|
| Status |
Public on Aug 22, 2024 |
| Title |
PML is a novel constitutive component of chromatin domains of enriched repetitive elements and duplicated gene clusters in cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Heterochromatin is a pivotal element in the functional organization of genomes. In our study, we delve into
the heterochromatin pattern of association by the PML (promyelocytic leukemia) protein. By using PML
chromatin immunoprecipitation and sequencing data and comparing computational methodologies to depict
PML chromatin association, we describe PML-associated domains or PADs as large heterochromatic
regions that exhibit similar genomic features across cancer cell lines. We show that PADs are specifically
enriched in non-coding genes, duplicated gene clusters, and repetitive DNA elements. Moreover, we find
enriched binding motifs of KZFPs, which are involved in orchestrating epigenetic repression at repetitive
DNA elements. Hence, our findings suggest that PML conservatively associates to heterochromatic
domains enriched in repetitive DNA elements and duplicated gene clusters in cancer. These findings
contribute to a broader understanding of the complex regulatory framework of genome organization by
heterochromatin in cancer.
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| |
|
| Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PML in RCC4 cells.
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| |
|
| Contributor(s) |
Cristina F, Matilde S, Morelli MJ, Rosa B, Uggè M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Mar 19, 2024 |
| Last update date |
Aug 22, 2024 |
| Contact name |
Rosa Bernardi |
| E-mail(s) |
bernardi.rosa@hsr.it
|
| Organization name |
San Raffaele Scientific Institute
|
| Street address |
via Olgettina 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (2) |
|
| Relations |
| BioProject |
PRJNA1089597 |
