Howard, J. M. | Search bioRxiv

bioRxiv2017

Precise, pan-cancer discovery of gene fusions reveals a signature of selection in primary tumors

Short AbstractThe extent to which gene fusions function as drivers of cancer remains a critical open question in cancer biology. In principle, transcriptome sequencing provided by The Cancer Genome Atlas (TCGA) enables unbiased discovery of gene fusions and post-analysis that informs the answer to this question. To date, such an analysis has been impossible because of performance limitations in fusion detection algorithms. By engineering a new, more precise, algorithm and statistical approaches to post-analysis of fusions called in TCGA data, we report new recurrent gene fusions, including those that could be druggable; new candidate pan-cancer oncogenes based on their profiles in fusions; and prevalent, previously overlooked, candidate oncogenic gene fusions in ovarian cancer, a disease with minimal treatment advances in recent decades. The novel and reproducible statistical algorithms and, more importantly, the biological conclusions open the door for increased attention to gene fusions as drivers of cancer and for future research into using fusions for targeted therapy.

cancer biology↗

bioRxiv2017

HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo

Alternative pre-mRNA splicing plays a major role in expanding the transcript output of human genes. This process is regulated, in part, by the interplay of trans-acting RNA binding proteins (RBPs) with myriad cis-regulatory elements scattered throughout pre-mRNAs. These molecular recognition events are critical for defining the protein coding sequences (exons) within pre-mRNAs and directing spliceosome assembly on non-coding regions (introns). One of the earliest events in this process is recognition of the 3 splice site by U2 small nuclear RNA auxiliary factor 2 (U2AF2). Splicing regulators, such as the heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), influence spliceosome assembly both in vitro and in vivo, but their mechanisms of action remain poorly described on a global scale. HNRNPA1 also promotes proof reading of 3ss sequences though a direct interaction with the U2AF heterodimer. To determine how HNRNPA1 regulates U2AF-RNA interactions in vivo, we analyzed U2AF2 RNA binding specificity using individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) in control- and HNRNPA1 over-expression cells. We observed changes in the distribution of U2AF2 crosslinking sites relative to the 3 splice sites of alternative cassette exons but not constitutive exons upon HNRNPA1 over-expression. A subset of these events shows a concomitant increase of U2AF2 crosslinking at distal intronic regions, suggesting a shift of U2AF2 to \"decoy\" binding sites. Of the many non-canonical U2AF2 binding sites, Alu-derived RNA sequences represented one of the most abundant classes of HNRNPA1-dependent decoys. Splicing reporter assays demonstrated that mutation of U2AF2 decoy sites inhibited HNRNPA1-dependent exon skipping in vivo. We propose that HNRNPA1 regulates exon definition by modulating the interaction of U2AF2 with decoy or bona fide 3 splice sites.

molecular biology↗