactive GAs (GA4, GA7) to inactive GAs. Therefore, our data suggesting that SlMBD5 is essential for tomato seeds germination. Together, our work provides an evidence of the essential function of MBDs in tomato plant growth and development, which would be helpful in further studies of these genes in tomato. Overall design: DAP-Seq