Additional file 12: of EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions

Analysis of ChIP-seq FUS and EWS enrichment peaks in the RCC1 and SNHG3 gene complex, including SNORA73A and SNORA73B genes. A. Graphic distribution of ChIP-seq reads aligned to the RCC1 and SNHG3 genes from the input, FUS, EWS and Ac-H3K9 ChIP-seq samples. The number of reads is shown on the scale to the left of each figure. The transcripts from the genes in the UCSC hg19 genomic database are shown in the bottom. The arrows beneath peaks illustrate location of the several qPCR amplicons used. The arrows above the transcripts illustrate location of RT-qPCR amplicons. Numbers above arrows denotes target exon numbers. B-C. FUS and EWS effect for RCC1, SNHG3 and snoRNA expression. The expression levels were determined by qPCR from HEK-293 cells transfected with siRNA for FUS and EWS or control siRNA. Three independent experiments were performed and error bars indicate standard deviation. In B., simultaneous depletion of FUS and EWS was performed, whereas in C. FUS and EWS were individually depleted. (PDF 552 kb)