Biology
Document Type
Article
Abstract
DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303-3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing. © 2023 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
Publication Title
NAR Genomics and BioInformatics
Publication Date
6-1-2023
Volume
5
Issue
2
ISSN
2631-9268
DOI
10.1093/nargab/lqad035
Keywords
DNA methylation, Dictyostelium, Dictyostelium discoideum, genomes, bisulfite sequencing
Repository Citation
Drewell, Robert; Cormier, Tayla C.; Steenwyk, Jacob L.; Denis, James St; Tabima, Javier F.; Dresch, Jacqueline; and Larochelle, Denis A., "The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing" (2023). Biology. 7.
https://commons.clarku.edu/faculty_biology/7
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright
Published source must be acknowledged with citation: Drewell, Robert A., et al. "The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing." NAR Genomics and Bioinformatics 5.2 (2023): lqad035.