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| 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
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| 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.
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| 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.
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| 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 |
| E-mail(s) |
alexmendozasoler@gmail.com
|
| 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 |
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| Platforms (5)
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| GPL22487 |
Illumina NextSeq 500 (Amphimedon queenslandica) |
| GPL25949 |
Illumina HiSeq 1500 (Amphimedon queenslandica) |
| GPL25950 |
Illumina HiSeq 1500 (Sycon ciliatum) |
| GPL25951 |
Illumina HiSeq 1500 (Mnemiopsis leidyi) |
| GPL25952 |
Illumina HiSeq 1500 (Nematostella vectensis) |
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| Samples (36)
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| Relations |
| BioProject |
PRJNA510589 |
| SRA |
SRP173795 |
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