Background: Epigenetic modifications, including chromatin accessibility, nucleosome positioning, and DNA methylation (5mC), are pivotal in shaping genome function. However, current short read sequencing approaches present challenges in characterising epigenetic patterns along repetitive genomic regions.
Results: We developed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq), a robust method utilising bacterial adenine methyltransferases (m6A-MTases) to mark accessible regions in purified plant nuclei. Coupled with Oxford Nanopore Technology sequencing, SAM-seq enables high-resolution profiling of cytosine methylation and m6A-tagged chromatin accessibility along individual chromatin fibres in A. thaliana and maize. Importantly, using naked genomic DNA we uncovered significant sequence preferences of m6A-MTases, which we show must be taken into account in order to obtain reliable accessibility profiles, particularly for the analysis of highly repetitive sequences such as centromeric repeats. Using this method we found intriguing antagonism between accessibility and DNA methylation within single molecules, somatic epigenetic variation at bivalent chromatin domains, periodicity of nucleosomal strings over centromeric repeats, and high-resolution methylation profiles over nucleosomes.
Conclusions: Our study highlights the importance of considering intrinsic substrate preferences of DNA modifying enzymes for their use in chromatin profiling. Hence, SAM-seq is a robust and cross-species method to chart high-resolution accessibility and DNA methylation genome-wide. This method and findings will enable the investigation of chromatin-based regulation across plant species, with implications for the study of non-model plant species with limited genomic and epigenomic information.