|
| Status |
Public on Jun 21, 2016 |
| Title |
Genome-wide map of DNA 5-Hydroxymethylcytosine in cardiomyocytes isolated from E14.5, Neonatal, Adult, pressure-overload (TAC), sh-control and sh-TET2 isolated cardiomyocytes |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Methylation at 5-cytosine (5-mC) is a fundamental epigenetic DNA modification associated recently with cardiac disease. In contrast, the role of 5-hydroxymethylcytosine (5-hmC) – 5-mC’s oxidation product – is unknown in the context of the heart. Here, we assess the hydroxymethylome in embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes, showing that dynamic modulation of hydroxymethylated DNA is associated with specific transcriptional networks during heart development and failure. DNA hydroxymethylation marks gene bodies of highly expressed genes and distal regulatory regions with enhanced activity. Pathological hypertrophy is characterized by a partial shift towards a fetal-like distribution pattern.
We further demonstrate a regulatory function of TET2 and provide evidence that the expression of key cardiac genes, such as Myh7 is modulated by TET2-mediated 5-hmC deposition on the gene body and at enhancers in cardiac cells.
We thus provide the first genome-wide analysis of 5-hmC in the cardiomyocyte, and establish the role of this epigenetic modification in heart development and disease
|
| |
|
| Overall design |
Profiling of 5hmC in E14.5, Neonatal, Adult, pressure-overload (TAC), sh-control and sh-TET2 isolated cardiomyocytes
|
| |
|
| Contributor(s) |
Kunderfranco P, Greco CM, Condorelli G |
| Citation(s) |
27489048 |
| |
| Submission date |
Apr 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Paolo Kunderfranco |
| E-mail(s) |
Paolo.Kunderfranco@humanitasresearch.it
|
| Organization name |
Humanitas Research Hospital
|
| Department |
Research
|
| Lab |
Bioinformatic Unit
|
| Street address |
Via Rita Levi Montalcini 4
|
| City |
Pieve Emanuele |
| State/province |
Milano |
| ZIP/Postal code |
20090 |
| Country |
Italy |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (22)
|
|
| This SubSeries is part of SuperSeries: |
| GSE66847 |
Dynamics of 5-hmC in cardiac maturation and hypertrophy |
|
| Relations |
| BioProject |
PRJNA317319 |
| SRA |
SRP072831 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE79882_5hmC_Adult.bigWig |
39.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_5hmC_E14.5.bigWig |
37.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_5hmC_Neonatal.bigWig |
40.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_5hmC_TAC.bigWig |
41.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_5hmC_sh-TET2.bigWig |
37.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_5hmC_sh-control.bigWig |
37.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_Differential_Analysis-1.xlsx |
2.4 Mb |
(ftp)(http) |
XLSX |
| GSE79882_Differential_Analysis-2.xlsx |
11.3 Mb |
(ftp)(http) |
XLSX |
| GSE79882_INPUT_DNA_Adult.bigWig |
37.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_INPUT_DNA_E14.5.bigWig |
37.1 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_INPUT_DNA_Neonatal.bigWig |
37.1 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_INPUT_DNA_TAC.bigWig |
36.7 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_INPUT_DNA_sh-TET2.bigWig |
31.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_INPUT_DNA_sh-control.bigWig |
32.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE79882_RAW.tar |
12.3 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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