Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: KAP1-Mediated Epigenetic Suppression in Anti-RNA Viral Responses by Direct Targeting RIG-I and MDA5.

doi: 10.4049/jimmunol.2100342

Figure Lengend Snippet: FIGURE 2. KAP1 inhibits RNA viralinduced IFN-b activation. (A) Luciferase analysis of IFN-b reporter activation in HEK293T cells trans- fected with IFN-b reporter plasmid with empty control, TRIM28 (KAP1), TRIM24, TRIM33, or TRIM66 expression plasmid and then infected with SeV for 12 h. (B) Luciferase analysis of IFN-b reporter activation in HEK293T cells transfected with IFN-b reporter plasmid, together with empty control plasmid or KAP1 expression plasmids, and then infected with VSV for 12 h. (C) Western blot analysis of KAP1 expression in mouse PMs from WT or CKO mice. Data shown are means ± SD [n 5 6 in (A), and n 5 5 in (B)]. All experiments were repeated three times. **p < 0.01, ***p < 0.001, by Student t test.

Article Snippet: TRIM33 plasmid (65398) and TRIM66 plasmid (65400) were purchased from Addgene and subcloned into the V5 tag to generate V5-TRIM33 and V5-TRIM66.

Techniques: Activation Assay, Luciferase, Plasmid Preparation, Control, Expressing, Infection, Transfection, Western Blot

Journal: bioRxiv

Article Title: TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination

doi: 10.1101/2025.02.14.638236

Figure Lengend Snippet: A PCA of AR and IgG RIME data in AR positive cell lines. B Barplot representing the enriched nuclear proteins (LFQ difference > 1 & p-value < 0.05) per cell line assigned to the displayed subsets. Shared = found in all AR positive cell lines and not in PC3. Sig in all = found across all cell lines. Sig in PC3 = proteins significant in PC3 and another cell line. AR dep unique = Shared between LNCaP, LAPC4 and no other. AR indep unique = shared between CWR-R1, 22Rv1, LNCaP-abl and 42D and no other. AR-V7 unique = proteins shared in cell lines that express the alternative AR splive variant AR-V7 (CWR-R1, 22Rv1, Supplementary Figure 3A ) C Over representation analysis of the AR core proteins against the CORUM protein complex database D Volcano plot displaying the TRIM33 RIME data with the AR core proteins highlighted in orange. Triangles depict proteins enriched in IgG with fold changes out of the axis limits. E Euler Diagram of the AR core, LNCaP AR and TRIM33 RIME nuclear enriched proteins.

Article Snippet: Guides targeting TRIM33 (T33-3: 5’-ACAGAGTCTGTTGGAGCATC-3, T33-4: 5’-ACTATGGCAAATGCAAACCG-3, T33-5: 5’-CTCCTCCTCCACCAGCACCG-3) or non-targeting control (NT: 5’-AACTACAAGTAAAAGTATCG-3) were cloned into lentiCRISPRv2 plasmids ( Addgene: #52961).

Techniques: Variant Assay

Journal: bioRxiv

Article Title: TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination

doi: 10.1101/2025.02.14.638236

Figure Lengend Snippet: A Feature distribution of peaks identified in the given ChIP-seq experiment. For AR, ChIP-seq data from GSE94682 was used B Over representation analysis of peak associated genes. Shown are only genesets that have a p.adjust < 0.05. C Tornado plot for the TRIM33 and AR shared and unique peaks at 4h stimulation. Data represents the average of QC passing replicates. D Tornado plot for the TRIM33 sites with dynamic behavior. Data represents the average of QC passing replicates. E Average signal intensity plots for the regions shown in D. Lighter colors represent the DMSO control whereas darker colors represent stimulated conditions with R1881. F GIGGLE results for the TRIM33 sites gained after 4h of R1881 treatment

Article Snippet: Guides targeting TRIM33 (T33-3: 5’-ACAGAGTCTGTTGGAGCATC-3, T33-4: 5’-ACTATGGCAAATGCAAACCG-3, T33-5: 5’-CTCCTCCTCCACCAGCACCG-3) or non-targeting control (NT: 5’-AACTACAAGTAAAAGTATCG-3) were cloned into lentiCRISPRv2 plasmids ( Addgene: #52961).

Techniques: ChIP-sequencing, Control

Journal: bioRxiv

Article Title: TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination

doi: 10.1101/2025.02.14.638236

Figure Lengend Snippet: A Western blot for TRIM33 across the generated monoclonal knockout cell lines of the TRIM33-5 guide. B Incucyte growth curves of monoclonal TRIM33 knockout cell lines in FBS. As an error SEM is shown. C Euler diagram for all DEGs in the represented cell lines between DMSO and 6h R1881 stimulation. D Heatmap for DEGs in the non-targeting control across all sequenced LNCaP cell lines. PC represents the TRIM33 polyclonal knockout parental cell line. E Volcano plot of gene expression levels between TRIM33 monoclonal knockout C2 and the non-targeting control at 6h stimulation with R1881. Genes in green are higher expressed in non-targeting cells than knockout cells. F GSEA of the data in E. Shown are only genesets that have a p.adjust < 0.05. G Scatterplot of the Cistrome-Go analysis. Used are the TRIM33 peaks at 4h stimulation and the RNA foldchange showed in E. Triangles depict AR response genes as defined by differential expression status in non-targeting control with and without AR stimulation. Cut-off for regulatory potential was set to 0.3. H Scatterplot comparing TRIM33 knockout (C2) to non-targeting foldchanges on RNA (x-axis) and protein (y-axis) levels. Genes or proteins just found in one dataset were set to 0 in the other. The dashed line represents the diagonal with a slope of 1. Cut-offs for classification were a foldchange > 1 for RNA and > 0.5 for proteomic data. I GSEA of proteomic data of all tested TRIM33 knockouts in R1881 treated conditions compared to the non-targeting. NTvs represents the comparison of non-targeting cells with and without stimulation.

Article Snippet: Guides targeting TRIM33 (T33-3: 5’-ACAGAGTCTGTTGGAGCATC-3, T33-4: 5’-ACTATGGCAAATGCAAACCG-3, T33-5: 5’-CTCCTCCTCCACCAGCACCG-3) or non-targeting control (NT: 5’-AACTACAAGTAAAAGTATCG-3) were cloned into lentiCRISPRv2 plasmids ( Addgene: #52961).

Techniques: Western Blot, Generated, Knock-Out, Control, Gene Expression, Quantitative Proteomics, Comparison

Journal: bioRxiv

Article Title: TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination

doi: 10.1101/2025.02.14.638236

Figure Lengend Snippet: A PCA plots for grouped and individual analysis of the TRIM33 C2 knockout ChIP-seq data. B Average signal intensity profiles of AR (top) and H3K18ac (bottom) across the tested cell lines on the TRIM33 R1881 treatment gained and lost regions of . TRIM33 C2 knockout cells are in green and non-targeting in blue. C Heatmap of H2Bub signal across gene bodies of differentially expressed genes from as well as the unresponsive genes. D Average signal intensity plots for the regions depicted in C. E Distribution of the sum of the H2Bub signals across the scaled gene body from the regions in C. Significance levels of Wilcoxon ranked sum test: * < 0.01, ** < 0.001

Article Snippet: Guides targeting TRIM33 (T33-3: 5’-ACAGAGTCTGTTGGAGCATC-3, T33-4: 5’-ACTATGGCAAATGCAAACCG-3, T33-5: 5’-CTCCTCCTCCACCAGCACCG-3) or non-targeting control (NT: 5’-AACTACAAGTAAAAGTATCG-3) were cloned into lentiCRISPRv2 plasmids ( Addgene: #52961).

Techniques: Knock-Out, ChIP-sequencing