Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs

in Arabidopsis

Weipeng Mo, Yi Shu, Bo Liu, Yanping Long, Tong Li, Xiaofeng Cao, Xian Deng & Jixian Zhai

Nature Plants (2023)Cite this article

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Abstract

The short read-length of next-generation sequencing makes it challenging to characterize highly

repetitive regions (HRRs) such as centromeres, telomeres and ribosomal DNAs. Based on recent
strategies that combined long-read sequencing and exogenous enzymatic labelling of open chromatin,
we developed single-molecule targeted accessibility and methylation sequencing (STAM-seq) in plants by
further integrating nanopore adaptive sampling to investigate the HRRs in wild-type Arabidopsis and
DNA methylation mutants that are defective in CG- or non-CG methylation. We found that CEN180
repeats show higher chromatin accessibility and lower DNA methylation on their forward strand,
individual rDNA units show a negative correlation between their DNA methylation and accessibility, and
both accessibility and CHH methylation levels are lower at telomere compared to adjacent subtelomeric
region. Moreover, DNA methylation-deficient mutants showed increased chromatin accessibility at HRRs,
consistent with the role of DNA methylation in maintaining heterochromatic status in plants. STAM-seq
can be applied to study accessibility and methylation of repetitive sequences across diverse plant
species.

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