A conserved short 3 ´UTR short motif regulates gene expression in vertebrates

The mRNA 3' untranslated region contains important regulatory elements of gene expression, including upstream sequence elements (USEs), which modulate pre-mRNA 3'end processing and alternative polyadenylation. One of the best functionally characterized USE, located in the 3'UTR of the Drosophila polo gene, when disrupted, leads to downregulation of its expression and critical phenotypes in adult flies. Here, we found that the most conserved region of this USE (DplUSE) is also present in the 3'UTR of vertebrate genes, including zebrafish, mouse and human genes. Using reporter assays, we show that DplUSE increases gene expression in vitro in human cell lines and in vivo in zebrafish embryos. Importantly, in humans, DplUSE-containing genes are enriched in processes associated with serious diseases such as Congenital abnormalities. Concomitantly, we show that proper zebrafish development is disrupted when sequestering the molecular machinery that operates at the DplUSE, using a dominant negative strategy. As part of this molecular machinery, we found that the RNA binding protein PTBP1, PTBP1/hnRNPI, which has been previously shown to control USE-mediated gene expression in human cells, is also required for the DplUSE function in human cells, as previously found for the fruit fly 31 orthologue Heph, suggesting an ultra-conserved mechanism present in distantly related bilateria. We also found that the SNP associated with malignant tumor of colon in the oncogene C11or53/POU2AF2, is located within a DplUSE creating an ectopic consensus of DplUSE, which causes a gain of function in zebrafish gut. Moreover, in human cells, this SNP leads to an increase in mRNA and protein levels, indicating a possible mechanism of disease in colon cancer driven by disruption of the DplUSE. Taken together, these results show that a short 3'UTR motif in diverse bilaterian genes controls their mRNA expression levels via conserved RBP binding, with human disease implications. Overall design: RNA-seq profiling of human HeLa cells with PTBP1 knockdown (siPTBP1) and a siRNA Non-target control (siNTC)