SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer [RNA-Seq]
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ABSTRACT:
PROVIDER: PRJNA1269943 | ENA |
REPOSITORIES: ENA
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Project description:Histone ubiquitination is a crucial post-translational modification (PTM) regulating chromatin function, yet many histone ubiquitination sites and their regulatory enzymes remain poorly understood. Here, we identify SMARCA3, a SWI/SNF-related protein frequently downregulated in colorectal cancer (CRC), as an E3 ubiquitin ligase that targets histone H3 at lysine 23 (H3K23). We demonstrate that SMARCA3 histone ubiquitination activity is stimulated by the repressive H3K9me3 mark. Loss of SMARCA3 reduces both H3K23Ub and H3K9me3, increasing chromatin accessibility at promoters and enhancers enriched for pioneer transcription factor motifs. This chromatin ‘rewiring’ alters the transcriptional landscape, driving upregulation of cancer-promoting genes. We validate this mechanism in CRC cell lines and patient-derived organoids, where SMARCA3 loss reduces H3K23Ub and H3K9me3. In xenograft mouse models, overexpression of wild type SMARCA3, but not a RING domain mutant, suppresses tumor growth. Together, our findings define SMARCA3 as a key chromatin regulator contributing to CRC pathogenesis through epigenetic mechanisms.
2025-07-01 | GSE298560 | GEO
Project description:Histone ubiquitination is a crucial post-translational modification (PTM) regulating chromatin function, yet many histone ubiquitination sites and their regulatory enzymes remain poorly understood. Here, we identify SMARCA3, a SWI/SNF-related protein frequently downregulated in colorectal cancer (CRC), as an E3 ubiquitin ligase that targets histone H3 at lysine 23 (H3K23). We demonstrate that SMARCA3 histone ubiquitination activity is stimulated by the repressive H3K9me3 mark. Loss of SMARCA3 reduces both H3K23Ub and H3K9me3, increasing chromatin accessibility at promoters and enhancers enriched for pioneer transcription factor motifs. This chromatin ‘rewiring’ alters the transcriptional landscape, driving upregulation of cancer-promoting genes. We validate this mechanism in CRC cell lines and patient-derived organoids, where SMARCA3 loss reduces H3K23Ub and H3K9me3. In xenograft mouse models, overexpression of wild type SMARCA3, but not a RING domain mutant, suppresses tumor growth. Together, our findings define SMARCA3 as a key chromatin regulator contributing to CRC pathogenesis through epigenetic mechanisms.
2025-07-01 | GSE298559 | GEO
Project description:Histone ubiquitination is a crucial post-translational modification (PTM) regulating chromatin function, yet many histone ubiquitination sites and their regulatory enzymes remain poorly understood. Here, we identify SMARCA3, a SWI/SNF-related protein frequently downregulated in colorectal cancer (CRC), as an E3 ubiquitin ligase that targets histone H3 at lysine 23 (H3K23). We demonstrate that SMARCA3 histone ubiquitination activity is stimulated by the repressive H3K9me3 mark. Loss of SMARCA3 reduces both H3K23Ub and H3K9me3, increasing chromatin accessibility at promoters and enhancers enriched for pioneer transcription factor motifs. This chromatin ‘rewiring’ alters the transcriptional landscape, driving upregulation of cancer-promoting genes. We validate this mechanism in CRC cell lines and patient-derived organoids, where SMARCA3 loss reduces H3K23Ub and H3K9me3. In xenograft mouse models, overexpression of wild type SMARCA3, but not a RING domain mutant, suppresses tumor growth. Together, our findings define SMARCA3 as a key chromatin regulator contributing to CRC pathogenesis through epigenetic mechanisms.
2025-07-01 | GSE298558 | GEO
Project description:Histone ubiquitination is an important post-translational modification (PTM) that mediates diverse chromatin functions1-3. However, our understanding of the enzymes that regulate histone ubiquitination, along with their relationships to human disease, remains limited. Here, we identify the tumor suppressor SMARCA3 as a histone H3K23 E3 ubiquitin ligase that functions through a distinct mechanism from its characterized role in post-replication repair. We show that cellular depletion of SMARCA3 results in reduced H3K9me3 levels and altered genomic distribution, leading to cancer-associated rewiring of cellular transcriptional programs . Using both cell lines and patient-derived organoids, we demonstrate that colorectal cancer tumors driven by downregulation of SMARCA3 display similar decreases in H3K9me3, as well as alterations in the expression of cancer-promoting genes. Taken together, our data indicate critical roles for SMARCA3 in maintaining chromatin integrity, and provide a mechanism through which its normal tumor-suppression function may precipitate colorectal cancer when perturbed.
2023-06-05 | GSE151913 | GEO
Project description:SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in colorectal cancer
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