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Related Experiment Video

Updated: Dec 30, 2025

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement
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SIMON: Simple methods for analyzing DNA methylation by targeted bisulfite next-generation sequencing.

Simon Vial-Pradel1, Yoshinori Hasegawa2, Ayami Nakagawa1

  • 1Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan.

Plant Biotechnology (Tokyo, Japan)
|January 28, 2020
PubMed
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We developed SIMON, a new DNA methylation analysis method using next-generation sequencing (NGS) and PCR. This cost-effective technique precisely measures DNA methylation variations at single nucleotide resolution for numerous samples and loci.

Area of Science:

  • Epigenetics and Molecular Biology
  • Genomics and Bioinformatics

Background:

  • DNA methylation is crucial for gene expression regulation in higher organisms.
  • Whole Genome Bisulfite Sequencing (WG-BS) is versatile but costly and lacks in-depth analysis for multiple samples.
  • Targeted bisulfite sequencing (BS) methods lack analytical depth for large-scale comparisons.

Purpose of the Study:

  • To develop a cost-effective, high-throughput method for precise DNA methylation analysis.
  • To combine the strengths of PCR-based targeted bisulfite sequencing and next-generation sequencing (NGS) with bioinformatics.
  • To enable in-depth analysis of DNA methylation patterns at specific loci across numerous samples.

Main Methods:

  • Developed SIMON (Simple Inference for Methylome based On NGS), a targeted BS method using NGS.
Keywords:
DNA methylationNGSbioinformaticssample size calculationtargeted BS sequencing

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  • Employed in silico size sieving of DNA fragments and primer matching for bioinformatics analysis.
  • Integrated PCR amplification with NGS for high specificity and throughput.

    • Main Results:

    • The SIMON method achieves precise and efficient measurement of DNA methylation patterns at single nucleotide resolution.
    • Demonstrated accurate quantification of small variations in DNA methylation levels.
    • Showcased the method's effectiveness for analyzing large numbers of samples and pre-identified loci.

    Conclusions:

    • SIMON offers a cost-effective solution for in-depth DNA methylation studies on targeted loci.
    • The method significantly improves workflow efficiency and the quality of DNA methylation data.
    • Enables precise determination of DNA methylation variations, even with extensive sample and locus numbers.