In undifferentiated cells, 1262 genes enriched in the ontology terms cell structure and motility, developmental processes, oncogenesis and cell cycle control were annotated (Fig 5C). were intermixed allowing a comparison of the localisation of the proteins in the two states. All scale bars 100 m.(TIF) pgen.1006600.s001.tif (3.4M) GUID:?0D861C90-D23C-458D-ACC6-F2016AAD60F1 S2 Fig: Tead4 occupancy in C2C12 cells. A. UCSC genome browser shot of Tead4 occupancy at the and loci in differentiated and non-differentiated C2C12 cells. The Tead4-bound sites are indicated with arrows. B. Read density maps showing comparison of Tead4 binding with that of Jun, Runx and Srf.(TIF) pgen.1006600.s002.tif (2.3M) GUID:?F025C92C-0ADA-4D8E-A35A-918F8145AFF1 S3 Fig: Tead1 genomic occupancy in C2C12 cells. A. Localisation of Tead1 occupied sites in non-differentiated C2C12 cells relative to genomic annotations and the TSS. B. Results of MEME analysis on the top 600 Tead1 occupied sites in non-differentiated C2C12 cells. Lower panel indicates the frequency of occurrence of DNA binding motifs for the indicated transcription factors at Tead1 occupied sites comparing the expected and observed values. C. Localisation of Tead1 occupied sites in differentiated C2C12 cells. D. UCSC genome browser view of Tead1 occupancy at the and loci in the non-differentiated and differentiated state. E. Read density cluster map to compare Tead1 and Tead4 occupancy in non-differentiated cells.(TIF) pgen.1006600.s003.tif (1.1M) GUID:?A4F5C729-B142-4FDF-865B-76D425F3F238 S4 Fig: Transcription factor occupancy at the and gene loci. A-B. UCSC screenshots showing Tead4 and Tead1 occupancy and H3K27ac at and gene loci in non-differentiated SRSF2 and differentiated C2C12 cells along with Myog and Myod1 occupancy in differentiated cells.(TIF) pgen.1006600.s004.tif (591K) GUID:?D27BD974-DE00-4FC9-B990-194C23540303 S5 Fig: Myog regulates Tead4 and Mef2c expression. A. Immunostaining for Myh expression to show inhibition of C2C12 and PM differentiation following siMyog. B. RT-qPCR analyses of gene expression in siControl and siMyog C2C12 cells. C. UCSC screenshots showing Tead4 and Myog occupancy and H3K27ac at the locus in differentiated C2C12 cells. Arrows indicate Tead4 or Myog bound sites that co-localise and/or co-localise with H3K27ac in differentiated cells.(TIF) pgen.1006600.s005.tif (1.9M) GUID:?B790B3EB-A610-40C5-AE4F-45BCF7968E2B S6 Fig: Integration of Tead1 genomic occupancy with chromatin modifications. A. Read density cluster map showing chromatin modifications at Tead1-occupied sites in non-differentiated cells. B. Venn diagrams illustrating the overlap of chromatin modifications with Tead1 genomic occupancy. C. Identification and ontology analysis of genes associated with Tead4 sites at active H3K27ac marked regulatory elements. D. UCSC screenshots showing Tead1, Tead4 occupancy and H3K4me3 and H3K27ac at a selection of loci illustrating constitutive and acquired chromatin marks and Tead binding during differentiation.(TIF) pgen.1006600.s006.tif (1.1M) GUID:?1B10677F-21B3-4353-9EC3-927CB7D8802B S7 Fig: Sites co-occupied by Tead4, Myod1 and Myog. A. Read density cluster maps showing sites occupied by Myog, Myod1 and Tead4 in differentiated C2C12 cells. The metaprofiles of selected Rivanicline oxalate clusters are shown to the right. B. Rivanicline oxalate Read density cluster map comparing sites occupied by Myog and Myod1 in differentiated cells with Tead1 in non-differentiated cells. Only a small set of common sites was identified. C. Frequency of occurrence of transcription factor binding motifs at the commonly occupied sites from panel A. D. Venn diagrams illustrating the overlap of genes associated with Tead4, Myod1 and Myog bound sites. E-F. Read density cluster maps showing sites co-occupied by Tead4 or Tead1 and Mef2a. The metaprofiles of selected clusters are shown to the right.(TIF) pgen.1006600.s007.tif (2.6M) GUID:?5AE0257E-6592-48AF-B14D-79FFBE74C800 S8 Fig: Rivanicline oxalate Gene expression programs in C2C12 cells and PMs. A-B. Venn diagrams illustrating the overlap of up and down-regulated genes in differentiating PMs and C2C12 cells. The ontology analyses of the commonly regulated genes of both categories are shown.(TIF) pgen.1006600.s008.tif (386K) GUID:?C1B5303B-9160-43AF-BEC8-0A25F668494D S9 Fig: Gene expression in differentiating C2C12 cells. A. Classification of gene expression changes into classes with different kinetics. B. GSEA analyses of genes up and down-regulated during C2C12 cell differentiation. The most significant categories are shown.(TIF) pgen.1006600.s009.tif (836K) GUID:?55FFBA14-DC05-4BEA-A497-CBCB6EC2B77F S10 Fig: Gene expression in differentiating PMs. A. Classification of gene expression changes into classes with different kinetics. B. GSEA analyses of genes up and down-regulated during PM differentiation. The most significant categories are shown.(TIF) pgen.1006600.s010.tif (915K) GUID:?FC92A279-DB79-4E53-B6AB-B49787FD1FAC S11 Fig: Genes regulated by siTead1/4 silencing in PMs and C2C12 cells. A. Venn diagram representing genes specifically or commonly down-regulated in C2C12 cells and PMs along with their BP-FAT ontology. B. Venn diagram representing genes specifically or commonly up-regulated in C2C12 cells and PMs along with their BP-FAT ontology.(TIF) pgen.1006600.s011.tif (435K) GUID:?5DBAECB0-CE65-4298-9EBB-C1669DE97D17 S12 Fig: Tead genome occupancy in muscle. A. Read density maps comparing Tead4 occupancy in muscle with that of Pol II and H3K27ac. The ontology of the genes associated with the subset of co-localising sites is indicated. B. Read density maps comparing Tead1 and Tead4 occupancy in muscle. The ontology of the genes associated with the subset of co-localising sites is indicated.(TIF) pgen.1006600.s012.tif (1.8M) GUID:?62475068-488A-4D83-8ABB-93368D329BE8 S13 Fig: Tead occupancy in muscle in vivo. UCSC genome browser view of the locus showing Tead1, Tead4, Pol II and H3K27ac ChIP-seq from WT and MT muscle. The arrow indicates the major Tead1/4 binding site.(TIF) pgen.1006600.s013.tif (381K) GUID:?BCDC396E-EC75-4E96-8F7E-D16A3560CBBC S14 Fig: Tead1/4 genome occupancy in C2C12 cells and.