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| Status |
Public on Mar 09, 2021 |
| Title |
Chromatin states in glioblastoma stem cell [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
In human, the 39 coding HOX genes and 18 referenced non-coding antisense transcripts are arranged in four genomic clusters named HOXA, B, C, and D. This highly conserved family belongs to the homeobox class of genes that encode transcription factors required for normal development. Therefore, HOX gene deregulation might contribute to the development of many cancer types. Here, we study HOX gene deregulation in adult glioma, a common type of primary brain tumor. We performed extensive molecular analysis of tumor samples, classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found widespread expression of sense and antisense HOX transcripts only in aggressive (IDHwt) glioma samples, although the four HOX clusters displayed DNA hypermethylation. Integrative analysis of expression-, DNA methylation- and histone modification signatures along the clusters revealed that HOX gene upregulation relies on canonical and alternative bivalent CpG island promoters that escape hypermethylation. H3K27me3 loss at these promoters emerges as the main cause of widespread HOX gene upregulation in IDHwt glioma cell lines and tumors. Our study provides the first comprehensive description of the epigenetic changes at HOX clusters and their contribution to the transcriptional changes observed in adult glioma. It also identified putative "master" HOX proteins that might contribute to the tumorigenic potential of glioma stem cells.
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| Overall design |
ChIP-seq
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| Contributor(s) |
Court F, Le Boiteux E, Guichet PO, Arnaud P |
| Citation(s) |
33720519, 35563134 |
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| Submission date |
Nov 13, 2020 |
| Last update date |
May 25, 2022 |
| Contact name |
franck court |
| Organization name |
GReD CNRS
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| Street address |
28 Place Henri Dunant
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| City |
Clermont-Ferrand |
| ZIP/Postal code |
63000 |
| Country |
France |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE161440 |
Chromatin states and Transcriptome in in glioblastoma stem cells |
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| Relations |
| BioProject |
PRJNA678318 |
| SRA |
SRP292507 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE161436_RAW.tar |
945.8 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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