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DNA Methylation of Intragenic CpG Islands are Required for Differentiation from iPSC to NPC

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Abstract

The effects of gene body DNA methylation on gene regulation still remains highly controversial. In this study, we generated whole genome bisulfite sequencing (WGBS) data with high sequencing depth in induced pluripotent stem cell (iPSC) and neuronal progentior cell (NPC), and investigated the relationship between DNA methylation changes in CpG islands (CGIs) and corresponding gene expression during NPC differentiation. Interestingly, differentially methylated CGIs were more abundant in intragenic regions compared to promoters and these methylated intragenic CGIs (iCGIs) were associated with neuronal development-related genes. When we compared gene expression level of methylated and unmethylated CGIs in intragenic regions, DNA methylation of iCGI was positively correlated with gene expression in contrast with promoter CGIs (pCGIs). To gain insight into regulatory mechanism mediated by iCGI DNA methylation, we executed motif searching in hypermethylated iCGIs and found NEUROD1 as a hypermethylated iCGI binding transcription factor. This study highlights give rise to possibility of activating role of hypermethylation in iCGIs and involvement of neuronal development related TFs.

The relationship between iCGI DNA methylation and expression of associated genes in neuronal developmental process. During iPSC to NPCdifferentiation, iCGI containing neural developmental genes show iCGI's DNA hypermethylation which is accompanied by gene activation and NEUROD1which is one of the core neuronal TFs interacts with hypermethylated iCGI regions.

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Acknowledgments

This work was supported by Samsung Science and Technology Foundation Project SSTF-BA1601-13.

Accession Codes

All Whole Genome Bisulfite sequencing (WGBS), mRNA-seq and ChIP-seq data for iPSC and NPC have been submitted to the Gene Expression Omnibus (GEO) under accession GSE156723.

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  1. Interdisciplinary Program of Integrated OMICS for Biomedical Science, The Graduate School, Yonsei University, Seoul, 03722, Republic of Korea

    Won-Young Choi, Ji-Hyun Hwang, Jungwoo Lee & Young-Joon Kim

  2. Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea

    Ann-Na Cho & Seung-Woo Cho

  3. Department of Biological Sciences, KAIST, Daejeon, Republic of Korea

    Andrew J Lee & Inkyung Jung

  4. Severance Biomedical Science Institute and BK21 PLUS Project for Medical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06230, Republic of Korea

    Lark Kyun Kim

  5. Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea

    Young-Joon Kim

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W.-Y.C. and Y.-J.K. conceived and designed the study. W.-Y.C., A.J.L and J.L. produced and processed next generation sequencing data and W.-Y.C. analyzed the data. A.-N.C. performed cellular work for iPSC maintaining and differentiation. I.-K.J. and S.-W.C. contributed advice in experiment and data analysis. W.-Y.C, J.-H.H. and L.K.K wrote the manuscript. L.K.K and Y.-J.K. supervised the project.

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Supplementary Fig. 1.

Characterization of function of genes according to localization of CGIs. (A-D) Gene Ontology analysis of genes containing hypermethylated promoter CGIs (pCGIs), hypomethylated pCGIs, hypermethylated intragenic CGIs (iCGIs) and hypomethylated iCGIs. The p-values were calculated using the Benjamini–Hochberg method in DAVID. Supplementary Table 1. The list of unmethylated iCGIs which were activated by neural differentiation (PDF 85 kb) (PDF 85 kb)

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Choi, WY., Hwang, JH., Cho, AN. et al. DNA Methylation of Intragenic CpG Islands are Required for Differentiation from iPSC to NPC. Stem Cell Rev and Rep 16, 1316–1327 (2020). https://doi.org/10.1007/s12015-020-10041-6

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