MCF10A cells expressing empty vector, siRNA-resistant wild-type and siRNA-resistant catalytically dead TIP60 treated with control or TIP60 siRNA
Alternative splicing of RNA transcripts can result in a multitude of variations from the genome. Since splicing can occur co-transcriptionally, chromatin structure has been reported to affect the choice of a splice site. TIP60 is a haploinsufficient tumor suppressor gene that is frequently downregulated in cancers. Since TIP60 is a writer of histone and non-histone modifications, we investigated TIP60's role in modulating alternative splicing. RNA sequencing was performed in TIP60-depleted MCF10A cells and with cells rescued with wild-type or catalytically inactive TIP60. The majority of the differential splicing events were skipped exon events, including exon 25 skipping event of ITGA6. To identify the splicing factor that regulates this event, a siRNA screen of 77 splicing factors was employed. TIP60 depletion results in an increase in the ITGA6 isoform that lacks exon 25 and the siRNA screen identified ESRP2 to regulate splicing of ITGA6 exon 25. This study suggests that alternative splicing of ITGA6 exon 25 is regulated by the TIP60-ESRP2 axis. Overall design: RNA-Seq of MCF10A cells stably expressing empty vector (MSCV), siRNA-resistant wild-type (*WT-TIP60) and siRNA-resistant catalytically dead (*KD-TIP60) TIP60 treated with control or TIP60 siRNA