A separate DESeq2 run was performed for siRNA against each element, comparing replicates treated with the siRNA against the given element versus replicates treated with the control siRNA. hypersensitive sites. ENCODE. ENCSR752EPHSupplementary MaterialsSupplementary file 1: Correlation between (A) biological replicates and (B) quantity of binding sites of YH249 the indicated proteins in ER-Src ethanol or tamoxifen; wild-type and YAP or TAZ knockout (KO) and MDA-MB-231 cells. elife-67312-supp1.pdf (32K) GUID:?CE0A10DC-F520-443E-9A81-1D3645B707F2 Supplementary file 2: Enriched GO groups for YAP-specific, TAZ-specific, or shared YAP/TAZ target genes. elife-67312-supp2.xlsx (73K) GUID:?B5941AEC-DBE6-4FFB-9D7D-42410E2CF628 Supplementary file 3: Gene signatures for the YH249 indicated categories of YAP/TAZ target sites. elife-67312-supp3.xlsx (33K) GUID:?59B3D732-4C91-4525-B73C-180204657F6B Supplementary file 4: Enriched GO terms with connected q-values for genes with YAP/TAZ target sites containing only AP-1, TEAD, or STAT motif but not combinations of motifs. elife-67312-supp4.xlsx (10K) GUID:?3277017D-5603-4086-8A6D-1537C476A62C Supplementary file 5: siRNAs, antibodies, qPCR primers, ChIP-seq primers, and list of datasets. elife-67312-supp5.xlsx (15K) GUID:?3002E497-1A39-4D0C-ADC0-3D9C3793FFA0 Transparent reporting form. elife-67312-transrepform1.pdf (322K) GUID:?5C117F60-D3C6-497C-B898-F3579054968C Data Availability StatementAll sequencing data were deposited about National Cancer for Biotechnology Info Gene Manifestation Omnibus (GEO). “type”:”entrez-geo”,”attrs”:”text”:”GSE166943″,”term_id”:”166943″GSE166943 is the accession quantity for all the data, with “type”:”entrez-geo”,”attrs”:”text”:”GSE166941″,”term_id”:”166941″GSE166941 becoming the subset for the ChIP-seq data and “type”:”entrez-geo”,”attrs”:”text”:”GSE166942″,”term_id”:”166942″GSE166942 for the RNA-seq data. The following dataset was generated: He L, Pratt H, Wei F, Gao M, Weng Z, Struhl K. 2021. YAP and TAZ are co-activators of AP-1 proteins and STAT3 during breast cellular transformation. NCBI Gene Manifestation Omnibus. GSE166943 The following previously published datasets were used: Fleming JD, Ji Z, Struhl K. 2018. Regulatory network controlling tumor-promoting swelling in human being cancers (ChIP-seq) NCBI Gene Manifestation Omnibus. GSE115597 He L, Ji Z, Struhl K. 2018. Regulatory network controlling tumor-promoting swelling in human being cancers (RNA-seq) NCBI Gene Manifestation Omnibus. GSE115598 Ji Z, He L, Rotem A, Janzer A, CC2D1B Cheng CS, Regev A, Struhl K. 2017. Genome-scale recognition of transcription factors that mediate an inflammatory network during breast cellular transformation. NCBI Gene Manifestation Omnibus. GSE100259 Meuleman W. 2017. Index and biological spectrum of human being DNase I hypersensitive sites. ENCODE. ENCSR752EPH Abstract The YAP and TAZ paralogs are transcriptional co-activators recruited to target sites by TEAD proteins. Here, we show that YAP and TAZ are also recruited by JUNB (a member of the AP-1 family) and STAT3, important transcription factors that mediate an epigenetic switch linking inflammation to cellular transformation. YAP and TAZ directly interact with JUNB and STAT3 via a WW domain name important for transformation, and they stimulate transcriptional activation by YH249 AP-1 proteins. JUNB, STAT3, and TEAD co-localize at virtually all YAP/TAZ target sites, yet many target sites only contain individual AP-1, TEAD, or STAT3 motifs. This observation and differences in relative crosslinking efficiencies of JUNB, TEAD, and STAT3 at YAP/TAZ target sites suggest that YAP/TAZ is usually recruited by different forms of an AP-1/STAT3/TEAD complex depending on the recruiting motif. The different classes of YAP/TAZ target sites are associated with largely non-overlapping genes with unique functions. A small minority of target sites are YAP- or TAZ-specific, and they are associated with different sequence motifs and gene classes from shared YAP/TAZ target sites. Genes made up of either the AP-1 or TEAD class of YAP/TAZ sites are associated with poor survival of breast malignancy patients with the triple-negative form of the disease. (Physique 3C). WW domains of YAP and TAZ are important for interacting with STAT3 and JUNB and for transformation YAP and TAZ have a TEAD domain name that interacts with TEAD1-4, and they contain WW domains (two for YAP and one for TAZ) that mediate interactions with a variety of other proteins. To map the regions of YAP and TAZ required for interacting with STAT3 and JUNB, we performed co-IP experiments in cells co-expressing YAP or TAZ derivatives lacking one or both WW domains along with FLAG-tagged STAT3 or JUNB (Physique 3D). The WW1 domain name of YAP is critical for the YH249 conversation with STAT3 and JUNB, whereas removal of the YAP WW2 domain name has no effect on these interactions. Deletion of the TAZ WW domain name reduces, but does not eliminate, the conversation with either JUNB or STAT3. Removal of any WW domain name has no effect on the conversation with the TEAD proteins, whereas removal of the TEAD domain name abolishes the conversation with the.