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| Status |
Public on Apr 01, 2018 |
| Title |
DNA 5-methylcytosine in Paramecium |
| Organism |
Paramecium tetraurelia |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
5-methyl-cytosine DNA methylation regulates gene expression and developmental programming in a broad range of eukaryotes. However, its presence and potential roles in ciliates, complex single-celled eukaryotes with germline-somatic genome specialization via nuclear dimorphism, are largely uncharted. While canonical cytosine methyltransferases have not been discovered in published ciliate genomes, recent studies performed in the stichotrichous ciliate Oxytricha trifallax suggest de novo cytosine methylation during macronuclear development. In this study, we applied bisfulfite genome sequencing, DNA mass spectrometry and antibody-based fluorescence detection to investigate the presence of DNA methylation in Paramecium tetraurelia. While the antibody-based methods suggest cytosine methylation, DNA mass spectrometry and bisulfite sequencing reveal that levels are actually below the limit of detection. Our results suggest that Paramecium does not utilize 5-methyl-cytosine DNA methylation as an integral part of its epigenetic arsenal.
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| Overall design |
We performed bisulfite conversion and Illumina DNA sequencing on 3 samples: one from vegetative cells, one from starved vegetative cells, and one from cells undergoing macronuclear development.
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| Contributor(s) |
Sigh A, Vancura A, Hogan DJ, Hendrick A, Woycicki R, Nowacki M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Mar 09, 2018 |
| Last update date |
Apr 02, 2018 |
| Contact name |
Daniel Hogan |
| Organization name |
none
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| Street address |
private address
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| City |
Foster City |
| State/province |
California |
| ZIP/Postal code |
94404 |
| Country |
USA |
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| Platforms (1) |
| GPL24715 |
Illumina HiSeq 2500 (Paramecium tetraurelia) |
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| Samples (3) |
| GSM3035201 |
Bisulfite conversion and whole genome sequencing_veg |
| GSM3035202 |
Bisulfite conversion and whole genome sequencing_starved |
| GSM3035203 |
Bisulfite conversion and whole genome sequencing_macdev |
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| Relations |
| BioProject |
PRJNA437583 |
| SRA |
SRP134240 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE111621_RAW.tar |
305.7 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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