|
| Status |
Public on Apr 21, 2011 |
| Title |
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
Other
|
| Summary |
5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution of 5hmC is limited. Here we describe two novel and specific approaches to profile the genomic localisation of 5hmC. The first approach, termed GLIB (GLucosylation, perIodate oxidation, Biotinylation) uses a combination of enzymatic and chemical steps to isolate DNA fragments containing as few as a single 5hmC. The second approach involves conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulphite, followed by immunoprecipitation of CMS-containing DNA with a specific antiserum to CMS. High-throughput sequencing of 5hmC-containing DNA from mouse embryonic stem (ES) cells showed strong enrichment within exons and near transcriptional start sites (TSS). 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Our results indicate that 5hmC has a likely role in transcriptional regulation, and suggest a model in which 5hmC contributes to the “poised” chromatin signature found at developmentally-regulated genes in ES cells.
|
| |
|
| Overall design |
Mapping of 5-hydroxymethylcytosine in ES cells by GLIB and anti-CMS methodologies
|
| |
|
| Contributor(s) |
Pastor WA, Pape UJ, Huang Y, Rao A |
| Citation(s) |
21552279 |
| Submission date |
Apr 18, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
William Abraham Pastor |
| E-mail(s) |
william.pastor@mcgill.ca
|
| Phone |
514-618-3348
|
| Organization name |
McGill University
|
| Department |
Biochemistry
|
| Lab |
Pastor
|
| Street address |
3655 Promenade Sir William Osler
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL14759 |
Helicos HeliScope (Mus musculus) |
|
| Samples (9)
|
|
| Relations |
| SRA |
SRP008984 |
| BioProject |
PRJNA138941 |
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