|
| Status |
Public on Oct 05, 2010 |
| Title |
Comprehensive analysis of orphan CpG islands identifes novel promoters with conserved DNA methylation dynamics |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
We report the application of single molecule-based sequencing technology in combination with CXXC affinity purifcation (CAP-seq), MBD affinity purification (MAP-seq) and chromatin immunoprecipitation (ChIP-seq) to generate reciprocal methylation and chromatin modifcation maps in human and mouse. We find that contrary to sequence based prediction methods that humans and mice possess highly equivalent compliments of CpG islands (CGIs). The majority of these CGIs are positive for the active histone modification; H3K4me3 in embryonic stem cells (ES cells) the magnitude of which is correlated with the local density of non-methylated CpG. Approximately half of the human and mouse CGIs are distal to annotated gene promoters, yet more than 40% identify unanticipated transcription start sites as defined by RNA polymerase occupancy and published RNA mapping data. These orphans CGIs preferentially acquire DNA methylation in somatic cells, and this corresponds with a loss of H3K4me3 and RNA polymerase II at these sites. Conversely abnormal CGI methylation found in colorectal tumours showed a distinct distribution relative to that found in normal somatic tissues displaying preferential association with loci marked by H3K27me3 in human ES cells. This study provides a comprehensive functional assessment of CGIs in normal and diseased tissues.
|
| |
|
| Overall design |
Examination of CGI methylation status in human and mouse primary tissues.
|
| |
|
| Contributor(s) |
Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr A, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP |
| Citation(s) |
20885785 |
| Submission date |
Apr 21, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Adrian P Bird |
| E-mail(s) |
A.Bird@ed.ac.uk
|
| Phone |
0131 6508695
|
| Fax |
0131 6505379
|
| Organization name |
The University of Edinburgh
|
| Department |
WTCCB
|
| Lab |
Bird Lab
|
| Street address |
Mayfield Road
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platforms (2) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
|
| Samples (32)
|
|
| Relations |
| SRA |
SRP002374 |
| BioProject |
PRJNA126345 |
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