title: DNA Methylation in Basal Metazoans: Insights from Ctenophores.
abstract: Epigenetic modifications control gene expression without altering the primary DNA sequence. However, little is known about DNA methylation in invertebrates and its evolution. Here, we characterize two types of genomic DNA methylation in ctenophores, 5-methyl cytosine (5-mC) and the unconventional form of methylation 6-methyl adenine (6-mA). Using both bisulfite sequencing and an ELISA-based colorimetric assay, we experimentally confirmed the presence of 5-mC DNA methylation in ctenophores. In contrast to other invertebrates studied, Mnemiopsis leidyi has lower levels of genome-wide 5-mC methylation, but higher levels of 5-mC methylation in promoters when compared with gene bodies. Phylogenetic analysis showed that ctenophores have distinct forms of DNA methyltransferase 1 (DNMT1); the zf-CXXC domain type, which localized DNMT1 to CpG sites, and is a metazoan specific innovation. We also show that ctenophores encode the full repertoire of putative enzymes for 6-mA DNA methylation, and these genes are expressed in the aboral organ of Mnemiopsis. Using an ELISA-based colorimetric assay, we experimentally confirmed the presence of 6-mA methylation in the genomes of three different species of ctenophores, M. leidyi, Beroe abyssicola, and Pleurobrachia bachei. The functional role of this novel epigenomic mark is currently unknown. In summary, despite their compact genomes, there is a wide variety of epigenomic mechanisms employed by basal metazoans that provide novel insights into the evolutionary origins of biological novelties.
authors.affiliation: *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Emily C
authors.initials: EC
authors.lastname: Dabe
authors.affiliation: *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Rachel S
authors.initials: RS
authors.lastname: Sanford
authors.affiliation: *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA;
authors.forename: Andrea B
authors.initials: AB
authors.lastname: Kohn
authors.affiliation: *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA;
authors.forename: Yelena
authors.initials: Y
authors.lastname: Bobkova
authors.affiliation: *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA moroz@whitney.ufl.edu.
authors.forename: Leonid L
authors.initials: LL
authors.lastname: Moroz
mesh_terms: D000818:Animals; D005075:Biological Evolution; D037302:Ctenophora / Q000378:metabolism*; D019175:DNA Methylation / Q000502:physiology*; D044127:Epigenesis, Genetic; D057890:Epigenomics