Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

Abstract

SummaryThere are ∼650,000 Alu elements in transcribed regions of the human genome. These elements contain cryptic splice sites, so they are in constant danger of aberrant incorporation into mature transcripts. Despite posing a major threat to transcriptome integrity, little is known about the molecular mechanisms preventing their inclusion. Here, we present a mechanism for protecting the human transcriptome from the aberrant exonization of transposable elements. Quantitative iCLIP data show that the RNA-binding protein hnRNP C competes with the splicing factor U2AF65 at many genuine and cryptic splice sites. Loss of hnRNP C leads to formation of previously suppressed Alu exons, which severely disrupt transcript function. Minigene experiments explain disease-associated mutations in Alu elements that hamper hnRNP C binding. Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-wide sentinel protecting the transcriptome. The findings have important implications for human evolution and disease.

Function of HNRNPC in breast cancer cells by controlling the dsRNA‐induced interferon response

“…Accumulation of some dsRNA regions was indeed observed after HNRNPC knock‐down. These elevated dsRNA species were mostly found in introns, corroborating known transcriptome‐wide HNRNPC binding regions (Konig et al , 2010; Zarnack et al , 2013). This differs from previous observation of elevated dsRNA derived from normally hypermethylated endogenous retroviruses (ERVs) that are activated by anti‐tumor inhibitors to trigger the IFN response as a therapeutic approach (Chiappinelli et al , 2015; Roulois et al , 2015; Goel et al , 2017).…”

“…Further studies revealed that HNRNPC is essential for repression of aberrant exonization of the Alu elements in the introns, and loss of HNRNPC resulted in abnormal inclusion of Alu in the transcripts (Zarnack et al , 2013). Therefore, we suspect that the newly discovered dsRNA‐controlling function of HNRNPC is a consequence of the well‐appreciated function of HNRNPC in regulating RNA splicing.…”

“…These transcripts are subjected to cytoplasmic RNA quality control mechanisms, e.g., nonsense‐mediated decay (NMD) of mRNAs with premature stop codons or truncated open reading frames (Zarnack et al , 2013; Attig et al , 2016), and thereby give rise to dsRNA fragments as a by‐product. Regulator of nonsense transcripts 1 (UPF1) is required for such RNA recycle machinery (Popp & Maquat, 2014).…”

“…The RBP HNRNPC has attracted much attention in the recent years, for its multiplex functions in regulating pre‐mRNA splicing (Konig et al , 2010; Zarnack et al , 2013), mRNA stabilization (Shetty, 2005), length‐dependent exportation (McCloskey et al , 2012), stability and translation (Holcik et al , 2003; Kim et al , 2003; Schepens et al , 2007), etc. Although HNRNPC has been shown to regulate multiple cancer‐related genes, mostly through RNA‐related processes, understanding about the accountable machinery for the function of HNRNPC in tumors is still limited.…”

“…This differs from previous observation of elevated dsRNA derived from normally hypermethylated endogenous retroviruses (ERVs) that are activated by anti‐tumor inhibitors to trigger the IFN response as a therapeutic approach (Chiappinelli et al , 2015; Roulois et al , 2015; Goel et al , 2017). Heterogeneous nuclear ribonucleoprotein C is well known for its function in regulating RNA splicing by binding with introns, especially the introns containing Alu (Konig et al , 2010; Zarnack et al , 2013). Indeed, almost all the up‐regulated dsRNA regions contain Alu or Alu fragments.…”