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The single-base resolution DNA methylation profiles for four developmental stages of Tribolium castaneum

ABSTRACT: Cytosine DNA methylation in the Tribolium castaneum has been controversial, its distribution pattern and functions have not been established yet. Here, using BS-Seq, we confirmed the existence of DNA methylation and described the methylation profiles for four life stages of T.castaneum. Interestingly, two types of DNA methylation had been discovered in T.castaneum genome. One was the symmetrical CpG methylation which was typically existed among eukaryotes methylomes, but occupied small part in methylome of T. castaneum. Another type was the non-CpG methylation which was uniquely and predominated in methylome of T. castaneum. While, the symmetrical CpG methylation which was catalyzed by the conserved DNA methyltransferase DNMT1 in T.castaneum mainly enriched in gene bodies and was positively correlated with the gene expression level. The asymmetrical nonCpG (most mCpA) methylation strongly concentrated in intergenic regions and introns while absent from the exons. Gene body methylation was negatively correlated with the gene expression level. The distribution pattern and functions of this type methylation only showed similarity with the methylome of Drosophila melanogaster, which further support that there existed a novel methyltransferase in these two specieces responsible for this methylation. The DNA methylome of T. castaneum possess two differential types and unique characterizations, which will contribute to our further understanding of the variety, origin and functions of DNA methylation in eukaryotes.

ORGANISM(S): Tribolium castaneum

PROVIDER: GSE84253 | GEO | 2017/07/11

SECONDARY ACCESSION(S): PRJNA328479

REPOSITORIES: GEO

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Project description:Cancer is characterised by DNA hypermethylation and gene silencing of CpG island-associated promoters, including tumour suppressor genes The methyl-CpG-binding domain (MBD) family of proteins bind to methylated DNA and can aid in the meditation of gene silencing by interaction with histone deacetylases and histone methyltransferases. However the mechanisms responsible for eliciting CpG island hypermethylation in cancer, and the potential role that MBD may proteins play in modulation of the methylome remain unclear. Our previous work demonstrated that MBD2 preferentially binds to the hypermethylated GSTP1 promoter CpG island in prostate cancer cells. Here, we use functional genetic approaches to investigate if MBD2 plays an active role in promoting DNA methylation. First, we show that loss of MBD2 results in inhibition of both maintenance and spread of de novo methylation of a transfected construct containing the GSTP1 promoter CpG island in prostate cancer cells and Mbd2-/- mouse fibroblasts. De novo methylation was rescued by transient expression of Mbd2 in Mbd2-/- cells. Second, we show that MBD2 depletion triggers significant hypomethylation genome-wide in prostate cancer cells with concomitant loss of MBD2 binding at promoter and enhancer regulatory regions. Finally, CpG islands and shores that become hypomethylated after MBD2 depletion in LNCaP cancer cells show significant hypermethylation in clinical prostate cancer, highlighting a potential active role of MBD2 in promoting cancer specific hypermethylation. Importantly, co-immunoprecipiation of MBD2 reveals that MBD2 associates with DNA methyltransferase (DNMT) enzymes 1 and 3A. Together our results demonstrate that MBD2 plays a critical role in â??rewritingâ?? the cancer methylome at specific regulatory regions. LNCaP prostate cancer cell line clones with reduced MBD2 expression were establised by using shRNA to MBD2 and scrambled control clones were established with scrambled control shRNA. To interrogate methylation changes induced by MBD2 knock-down we profiled three stably transfected scrambled control clones and three MBD2 knockdown clones on Illumina HumanMethylation450K arrays. Differential methylation analysis was carried out to identified CpG sites hypo-/hyper-methylated as a result of MBD2 knockdown.

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The single-base resolution DNA methylation profiles for four developmental stages of Tribolium castaneum

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