Most methylation-susceptible DNA sequences in human embryonic stem cells undergo a change in conformation or flexibility upon methylation

Yasutoshi Shimooka, Jun Ichi Nishikawa, Takashi Ohyama

    Research output: Contribution to journalArticle

    9 Citations (Scopus)

    Abstract

    DNA methylation in eukaryotes occurs on the cytosine bases in CG, CHG, and CHH (where H indicates non-G nucleotides) contexts and provides an important epigenetic mark in various biological processes. However, the structural and physical properties of methylated DNA are poorly understood. Using nondenaturing polyacrylamide gel electrophoresis, we performed a systematic study of the influence of DNA methylation on the conformation and physical properties of DNA for all CG, CHG, and CHH contexts. In the CG context, methylated multimers of the CG/CG-containing unit fragment migrated in gels slightly faster than their unmethylated counterparts. In the CHG context, both homo- and hemimethylation caused retarded migration of multimers of the CAG/CTG-containing fragment. In the CHH context, methylation caused or enhanced retarded migration of the multimers of CAA/TTG-, CAT/ATG-, CAC/GTG-, CTA/TAG-, or CTT/AAG-containing fragments. These results suggest that methylation increases DNA rigidity in the CG context and introduces distortions into several CHG and CHH sequences. More interestingly, we found that nearly all of the methylation repertoires in the CHG context and 98% of those in the CHH context in human embryonic stem cells were species that undergo conformational changes upon methylation. Similarly, most of the methylation repertoires in the Arabidopsis CHG and CHH contexts were sequences with methylation-induced distortion. We hypothesize that the methylation-induced properties or conformational changes in DNA may facilitate nucleosome formation, which provides the essential mechanism for alterations of chromatin density.

    Original languageEnglish
    Pages (from-to)1344-1353
    Number of pages10
    JournalBiochemistry
    Volume52
    Issue number8
    DOIs
    Publication statusPublished - 2013 Feb 26

    Fingerprint

    Methylation
    DNA sequences
    Stem cells
    Conformations
    DNA Methylation
    DNA
    Physical properties
    Biological Phenomena
    Nucleosomes
    Cytosine
    Electrophoresis
    Eukaryota
    Arabidopsis
    Epigenomics
    Rigidity
    Chromatin
    Human Embryonic Stem Cells
    Structural properties
    Polyacrylamide Gel Electrophoresis
    Cats

    ASJC Scopus subject areas

    • Biochemistry

    Cite this

    Most methylation-susceptible DNA sequences in human embryonic stem cells undergo a change in conformation or flexibility upon methylation. / Shimooka, Yasutoshi; Nishikawa, Jun Ichi; Ohyama, Takashi.

    In: Biochemistry, Vol. 52, No. 8, 26.02.2013, p. 1344-1353.

    Research output: Contribution to journalArticle

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