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Genome-wide analysis of DNA methylation in the sexual stage of the insect pathogenic fungus Cordyceps militaris

ABSTRACT: Genome-wide analysis of DNA methylation for asexual and sexual stages of Cordyceps militaris DNA methylation is a basic epigenetic mechanism found in eukaryotes, but its patterns and roles vary significantly among diverse taxa. In fungi, DNA methylation has various effects on diverse biological processes; however, its function underlying the sexual development of fungi remains unclear. Cordyceps militaris, readily performing sexual reproduction, provides a remarkably rich model for understanding epigenetic processes in sexual development. The methylome was surveyed to assess DNA methylation patterns of the nascent fruiting body in C. militaris at single-base resolution by genomic bisulfite sequencing (BS-Seq). The results showed that around 0.4 % of cytosines are methylated, and that there is no difference compared with the DNA methylation level (0.39 %) during asexual development. However, 225 differentially methylated regions (DMRs) were identified between the stages. Moreover, RNA-Seq analysis indicated that the DMRs have no direct relation with the genes for fungal sexual development in C. militaris. DNA methylation regions from the BS-Seq show a striking correspondence to regions predicted to be repetitive and repeat-induced point mutation (RIP) mutated, suggesting that DNA methylation functions as a genome defense mechanism in sexual development. These results provide a comprehensive characterization of DNA methylation in the sexual development of C. militaris, which will contribute to future investigations of epigenetics in fungi.

ORGANISM(S): Cordyceps militaris

PROVIDER: GSE66919 | GEO | 2016/05/13

SECONDARY ACCESSION(S): PRJNA278366

REPOSITORIES: GEO

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Project description:To further our understanding of the role of DNA methylation in development, Methylated DNA Immunoprecipitation (MeDIP) was used in conjunction with a NimbleGen promoter plus CpG island array to identify Tissue and Developmental Stage specific Differentially Methylated DNA Regions (T-DMRs and DS-DMRs) on a genome-wide basis. Four tissues (brain, heart, liver, and testis) from C57BL/6J mice were analyzed at three developmental stages (15 day embryo, E15; new born, NB; 12 week adult, AD). Almost 5,000 adult T-DMRs and 10,000 DS-DMRs were identified. Surprisingly, almost all DS-DMRs were tissue specific (i.e., methylated and ummenthylated in one or more non-overlapping tissues), indicating that the vast majority of unique sequence DNA methylation has tissue specificity. Also, many DS-DMRs were methylated at early development stages (E15 and NB) but unmethylated in adult, indicating “demethylation” has a prominent role in tissue differentiation. The pattern of DNA methylation in adult testis was dramatically different from somatic tissues in many aspects, mostly notably with a very strong bias of methylation in non-CpGi (CpG island) promoter regions (94%). Although the majority of T-DMRs and DS-DMRs tended to be in non-CpGi promoter regions, a relatively large number were also located in CpGi in promoter, intra-genic and inter-genic regions (>15% of all CpGi). Gene Ontology analysis of genes with methylation in non-CpGi promoters indicates enrichment of genes related to membrane proteins and G-protein coupled receptors. Our data also suggest regulatory roles of DNA methylation outside of promoter regions and in alternative promoter selection. Overall, our studies indicate that change in DNA methylation during development is a dynamic, widespread and tissue-specific process involving both DNA methylation and demethylation. Comparison of DNA methylation across 3 developmental stages (15 day embryo, newborn, and adult) for four tissues (brain, heart, liver and testis)

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Genome-wide analysis of DNA methylation in the sexual stage of the insect pathogenic fungus Cordyceps militaris

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