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| Status |
Public on Jan 23, 2019 |
| Title |
Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.
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| |
|
| Overall design |
ChIP-seq was conducted in 2 human prostate cell lines: normal prostate epithelial cells (PrEC) and prostate cancer cells (LNCaP)
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| |
|
| Contributor(s) |
Du Q, Clark SJ |
| Citation(s) |
30679435 |
| Submission date |
May 09, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Qian Du |
| E-mail(s) |
q.du@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE98732 |
Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer |
|
| Relations |
| Reanalysis of |
GSM947525 |
| Reanalysis of |
GSM947526 |
| BioProject |
PRJNA386038 |
| SRA |
SRP106747 |
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