Table summarizing the RNA-seq results. Differential gene expression results in BAP1-knockdown compared to control OCM-1A cells are shown from the RNA-seq data. Each row gives the unique Ensembl identifier, gene name, and description for each gene, as well as the log of the fold change (logFC), average expression, adjusted p-value, and linear fold change. (XLSX 1392 kb

Chen, Xuhua

Cooper, John A

Mitra, Robi D

Onken, Michael D

Qi, Zongtai

Yen, Matthew

BMC Medical Genomics

English

GSEA terms associated with top BAP1 target genes. Gene set enrichment analysis on the subset of 79 BAP1 targets that were able to discriminate molecular class in primary tumors. Each row gives the name of the curated GSEA term, the number of overlapping genes (size), enrichment score (ES), nominal enrichment score (NES), nominal p-value, false discovery rate (FDR), family-wise error rate (FWER), and rank-at-max value calculated by the GSEA software. (XLSX 12 kb

Matthew Yen (5940104)

Zongtai Qi (2068426)

Xuhua Chen (5940107)

John Cooper (274237)

Robi Mitra (5940110)

Michael Onken (834122)

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Additional file 10: of Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma

Abstract Background BAP1 is a histone deubiquitinase that acts as a tumor and metastasis suppressor associated with disease progression in human cancer. We have used the “Calling Card System” of transposase-directed transposon insertion mapping to identify the genomic targets of BAP1 in uveal melanoma (UM). This system was developed to identify the genomic loci visited by transcription factors that bind directly to DNA; our study is the first use of the system with a chromatin-remodeling factor that binds to histones but does not interact directly with DNA. Methods The transposase piggyBac (PBase) was fused to BAP1 and expressed in OCM-1A UM cells. The insertion of transposons near BAP1 binding sites in UM cells were identified by genomic sequencing. We also examined RNA expression in the same OCM-1A UM cells after BAP1 depletion to identify BAP1 binding sites associated with BAP1-responsive genes. Sets of significant genes were analyzed for common pathways, transcription factor binding sites, and ability to identify molecular tumor classes. Results We found a strong correlation between multiple calling-card transposon insertions targeted by BAP1-PBase and BAP1-responsive expression of adjacent genes. BAP1-bound genomic loci showed narrow distributions of insertions and were near transcription start sites, consistent with recruitment of BAP1 to these sites by specific DNA-binding proteins. Sequence consensus analysis of BAP1-bound sites showed enrichment of motifs specific for YY1, NRF1 and Ets transcription factors, which have been shown to interact with BAP1 in other cell types. Further, a subset of the BAP1 genomic target genes was able to discriminate aggressive tumors in published gene expression data from primary UM tumors. Conclusions The calling card methodology works equally well for chromatin regulatory factors that do not interact directly with DNA as for transcription factors. This technique has generated a new and expanded list of BAP1 targets in UM that provides important insight into metastasis pathways and identifies novel potential therapeutic targets

Matthew Yen

Zongtai Qi

Xuhua Chen

John A. Cooper

Robi D. Mitra

Michael D. Onken

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