The Bioinformatic Analysis Of MYB13 And SUVR5 Involved In Modulating Genomic DNA Methylation In Arabidopsis Thaliana

DNA methylation is an important epigenetic modification.DNA methylome is ultimately formed through the combined action of establishment of DNA methylation,maintenance of DNA methylation and DNA demethylation.Our previous study had identified two stable low-fluorescence mutants,named YJ myb13(myb domain protein 13)and YJ suvr5(SU(VAR)3-9-RELATED protein 5),though a genetic screen of an EMS-mutagenized YJ(YJ11-3F)population.By Y2H(yeast two hybrid)assays for testing interactions between MYB13 or SUVR5 and tens of known proteins,we found that MYB 13 is able to physically interact with DMS3(DEFECTIVE IN MERISTEM SILENCING 3),RDM1(RNA-DIRECTED DNA METHYLATION 1),MET18(homolog of yeast MET18)and NRPB4,while SUVR5 is capable of physically interacting with DMS3,ROS1(REPRESSOR OF SILENCING1),IDM3(Increased DNA Methylation 3),SDJ1(SUVH1/3-interacting DNAJ domain-containing protein 1)and SDJ3.In addition,it was also found that there also exists a physical interaction between SUVR5 and MYB 13.It has been known that MET18,ROS1 and IDM3 are all components of DNA demethylation pathway,and DMS3,RDM1 and Pol ?(RNA polymerase II)are all involved in RdDM(RNA-directed DNA methylation)pathway;SDJ1 and SDJ3 protein are constituents of the newly discovered DNA methylation reader complex SUVH-SDJ.Hence,it seems that MYB 13 and SUVR5 are both multifunctional proteins,but their detailed roles in DNA methylome in planta remain unclear.In this study,we analyzed the WGBS(whole genome bisulfite sequencing)data and ChIP-seq(Chromatin Immunoprecipitation Sequencing)data,and came to several conclusions from these results together with protein-protein interaction data,which are listed as follows:1.MYB 13 is a bi-functional protein and it mainly works in RdDM pathway.Bioinformatic analysis of DNA methylome and protein binding data relevant to MYB 13 indicate that although MYB 13 can interact physically with Pol ? subunit NRPB4,it's Pol ?,other than Pol ?,exhibits enrichment in the vicinity of MYB 13 binding sites.The mechanism underlying this phenomenon remains to be investigated.2.SUVR5 is also a bi-functional protein,as does MYB13.Analysis of DNA methylome and protein binding data suggest that there is a high enrichment of Pol ? in the vicinity of SUVR5 peaks.Whereas SUVH-SDJ complex facilitate transcription of promoter-methylated genes via physical binding of such genes,and SUVR5 interacts with DNA demethylase ROS1 as well as DMS3 that is implicated in RdDM,we speculate that SUVR5 may function as a bridge protein to link DNA methylation,DNA demethylation and Pol ?-directed transcription.Futher study needs to be conducted to confirm such speculation.3.In addition to assisting transcription of the genes with highly methylated promoters,the SUVH-SDJ complex is also involved in RdDM pathway.4.IDM3 not only works as a component of DNA demethylation pathway,but also takes part in RdDM pathway.In summary,this study discovered that MYB13 and SUVR5 are both bi-functional proteins that play roles in both DNA methylation and DNA demethylation pathways by means of analysing the data of WGBS and ChIP-seq data.Besides,IDM3,a member of the DNA demethylation pathway,and the SUVH-SDJ complex,a methylation reader that assists in the transcription of promoter-methylated genes,can also play a role in the RdDM pathway.These study increase understanding of mechanism of the formation of DNA methylome and lays a solid foundation for further understanding of interrelationships between DNA methylation and DNA demethylation.