Biology subjects

Kebede, A. F.

Publications and source records attributed to Kebede, A. F..

3 recordsLinked to original sources

bioRxiv2026

Elongin B orchestrates chromatin and transcriptional programs in H3K27M-mutant diffuse midline glioma

Recurrent driver mutations in genes encoding histone H3 (H3.3K27M and H3.1K27M) are observed in [~]80% of diffuse midline gliomas (DMG), which lead to aberrant gene regulation, yet the specific RNA polymerase II (Pol2) regulators that induce transcriptional dysregulation in DMG are not fully defined. We identified multiple regulators of Pol2 elongation as DMG genetic dependencies in a chromatin-focused CRISPR screen. Additional studies confirm that knockout (KO) of the Pol2 SIII complex gene elongin B (ELOB) inhibits DMG cell proliferation in tissue culture and tumor growth in xenograft models. Further genomic analyses reveal that ELOB binding sites are enriched in H3K27M oncohistones and that ELOB KO alters H3K27me3 and H3K27M incorporation at thousands of genomic regions, implicating ELOB in the maintenance of dysfunctional chromatin states in DMG. Correspondingly, PRO-seq and RNA-seq profiling reveal that ELOB loss disrupts Pol2 transcriptional activity and alters the expression of transcripts involved in metabolism, proliferation, and brain development. These findings suggest that Pol2 elongation factors like ELOB cooperate with H3K27M oncohistones to maintain the epigenetic and transcriptional landscape driving DMG malignancy.

cancer biology↗

bioRxiv2026

SAGA/ATAC complexes sustain aberrant chromatin regulation and promote tumorigenesis in diffuse midline glioma

Diffuse midline gliomas (DMG) are aggressive pediatric brain tumors characterized by chromatin and transcriptional dysregulation induced by H3K27M mutations, with a median survival of 11-15 months. We identified multiple components of the SAGA and ATAC chromatin regulatory complexes as DMG genetic dependencies and found that genetic or pharmacological inhibition of the SAGA/ATAC-associated chromatin reader SGF29 reduces DMG proliferation in vitro and prolongs survival in xenograft models. Small molecule inhibitors targeting SAGA/ATAC-associated histone acetylation, ubiquitination, and methylation similarly suppress DMG growth. Integrative chromatin and transcriptomic profiling reveals that disruption of SAGA/ATAC through SGF29 knockout remodels the DMG chromatin landscape, producing distinct alterations at metabolic genes (loss of H3K9ac) and at embryonic/neurodevelopmental genes (redistribution of H3K4me3 and H3K27me3) and accompanying transcriptional changes. We further show that inhibition of the SAGA/ATAC-associated KAT2A/2B histone acetyltransferases represses cholesterol metabolism gene expression and that combined KAT2A/2B and cholesterol synthesis inhibition synergistically suppresses DMG growth in vitro and in a xenograft model. Together, these findings establish a mechanistic link between SAGA/ATAC-dependent chromatin regulation and the transcriptional and metabolic dysregulation underlying DMG malignancy. SignificanceWe demonstrate that SAGA/ATAC-dependent chromatin regulation sustains malignant transcription controlling cholesterol metabolism, proliferation, and cell fate in DMG, suggesting that a SAGA/ATAC-regulated epigenome-metabolome axis may be targeted to treat DMG.

cancer biology↗

bioRxiv2025

N-terminal modification of Histone H3 inhibits H3K27M-mediated loss of H3K27 trimethylation

The use of short epitope tags is widespread in the study of histone H3 biology as they allow for the antibody-mediated detection and pulldown of particular histone post-translational modifications (PTM) or exogenous histone transgenes. However, H3 is particularly sensitive to sequence modification and the addition of epitope tags may interfere with the native function of H3. Here, we use the known relationship between lysine-to-methionine K27M mutations and the loss of trimethylation at the H3 K27 residue to test whether the addition of epitope tags to the N or C terminus of H3 affects the levels of histone H3 PTMs. We find that all tested N-terminal tags abrogate the H3K27M-mediated loss of H3K27 trimethylation. These results suggest that the addition of epitope tags to the N-terminus of H3 should be performed with caution, and these findings may be of particular interest for the study of H3-driven cancers, like diffuse midline gliomas.

cell biology↗