BRD2 and BRD3 genes independently evolved RNA structures to control unproductive splicing

Abstract

AbstractThe mammalianBRD2andBRD3genes encode structurally related proteins from the bromodomain and extraterminal domain (BET) protein family. The expression ofBRD2is regulated by unproductive splicing upon inclusion of exon 3b, which is located in the region encoding a bromodomain. Bioinformatic analysis indicated thatBRD2exon 3b inclusion is controlled by a pair of conserved complementary regions (PCCR) located in the flanking introns. Furthermore, we identified a highly conserved element encoding a cryptic poison exon 5b and a previously unknown PCCR in the intron between exons 5 and 6 ofBRD3, however outside of the homologous bromodomain. Minigene mutagenesis and blockage of RNA structure by antisense oligonucleotides demonstrated that RNA structure controls the rate of inclusion of poison exons. The patterns ofBRD2andBRD3expression and splicing show downregulation upon inclusion of poison exons, which become skipped in response to transcription elongation slowdown, further confirming a role of PCCRs in unproductive splicing regulation. We conclude thatBRD2andBRD3independently acquired poison exons and RNA structures to dynamically control unproductive splicing. This study describes a convergent evolution of regulatory unproductive splicing mechanisms in these genes providing implications for selective modulation of their expression in therapeutic applications.