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Brigham and Women's Hospital</center_name><full_dataset_link>https://www.ebi.ac.uk/ena/browser/view/PRJNA947105</full_dataset_link><scientific_name>Homo sapiens</scientific_name><tag>xref:PubMed:37425921</tag><long_description>A growing number of studies describe multiple functions of lncRNAs in chromatin that support their active roles in normal and disease-specific gene expression. We identified a specific enhancer-associated LINC01116 (named HOXDeRNA), which targeted activation transformed human astrocytes into glioma-like cells. Using a combination of RNA-Seq, ChIRP-Seq, and ChIP-Seq, we defined the transcriptomic and epigenetic changes underlying the transformation. We demonstrate that HOXDeRNA binds in trans to the promoters of 44 glioma-specific transcription factors distributed throughout the genome and derepresses them by removing the Polycomb 2 complex. This process is mediated by the RNA G-quadruplex structure of HOXDeRNA. Moreover, HOXDeRNA-induced astrocyte transformation is accompanied by the activation of glioma-specific super-enhancers enriched for binding sites of glioma master transcription factors SOX2 and OLIG2, and multiple oncogenes such as EGFR, PDGFR, BRAF, and miR-21. Our results help reconstruct the sequence of events underlying the process of astrocyte transformation and suggest a driving role of HOXDeRNA eRNA in gliomagenesis. Overall design: mRNA-Seq was performed on fetal human astrocytes, Immortalized dCas9 expressing astrocytes (NHA) transduced with sgRNA non-targeting control and custom-made Edit-R CRISPRa human HOXDeRNA lentiviral sgRNAs</long_description><repository>ENA</repository></additional><is_claimable>false</is_claimable><name>Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA [RNA-seq]</name><description>Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA [RNA-seq]</description><dates><last_updated>2025-09-24</last_updated><first_public>2023-04-05</first_public></dates><accession>PRJNA947105</accession><cross_references><GEO>GSE227802</GEO><taxon>9606</taxon><PubMed>37425921</PubMed></cross_references></HashMap>