The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells
- CRBM, University of Montpellier, CNRS, France
Figures
Figure 1 with 2 supplements
TELO2 promotes TRRAP assembly into the SAGA and TIP60 complexes.
(A, B) Western blot analyses of total extracts from TELO2AID (A) or AIDTRRAP (B) cell lines harvested at different time points after auxin addition, as indicated (hours). Blots were probed with an …
Figure 1—figure supplement 1
Characterization of TELO2-AID and AID-TRRAP cell lines.
(A, B) Schematic depiction of the strategy designed to tag endogenous TELO2 (A) and TRRAP (B) with an auxin-inducible degron (AID) in in an HCT116 cell line stably expressing Oryza sativa TIR1. Gene …
Figure 1—figure supplement 2
TRRAP is not involved in SAGA-dependent endoplasmic reticulum (ER) stress gene induction.
(A) Expression of CHOP and HERPUD using quantitative RT-PCR of RNA extracted from AIDTRRAP cells treated with either thapsigargin (red dots) or DMSO (blue dots) for 3 hr. Prior to ER stress …
Figure 2 with 3 supplements
TELO2 and TRRAP regulate an overlapping set of genes and repress type I interferon-stimulated genes.
(A) Density scatter plot comparing gene expression changes between TELO2 and TRRAP-depleted cells. The Pearson correlation coefficient and corresponding p-value are indicated. (B) Venn diagrams …
Figure 2—figure supplement 1
Gene expression changes upon TELO2 and TRRAP depletion.
(A, B) Scaled Integrative Genomics Viewer (IGV) snapshots of two differentially expressed genes, MCIDAS (A) and KRT20 (B), from RNA sequencing (RNA-seq) performed in three distinct TELO2AID and AIDTR…
Figure 2—figure supplement 2
Auxin treatment induces aryl hydrocarbon receptor (AHR)-responsive genes.
(A) Gene Set Enrichment Analysis (GSEA) showing the enrichment of genes encoding MTORC1 signaling components in the ranked transcriptome profiles of TELO2-depleted cells. Green lines represent …
Figure 2—figure supplement 3
TELO2 and TRRAP repress type I interferon-stimulated genes (ISGs).
Heatmap representation of the expression of a list of IFN-I-stimulated genes (113 ISGs) in TELO2 and TRRAP-depleted cells. The list of 113 ISGs results from merging the list of 97 genes from the IFN …
Figure 3
Interferon-stimulated gene (ISG) induction in the absence of an innate immune response.
(A) Schematic representation of the innate immune and IFN-I signaling pathways. (B) Western blot analyses of phosphorylated and total STAT1 and IRF3 levels in extracts from AIDTRRAP cells treated …
Figure 4
TRRAP specifically represses U-ISGF3-regulated genes.
(A) Schematic representation of the transcription regulation of distinct subsets of interferon-stimulated genes (ISGs), depending on whether ISGF3 unphosphorylated, in basal conditions (U-ISGF3, …
Figure 5 with 1 supplement
Genome-wide profiling of TRRAP occupancy.
(A) Histogram showing the frequency distribution of TRRAP-bound loci across the genome, relative to annotated transcription start sites (TSS). Shown are the number of peaks computed by MACS2 in bins …
Figure 5—figure supplement 1
Implementation of the CUT&RUN procedure.
(A, B) CUT&RUN-qPCR analysis of MYC (A) and TRRAP (B) occupancy at the MIR17-HG locus in HCT116 cells. Parental TIR-1-expressing and -derived AIDTRRAP cell lines were treated with either NaOH (gray) …
Figure 6
TRRAP directly represses the transcription of IRF7 and IRF9.
(A) RT-qPCR analysis of newly synthesized IRF7, IRF9, and OAS1. AIDTRRAP cells were treated with either NaOH (gray) or auxin (purple) for 10 hr, prior to a 20 min incubation with 4-thiouridine …
Figure 7
Dynamics of interferon-stimulated gene (ISG) regulation by TRRAP.
(A) Experimental strategy: AIDTRRAP cells were harvested before auxin addition, after incubation with auxin for 10 hr (purple), and at various time points up to 5 hr after auxin removal (blue), as …
Additional files
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Supplementary file 1
Gene expression changes upon TELO2 depletion.
Shown are DESeq2 results from RNA-seq experiments comparing HCT116 TELO2-AID cells treated with either NaOH or auxin for 48 hr. log2FoldChange indicates the Log2 fold change of the ratio of RNA-seq counts in auxin-treated cells over NaOH-treated cells, averaged from three independent clones. padj indicates the p-values after Benjamin–Hochberg correction for multiple testing.
- https://cdn.elifesciences.org/articles/69705/elife-69705-supp1-v2.csv
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Supplementary file 2
Gene expression changes upon TRRAP depletion.
Shown are DESeq2 results from RNA-seq experiments comparing HCT116 AID-TRRAP cells treated with either NaOH or auxin for 24 hr. log2FoldChange indicates the Log2 fold change of the ratio of RNA-seq counts in auxin-treated cells over NaOH-treated cells, averaged from three independent clones. padj indicates the p-values after Benjamin–Hochberg correction for multiple testing.
- https://cdn.elifesciences.org/articles/69705/elife-69705-supp2-v2.csv
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Supplementary file 3
Interferon-stimulated gene (ISG) expression changes upon TELO2 and TRRAP depletion.
Shown are DESeq2 results as in Tables S1 and S2, filtered for IFN-I stimulated genes (113 ISGs). The list of 113 ISGs results from merging the 97 genes from the HALLMARK_INTERFERON_ALPHA_RESPONSE (MSigDB) with all non-redundant U-ISGF3- and ISGF3-regulated genes. Source data for Figure 4 and Figure 2—figure supplement 3.
- https://cdn.elifesciences.org/articles/69705/elife-69705-supp3-v2.csv
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Supplementary file 4
Supplementary file 4.Genome-wide occupancy profile of TRRAP in HCT116 cells.
'NarrowPeaks' output files from MACS2 peak calling analyses of duplicate anti-HA CUT&RUN-seq experiments performed in AID-TRRAP cells, treated with either NaOH or auxin (IAA) for 12 hr, compared to a control IgG CUT&RUN-seq sample.
- https://cdn.elifesciences.org/articles/69705/elife-69705-supp4-v2.xlsx
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Supplementary file 5
List of oligonucleotides used in this study.
- https://cdn.elifesciences.org/articles/69705/elife-69705-supp5-v2.xlsx
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Supplementary file 6
List of antibodies used in this study.
- https://cdn.elifesciences.org/articles/69705/elife-69705-supp6-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/69705/elife-69705-transrepform1-v2.pdf
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Source data 1
This contains all original uncropped scans of all Western blots.
- https://cdn.elifesciences.org/articles/69705/elife-69705-data1-v2.zip
