HNRNPH1-mediated splicing events regulate EIF4G1 transcript variant composition and the organization of the AURKA 5' UTR

Abstract

HNRNPH1 is a regulator of alternative splicing, but few studies have defined the splicing events it mediates. Here, we used short- and long-read RNA sequencing to interrogate the transcriptome-wide effects of HNRNPH1 depletion and its regulation of specific splicing events. Differential alternative splicing analysis revealed effects on the transcriptome that involved all splice event categories. We confirmed HNRNPH1s regulation of a splicing event involving TCF3-exons 18a and 18b that encode distinct TCF3 transcription factor isoforms. Extending this finding, we present evidence that in neuroblastoma, HNRNPH1 is a MYCN target, potentially explaining the higher levels of HNRNPH1 and TCF3-exon 18a transcript variants in this tumor type. Analysis of two skipped exon events determined that HNRNPH1 regulates the splicing of exons encoding part of the EIF4G1 translation initiation factors N-terminus and an exon included in the 5UTR of specific transcript variants encoding the mitotic kinase AURKA. Using reporter constructs, we show this AURKA 5UTR exon enhances expression, suggesting HNRNPH1 could contribute to regulating AURKA protein levels. Our findings highlight HNRNPH1s roles in regulating the expression of proteins with diverse cellular functions. Key pointsO_LIHNRNPH1 regulates the expression of proteins with diverse cellular functions, including proteins involved in the regulation of gene expression and essential cellular mechanisms. C_LIO_LIDepletion of HNRNPH1 alters the expression of specific protein-coding EIF4G1 transcript variants. C_LIO_LIHNRNPH1 mediates the inclusion of an AURKA 5UTR exon that enhances protein expression. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/667222v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@13780f1org.highwire.dtl.DTLVardef@f276d8org.highwire.dtl.DTLVardef@588245org.highwire.dtl.DTLVardef@d08551_HPS_FORMAT_FIGEXP M_FIG C_FIG