Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice

Mayumi Oda, Shunichi Wakabayashi, N. Ari Wijetunga, Shinsuke Yuasa, Hirokazu Enomoto, Ruri Kaneda, Sung Han Yoon, Nishant Mittal, Qiang Jing, Masako Suzuki, John M. Greally, Keiichi Fukuda, Shinji Makino

Research output: Contribution to journalArticle

Abstract

Background: Cell-type-specific genes exhibit heterogeneity in genomic contexts and may be subject to different epigenetic regulations through different gene transcriptional processes depending on the cell type involved. The gene-body regions (GBRs) of some cardiomyocyte (CM)-specific genes are long and highly hypomethylated in CMs. To explore the cell-type specificities of epigenetic patterns and functions, multiple epigenetic modifications of GBRs were compared among CMs, liver cells and embryonic stem cells (ESCs). Results: We found that most genes show a moderately negative correlation between transcript levels and gene lengths. As CM-specific genes are generally longer than other cell-type-specific genes, we hypothesized that the gene-body epigenetic features of CMs may support the transcriptional regulation of CM-specific genes. We found gene-body DNA hypomethylation in a CM-specific gene subset co-localized with rare gene-body marks, including RNA polymerase II (Pol II) and p300. Interestingly, 5-hydroxymethylcytosine (5hmC) within the gene body marked cell-type-specific genes at neonatal stages and active gene-body histone mark H3K36 trimethylation declined and overlapped with cell-type-specific gene-body DNA hypomethylation and selective Pol II/p300 accumulation in adulthood. Different combinations of gene-body epigenetic modifications were also observed with genome-wide scale cell-type specificity, revealing the occurrence of dynamic epigenetic rearrangements in GBRs across different cell types. Conclusions: As 5hmC enrichment proceeded to hypomethylated GBRs, we considered that hypomethylation may not represent a static state but rather an equilibrium state of turnover due to the balance between local methylation linked to transcription and Tet oxidative modification causing demethylation. Accordingly, we conclude that demethylation in CMs can be a used to establish such cell-type-specific epigenetic domains in relation to liver cells. The establishment of cell-type-specific epigenetic control may also change genomic contexts of evolution and may contribute to the development of cell-type-specific transcriptional coordination.

Original languageEnglish (US)
Article number349
JournalBMC Genomics
Volume19
Issue number1
DOIs
StatePublished - May 10 2018

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Cardiac Myocytes
Epigenomics
Genes
Body Regions
Histone Code
Gene Rearrangement
RNA Polymerase II
Liver
DNA
Embryonic Stem Cells

Keywords

  • 5-hydroxymethylation
  • Cardiomyocytes
  • DNA methylation
  • Epigenome
  • Gene length

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice. / Oda, Mayumi; Wakabayashi, Shunichi; Ari Wijetunga, N.; Yuasa, Shinsuke; Enomoto, Hirokazu; Kaneda, Ruri; Yoon, Sung Han; Mittal, Nishant; Jing, Qiang; Suzuki, Masako; Greally, John M.; Fukuda, Keiichi; Makino, Shinji.

In: BMC Genomics, Vol. 19, No. 1, 349, 10.05.2018.

Research output: Contribution to journalArticle

Oda, Mayumi ; Wakabayashi, Shunichi ; Ari Wijetunga, N. ; Yuasa, Shinsuke ; Enomoto, Hirokazu ; Kaneda, Ruri ; Yoon, Sung Han ; Mittal, Nishant ; Jing, Qiang ; Suzuki, Masako ; Greally, John M. ; Fukuda, Keiichi ; Makino, Shinji. / Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice. In: BMC Genomics. 2018 ; Vol. 19, No. 1.
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AU - Yuasa, Shinsuke

AU - Enomoto, Hirokazu

AU - Kaneda, Ruri

AU - Yoon, Sung Han

AU - Mittal, Nishant

AU - Jing, Qiang

AU - Suzuki, Masako

AU - Greally, John M.

AU - Fukuda, Keiichi

AU - Makino, Shinji

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