The Regulation Of Genetic Imprinting In Maize Endosperm And Its Stability And Conservation

Genomic imprinting mainly occurs in endosperm tissues in plants,which is often associated with allele-specific epigenetic modifications.Although there are many reports suggesting the potential roles of DNA methylation and H3K27me3 in regulating of genomic imprinting,research about the contributions of allele-specific active histone modifications to imprinting has been highly limited in plant.So far in several organisms of plant,hundreds of imprinted genes have been identified in one specific periods of endosperm.However,how the expression and imprinting profile of these imprinted genes look across the whole endosperm development in the transcriptome-wide scale is still unknown so far.Here we identified 337 high-stringency allele-specific H3K4me3 and H3K36me3 peaks in 12 DAP maize endosperm.Paternally expressed genes(PEGs)were correlated with paternally preferred H3K4me3 and H3K36me3 peaks while maternally expressed genes that are specifically expressed in endosperm(endo-MEGs)were associated with maternally preferred H3K4me3 and H3K36me3 peaks.Taken H3K4me3,H3K36me3 and H3K27me3 together,a pattern unique for PEGs was observed,where the active H3K4me4,H3K36me3(preferentially enriched on paternal alleles)and repressive H3K27me3(specifically enriched on maternal alleles)peaks showed up altogether.H3K27me3 and H3K36me3 specifically deposited at the gene body of con-PEGs(constitutively expressed PEG)on hypomethylated maternal alleles and hypermethylated paternal alleles respectively.For endo-MEGs,DNA methylation and H3K4me3 specifically marked around TSS on paternal and maternal alleles respectively.Additionally,35 maternally expressed non-coding RNAs(MNCs)were identified,which exhibited same allele-specific epigenetic features with endo-MEGs,indicating similar mechanism for regulation of imprinted genes and non-coding RNAs.Additionally,we performed RNA sequencing of 4,6,8,10,12,16,24 and 32 days-after-pollination(DAP)maize endosperm from the reciprocal crosses of B73 and Mo 17 inbred,which almost represents the main developmental stages of maize endosperm.As a result,92 high-striengency MEGs and 180 PEGs were uncovered in eight developmental-stages endosperm.Comparing parental bias of imprinted genes in developmental stages endosperm,62.5%of MEG and 68.6%of PEGs showed continuously imprinted expression,which were called all-stages MEGs/PEGs.20.8%of MEGs and 16.3%of PEGs showed allelic expression mainly before 16 DAP endosperm,16.7%of MEGs and 11.6%of PEGs showed allelic expression mainly after 8 DAP endosperm,which were called stage-specific MEGs/PEGs.Interestingly,we found that the parental-bias dynamic of stage-specific MEGs/PEGs changes gradually according to endosperm development.The rice and maize,sorghum and maize are diverged～50 and～12 million years ago.We found 48.4%/54.3%of rice MEGs/PEGs and 65.7%/61.3%of sorghum MEGs/PEGs with their synthenic/homolog genes being imprinted in maize.In this study,the complex patterns of mutually exclusive epigenetic modifications deposited at different alleles of imprinted genes that are required for the genomic imprinting in maize endosperm.And,our results not only provided a resource about imprinted genes and their allelic expression patterns in maize endosperm from 4 DAP to 32 DAP,but also uncover the imprinting stability and conservation.