Similar Datasets
Project description:Aire-sensitive genes escape the inclusion of alternative splicing events that Raver2 and Setd2 promote in mTECs
2022-01-07 | GSE177063 | GEO
Project description:To evaluate the effect of SETD2 and METTL14 on mRNA stability, we conducted RNA-seq in SETD2 or METTL14 knockdown HepG2 cells as well as control cells with or without actinomycin D treatment. Our RNA stability profiling revealed that depletion of SETD2 and METTL14 resulted in global reduction of RNA stability, and the changes were correlated between SETD2 and METTL14 knockdown cells.
2019-02-21 | GSE121949 | GEO
Project description:SETD2 is the specific methyltransferase of H3K36me3, while METTL14 is a critical subunit of the m6A methyltransferase complex. To evaluate the effect of SETD2 and METTL14 on translation, we conducted robosome profiling in SETD2 and METTL14 knockdown and control HepG2 cells. Our RNA ribosome profiling revealed that depletion of SETD2 and METTL14 resulted in a global reduction in RNA translation and the changes of translation efficiency were correlated between SETD2 and METTL14 knockdown cells.
2019-02-21 | GSE121952 | GEO
Project description:Histone-Lysine N-methyltransferase SETD2 is an evolutionarily conserved histone methyltransferase that associates with RNA Polymerase II (RNAPII) and catalyzes trimethylation of histone H3 lysine 36 (H3K36me3) in transcribed regions. Interestingly, SETD2 is frequently mutated in cancers. Clear cell renal cell carcinomas (ccRCCs) have extensive mutation of SETD2, implicating SETD2 as a tumor suppressor. ccRCCs are known for early driving events where the 3p chromosomal arm is lost, deleting one copy of SETD2, resulting in haploinsufficiency. While the role of SETD2 mediated H3K36me3 and interaction of RNAPII has been the focus of many studies, haploinsufficient SETD2 tumors retain H3K36me3, yet have drastic genome stability defects. The C-terminus of SETD2 is required for H3K36me3 while the N-terminus of SETD2 remains poorly characterized compared to the C-terminus. The N-terminus is highly disordered and has recently been shown to contribute to SETD2 stability, implicating regulatory functions. To better understand how SETD2 contributes to chromatin biology, we first sought to identify SETD2 protein interactors. A stable, immortalized normal human kidney epithelial cell (HKC) line with a dox inducible SETD2-APEX2 construct was used for a proximity-based biotinylation assay. Initial analysis yielded 2083 biotinylated proteins with significant enrichment (log2 fold change > 2 p-value < 0.05) in SETD2-APEX2 compared to control. Gene Ontology analysis of these interactors revealed enrichment of proteins involved in nuclear envelope functions, including lamin A/C, lamin B1, lamin B2 and emerin. These interactions were confirmed via western and reciprocal immunoprecipitation (IP). To determine effect of SETD2 depletion on lamin A/C and lamin B1 phosphorylation, we performed lamin A/C or lamin B1 IP from control or SETD2-knockdown (KD) cells and interrogated via LC-MS/MS. Mass spectrometry analysis revealed a significant decrease in lamin A/C S22 phosphorylation, and modest decrease in S390 phosphorylation, in SETD2 depleted cells compared to controls. While lamin B1 S23 phosphorylation was detected in control cells, we did not detect it in SETD2-KD cells, indicating a significant reduction in S23 phosphorylation upon SETD2 depletion. Next, we sought to identify the effect of SETD2 N-terminal deletion on the SETD2 protein interactome. We compared the protein interactors of dox inducible WT-SETD2 APEX2 fusion to an N-terminal deletion mutant of SETD2 (tSETD2-APEX2). Deletion of the N-terminus resulted in loss of lamin B1 and emerin interaction. Intriguingly, tSETD2 selectively associated with lamin C, whereas WT SETD2 interacted with both lamin A and C. These data together reveal an interaction with SETD2 and nuclear lamins. Further experiments revealed a role for the SETD2 N-terminus in facilitating the association of lamins with CDK1, thereby promoting lamin phosphorylation and depolymerization required for nuclear envelope disassembly during mitosis. Together, the data reveal a non-catalytic role of SETD2 during mitosis.
2025-06-04 | PXD040771 | Pride
Project description:Setd2 is the only enzyme that catalyzes histone H3 lysine 36 trimethylation (H3K36me3) on virtually all actively transcribed protein-coding genes, and this mechanism is evolutionarily conserved from yeast to human. Setd2 and H3K36me3 have been revealed to be involved in many important biochemical mechanisms, including DNA repair, alternative mRNA splicing and transcription elongation. However, physiological function of Setd2 in the context of zebrafish development remains elusive. Here we generated zebrafish setd2 mutant lines through disrupting the majority of the protein. And mRNA profiles of wild-type (WT), Setd2(+/-) and Setd2(-/-) zebrafish embryos at 36hpf were generated by deep sequencing, providing an opportunity to uncover molecular programs and functions of Setd2.
2020-05-27 | GSE151238 | GEO
Project description:SETD2 is the specific methyltransferase of H3K36me3, while METTL3, METTL14 and WTAP are the components of m6A methyltransferase complex. To understand the global effect of H3K36me3 on m6A modification, we compared the m6A profiling in SETD2 and METTL3, METTL14 or WTAP knockdown HepG2 cells, and found depletion of H3K36me3 by SETD2 silencing globally reduced m6A in human transcriptome. What’s more, most of the SETD2-dependent hypomethylation sites also responded to knockdown of METTL3, METTL14, or WTAP.
2019-02-21 | GSE110320 | GEO
Project description:Setd2 is the specific methyltransferase of H3K36me3. To understand the global effect of H3K36me3 on m6A modification, we used mouse embryonic stem cells (mESCs) model with doxycycline (Dox)-induced Setd2 knockdown, and performed m6A-IP followed by sequencing in mESCs with or without Dox treatment. We found that depletion of H3K36me3 by Setd2 silencing globally reduced m6A in mouse transcriptome.
2019-02-21 | GSE110322 | GEO
Project description:To understand the global effect of H3K36me3 on m6A modification, we compared the m6A profiling in SETD2 knockdown and control HepG2 cells by miCLIP-seq, and found the depletion of H3K36me3 by SETD2 silencing globally reduced m6A in the human transcriptome.
2019-02-21 | GSE121942 | GEO
Project description:SETD2 is a key histone methyltransferase responsible for depositing histone H3 lysine 36 trimethylation (H3K36me3). Loss of its enzymatic activity has been implicated in various cancers, including renal cell carcinoma (RCC). In RCC, SETD2 mutations have been linked to defects in transcription termination, though the underlying mechanism remains unclear. Here, using nascent transcriptomics in SETD2 knockouts and RCC patient-derived cells, we show that SETD2 loss leads to delayed transcription termination, but only in a subset of genes. POINT-seq analysis reveals widespread transcriptional readthrough beyond canonical termination sites upon SETD2 loss/mutation, affecting 15–24% of genes. We demonstrate that defective termination following SETD2 loss/mutation is driven by a combination of increased cryptic transcription initiation and impaired 3′ pre-mRNA cleavage. In contrast, genes that maintain proper termination show significant downregulation. Additionally, we find that SETD2 ensures proper termination independently of alternative polyadenylation, underscoring the distinction between transcription termination and 3′ end processing. Our findings highlight that methyltransferase activity of SETD2 is a crucial regulator of transcriptional integrity, preventing cryptic initiation and promoting efficient 3′ end processing
2026-02-09 | GSE301035 | GEO