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Series GSE124016 Query DataSets for GSE124016
Status Public on Aug 02, 2019
Title Convergent evolution of a vertebrate-like methylome in a marine sponge
Organisms Mnemiopsis leidyi; Sycon ciliatum; Nematostella vectensis; Amphimedon queenslandica
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Vertebrates have highly methylated genomes at CpG positions while most invertebrates have sparsely methylated genomes. Therefore, hypermethylation is considered a major innovation that shaped the genome and the regulatory roles of DNA methylation in vertebrates. However, here we report that the marine sponge Amphimedon queenslandica, belonging to one of the earliest branching animal lineages, has evolved a hypermethylated genome with remarkable similarities to that of a vertebrate. Despite major differences in genome size and architecture, independent acquisition of hypermethylation reveal common distribution patterns and repercussions for genome regulation between both lineages. Genome wide depletion of CpGs is counterbalanced by CpG enrichment at unmethylated promoters, mirroring CpG islands. Furthermore, a subset of CpG-bearing transcription factor motifs are enriched at Amphimedon unmethylated promoters. We find that the animal-specific transcription factor NRF has conserved methyl-sensitivity over 700 million years, indicating an ancient cross-talk between transcription factors and DNA methylation. Finally, the sponge shows vertebrate-like levels of 5-hydroxymethylcytosine, the oxidative derivative of cytosine methylation involved in active demethylation. Hydroxymethylation is concentrated in regions that are enriched for transcription factor motifs and show developmentally dynamic demethylation. Together, these findings push back the links between DNA methylation and its regulatory roles to the early steps of animal evolution. Thus, the Amphimedon methylome challenges the prior hypotheses about the origins of vertebrate genome hypermethylation and its implications for regulatory complexity.
Overall design Profiling of cytosine methylation for Amphimedon queenslandica, Sycon ciliatum, Mnemiopsis leidyi and Nematostella vectensis. Profiling hydroxymethylation with TAB-seq for Amphimedon queenslandica and Nematostella vectensis. DAP-seq and ampDAP-seq for Amphimedon transcription factors on Amphimedon queenslandica genomic DNA.
Contributor(s) de Mendoza A, Lister R
Citation(s) 31558833
Submission date Dec 18, 2018
Last update date Nov 01, 2019
Contact name Alex de Mendoza
Organization name Queen Mary University of London
Department School of Biological and Behavioural Sciences
Lab de Mendoza Lab
Street address Mile End Road. Fogg Building 5.14
City London
ZIP/Postal code E1 4NS
Country United Kingdom
Platforms (5)
GPL22487 Illumina NextSeq 500 (Amphimedon queenslandica)
GPL25949 Illumina HiSeq 1500 (Amphimedon queenslandica)
GPL25950 Illumina HiSeq 1500 (Sycon ciliatum)
Samples (36)
GSM3518725 mC_Aqueenslandica_cleavage
GSM3518726 mC_Aqueenslandica_precompetent_larva
GSM3518727 mC_Aqueenslandica_competent_larva
BioProject PRJNA510589
SRA SRP173795

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE124016_RAW.tar 4.5 Gb (http)(custom) TAR (of CGMAP, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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