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| Status |
Public on Mar 24, 2017 |
| Title |
The methylome of a cartilaginous fish, Callorhinchus milii, reveals conservation of epigenetic regulation across jawed vertebrates |
| Organism |
Callorhinchus milii |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Background
Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates.
Methods
We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data.
Results
Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates.
Conclusions
Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.
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| Overall design |
Whole-genome bisulfite sequencing was used to generate genome-wide methylation profiles from one male and one female liver sample. Low-coverage sequencing was also performed on additional liver, spleen and pancreas samples.
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| Contributor(s) |
Peat JR, Ortega-Recalde O, Kardailsky O, Hore TA |
| Citation(s) |
28580133 |
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| Submission date |
Mar 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim Hore |
| Organization name |
University of Otago
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| Department |
Department of Anatomy
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| Street address |
270 Great King Street
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| City |
Dunedin |
| ZIP/Postal code |
9016 |
| Country |
New Zealand |
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| Platforms (2) |
| GPL23184 |
Illumina HiSeq 2000 (Callorhinchus milii) |
| GPL23272 |
Illumina MiSeq (Callorhinchus milii) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA379367 |
| SRA |
SRP101988 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE96683_RAW.tar |
593.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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