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Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis.

ABSTRACT: Cytosine methylome data is commonly generated through next-generation sequencing, with analyses averaging methylation states of individual reads. We propose an alternative method of analysing single-read methylome data. Using this method, we identify patterns relating to the mechanism of two plant non-CG-methylating enzymes, CMT2 and DRM2. CMT2-methylated regions show higher stochasticity, while DRM2-methylated regions have higher variation among cells. Based on these patterns, we develop a classifier that predicts enzyme activity in different species and tissues. To facilitate further single-read analyses, we develop a genome browser, SRBrowse, optimised for visualising and analysing sequencing data at single-read resolution.

SUBMITTER: Harris KD

PROVIDER: S-EPMC7412668 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis.

Harris Keith D KD Zemach Assaf A

Genome biology 20200806 1

Cytosine methylome data is commonly generated through next-generation sequencing, with analyses averaging methylation states of individual reads. We propose an alternative method of analysing single-read methylome data. Using this method, we identify patterns relating to the mechanism of two plant non-CG-methylating enzymes, CMT2 and DRM2. CMT2-methylated regions show higher stochasticity, while DRM2-methylated regions have higher variation among cells. Based on these patterns, we develop a clas ...[more]

PMID: 32762764

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