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| Status |
Public on Dec 08, 2016 |
| Title |
Establishment of monkey imprinted differentially methylated regions map by comparative analysis of parthenogenetic haploid embryonic stem cells and sperms |
| Organism |
Macaca mulatta |
| Experiment type |
Methylation profiling by high throughput sequencing
Other
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| Summary |
Genomic imprinting is a important biological process, which leads to parental specific gene expressions. Improper gene imprinting results in several developmental abnormalities, cancer and other diseases. Studies in mice indicated genomic imprinting establishment relied on parental allele-specific DNA methylation during gametogenesis. Despite the fact that genomic imprinting is highly conserved in mammalian, the species specific pattern exists. Until now, except that of in mouse, informations about imprinting patterns is little, especially in primates. Through generation genome-wide 5mC and 5hmC profiles for two types of haploid genomes from rhesus monkeys, including parthenogenetic haploid ESCs ( PG ha ESCs) (derived from rhesus monkey parthenogenetic embryos) and sperms. We clearly characterized and distinguished methylome (5mC) from hydroxymethylome (5hmC)(which can not discriminate from methylome in traditional bisulfite (BS) sequencing) in haploid genomes. Based on these information, we determined distribution patterns of 5mC and 5hmC in ha ESCs and sperms. Interestingly, both 5hmC levels and distribution patterns were similar in ha ESCs and sperms, and 5hmC which is enriched in the regions with low 5mC frequency. Meanwhile through comparing DNA methylation and hydroxymethylation status between sperms and ha ESCs, we first provided a fundamental information of monkey imprinted differentially methylated regions (DMRs) distribution in monkey chromosomes. Second, we observed that DMRs did not overlap with hydroxymethylated regions (DMR or DhMR), suggesting that establishment of imprinted regions was not interfered by 5hmC. Our results demonstrate DNA methylation profiling of PG ha ESCs and sperms can be uesed as a powerful and effective method to map and characterize imprinted regions in non-human primates genome.
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| Overall design |
DNA methylation sequencing of monkey ha ESCs and sperms
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| Contributor(s) |
Xia Y, Gao F, Tan T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Dec 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Tan |
| E-mail(s) |
tant@lpbr.cn
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| Organization name |
Primate Translational Medicine Research Center, Kunming University of Science and Technology
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| Street address |
No. 1 Boda Road, Yuhua Area, Chenggong District, Kunming, Yunnan,
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| City |
Kunming |
| ZIP/Postal code |
650500 |
| Country |
China |
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| Platforms (1) |
| GPL14954 |
Illumina HiSeq 2000 (Macaca mulatta) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA305424 |
| SRA |
SRP067147 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE75817_Sperm.modified.sites.txt.gz |
73.1 Mb |
(ftp)(http) |
TXT |
| GSE75817_haESC.modified.sites.txt.gz |
77.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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