TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex
- Department of Pathology, University of Iowa, United States
- Cancer Biology Graduate Program, University of Iowa, United States
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, United States
- Peter MacCallum Cancer Centre, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Australia
- Department of Pathology and Immunology, Washington University, United States
- Iowa Institute of Human Genetics, Carver College of Medicine, University of Iowa, United States
- Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Australia
- Holden Comprehensive Cancer Center, University of Iowa, United States
- Pathology and Laboratory Medicine, Veterans Affairs Medical Center, United States
Figures
Figure 1 with 3 supplements
YAP-TFE3 transforms cells in vitro and in vivo and combines properties of both YAP and TFE3.
(A) Structure of full-length TAZ, CAMTA1, TAZ-CAMTA1 (TC), YAP, TFE3, YAP-TFE3 (YT), truncated portion of YAP (YAP trunc) and the truncated portion of TFE3 (TFE3 trunc). (B) Soft agar assay in NIH …
Figure 1—figure supplement 1
YAP-TFE3, TAZ-CAMTA1, and controls are expressed in NIH 3T3 cells, SW 872 cells, and HEK293 cells.
(A) Western blot for Flag tagged YAP5SA, YAP-TFE3, TFE3, TAZ4SA, TAZ-CAMTA1, CAMTA1 in NIH 3T3 cells (B) Western blot for Flag-tagged YAP, YAP-TFE3 S94A, YAP S94A, YAP-Trunc, and TFE3-Trunc in NIH …
Figure 1—figure supplement 2
YAP-TFE3 is not regulated by the Hippo pathway and required binding to TEAD transcription factors to drive its oncogenic transcriptional program.
(A) YAP and YAP-TFE3 are localized within the nucleus under spare conditions in SW872 cells. YAP-TFE3 but not YAP is localized within the nucleus under confluent conditions in SW872 cells. (B) …
Figure 1—figure supplement 3
YAP-TFE3 and TAZ-CAMTA1 driven xenografts in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice form tumors in vivo.
(A) H and E sections of NIH 3T3 xenografts transduced with EV, YAP-TFE3 or TAZ-CAMTA1. Tumors expressing YAP-TFE3 or TAZ-CAMTA1 showed a more epithelioid cytomorphology and a greater degree of …
Figure 2
Tead1 mediates the oncogenic transcriptional program of YAP-TFE3.
(A) Knockdown of Tead1 in NIH 3T3 YAP-TFE3 cells. (B) Poly-HEMA analysis in NIH 3T3 YAP-TFE3 cells with Tead1 knock-down. Spheroid formation on poly-HEMA is shown below. (C) Soft agar assay in NIH …
-
Figure 2—source data 1
Tead1 shRNA sequences.
- https://cdn.elifesciences.org/articles/62857/elife-62857-fig2-data1-v2.xlsx
Figure 3 with 1 supplement
TAZ-CAMTA1 and YAP-TFE3 induce different but overlapping transcriptomes compared to TAZ and YAP.
(A) Number of differentially expressed genes (FDR = 5%) in NIH 3T3 cells expressing TAZ-CAMTA1 and full-length controls. HG density represents the –log10(hypergeometric density). p Value for …
-
Figure 3—source data 1
Differentially expressed genes in NIH 3T3 cells expressing fusion proteins and full length controls.
- https://cdn.elifesciences.org/articles/62857/elife-62857-fig3-data1-v2.xlsx
-
Figure 3—source data 2
Differentially expressed genes in SW872 cells expressing fusion proteins and full length controls.
- https://cdn.elifesciences.org/articles/62857/elife-62857-fig3-data2-v2.xlsx
Figure 3—figure supplement 1
Differentially expressed genes in SW872 cells expressing fusion proteins and full length controls.
(A) Principal component analysis of RNA expression after variance stabilizing transformation in SW872 cells. (B) iPathwayGuide analysis showing enrichment of Hippo pathway genes in DE expression …
Figure 4 with 3 supplements
TAZ-CAMTA1 and YAP-TFE3 occupy TEAD and non-TEAD transcription factor motifs.
(A) Heat map of ChIP binding to transcriptional start site (TSS) regions and average TSS profile histogram for TAZ-CAMTA1 and controls. (B) Heat map and histogram for YAP-TFE3 and controls. (C) …
-
Figure 4—source data 1
ChIP AME Motif Enrichment Analysis.
- https://cdn.elifesciences.org/articles/62857/elife-62857-fig4-data1-v2.xlsx
-
Figure 4—source data 2
Differentially expressed genes also bound by fusion proteins and controls as determined by ChIP-Seq.
- https://cdn.elifesciences.org/articles/62857/elife-62857-fig4-data2-v2.xlsx
Figure 4—figure supplement 1
Distribution of overlapping transcription factor and H3K27ac ChIP peaks among annotated functional DNA-binding sites.
Overlapping transcription factor/coactivator ChIP peaks shown for annotated functional DNA binding sites in SW872 cells expressing (A) TAZ4SA, (B) CAMTA1, (C) YAP5SA, and (D) TFE3. (E) Combined …
Figure 4—figure supplement 2
Characterization of YAP-TFE3 and TAZ-CAMTA1 DNA binding in SW872 cells.
(A) Pull-down of TFE3 reveals interaction with Flag-YAP-TFE3 by co-immunoprecipitation, consistent with enrichment of the MiTF consensus DNA binding sequence and mass spectrometry data. Soft agar …
Figure 4—figure supplement 3
TAZ-CAMTA1 and YAP-TFE3-bound genes are differentially expressed.
(A) Venn diagram showing intersection of DE expressed genes in SW872 TAZ-CAMTA1 with TAZ-CAMTA1-bound genes. (B) Venn diagram showing intersection of DE expressed genes in SW872 YAP-TFE3 with …
Figure 5 with 1 supplement
TAZ-CAMTA1 and YAP-TFE3 promote the formation of chromatin accessible to transcriptional regulation.
(A) Heat map of ATAC peak distribution around the transcriptional start site (TSS) region and average ATAC TSS profile for TAZ-CAMTA1 and controls and (B) for YAP-TFE3 and controls. (C) Intersection …
Figure 5—figure supplement 1
TAZ-CAMTA1 and YAP-TFE3 alter the chromatin landscape.
Distribution of transposase accessible chromatin relative to transcriptional start site (A) and functional annotation (B). (C) Venn diagram analysis for TAZ-CAMTA1 after ATAC peaks annotated to …
Figure 6 with 1 supplement
The TAZ-CAMTA1 and YAP-TFE3 interactomes are enriched for transcriptional regulators and chromatin modifiers.
(A) Overview of BioID method. (B) Summary of YAP-TFE3 and TAZ-CAMTA1 interactomes. (C) Dot plot representation of chromatin modifiers shared by YAP-TFE3 and TAZ-CAMTA1 interactomes. (D) Table of …
Figure 6—figure supplement 1
BioID Mass Spectrometry shows that YAP-TFE3 and TAZ-CAMTA1 have an altered interactome compared to YAP and TAZ.
Group (A) prey proteins often demonstrated a loss of interaction with the fusion proteins. Group (B) prey proteins demonstrated enhanced interaction with the fusion proteins relative to TAZ and YAP …
Figure 7 with 1 supplement
RNAi screen shows subunits of the ATAC complex mediate the transforming capacity of TAZ-CAMTA1 and YAP-TFE3.
(A) Overview of RNAi screen. SW872 cells expressing TAZ-CAMTA1 are transduced with five shRNAs for each gene in the shared TAZ-CAMTA1/YAP-TFE3 interactome and proliferation assayed on …
-
Figure 7—source data 1
Oligonucleotide sequences for shRNA constructs used in the RNAi screen.
- https://cdn.elifesciences.org/articles/62857/elife-62857-fig7-data1-v2.xlsx
Figure 7—figure supplement 1
RNAi screen identifies epigenetic modifiers important for the activity of TAZ-CAMTA1 and YAP-TFE3.
(A–F) Additional epigenetic modifiers with at least one shRNA showing a deficit in anchorage-independent growth in SW872 TAZ-CAMTA1 cells. (G) Knock-down of YEATS2 in SW872 YAP-TFE3 cells by …
Figure 8 with 2 supplements
The ATAC complex is critical for the oncogenic transcriptomes of the fusion proteins.
(A) Principal component analysis showing the effect of knock-down of YEATS2 or ZZZ3 on the TAZ-CAMTA1 and YAP-TFE3 transcriptomes. (B) Genes with at least a two-fold decrease in at least two of the …
-
Figure 8—source data 1
Differentially expressed genes in SW872 cells expressing TAZ-CAMTA1 or YAP-TFE3 after YEATS2 or ZZZ3 knock-down.
- https://cdn.elifesciences.org/articles/62857/elife-62857-fig8-data1-v2.xlsx
Figure 8—figure supplement 1
Validation of mass spectrometry/RNAi screen.
(A) Knock-down of YEATS2 in SW872 TAZ-CAMTA1 cells by qRT-PCR. (B) Soft agar assay for SW872 TAZ-CAMTA1 cells after YEATS2 knock-down. (C) Knock-down of ZZZ3 in SW872 TAZ-CAMTA1 cells evaluated by …
Figure 8—figure supplement 2
The ATAC complex modulates expression of the MAPK signaling pathway, the PI3K signaling pathway, and extracellular matrix (ECM) proteins.
(A) Knock-down of YEATS2 in YAP-TFE3 expressing SW872 cells inhibited expression of components of MAPK signaling by iPathwayGuide analysis. (B) Upregulation of PI3K-Akt signaling in SW872 cells …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Mus musculus) | NIH 3T3 cells | ATCC | CRL-1658; RRID:CVCL_0594 | Mycoplasma negative |
| Cell line (Homo sapiens) | SW872 cells | ATCC | HTB92; RRID:CVCL_1730 | Mycoplasma negative |
| Transfected construct (H. sapiens) | pPGS-3HA-TEAD1 | Dr. Kunliang Guan (Addgene) | #33055; RRID:Addgene_33055 | |
| Transfected construct (H. sapiens) | 8xGTIIC-luciferase | Dr. Stefano Piccolo (Addgene) | #34615; RRID:Addgene_34615 | |
| Transfected construct (H. sapiens) | pRP-CMV-3xMyc-KAT14 | Vector builder | ||
| Commercial assay or kit | SimpleChIP Enzymatic Chromatin IP Kit | Cell Signaling | #9003 | |
| Antibody | Anti-DYKDDDDK antibody | Cell Signaling | #14793; RRID:AB_2572291 | ChIP grade antibody |
