Talk abstracts
Talk on Friday 01:15-01:30pm submitted by Cassia Williams-Rogers
RNA binding proteins, upstream open reading frames, and translational control of human gene expression
Cassia Williams-Rogers (Department of Biological Sciences, Carnegie Mellon University), Matthew Agar-Johnson (Department of Biological Sciences, Carnegie Mellon University), Gemma May (Department of Biological Sciences, Carnegie Mellon University), Joel McManus (Department of Biological Sciences, Carnegie Mellon University)
Abstract:
Translation is an integral part of the conversion of DNA’s genetic information into functional proteins. Translation is controlled at the initiation step by the scanning of the preinitiation complex (PIC) along the 5’ transcript leader until the start codon is recognized. Upstream open reading frames (uORFs) that present potential start sites for translation in the 5’ transcript leader generally suppress translation of downstream genes, but the mechanisms by which uORF usage is regulated are not well defined. Previous work in Drosophila has proposed a translational control mechanism in which the RNA binding protein (RBP) Sex-lethal increases uORF usage in msl-2 and other transcripts by binding immediately downstream of uORF start codons (Medenbach, et al., 2011). However, whether uORF regulation in humans occurs by the same mechanism remains unknown. To address this, we performed large scale computational analyses of human transcript annotations and RBP site conservation and frequency data from GENCODE and the ENCODE project (Van Nostrand, et al., 2020) to investigate the potential role of RBPs in human uORF regulation. We found 5,963 genes with highly conserved AUG uORFs that are enriched for functions and processes related to control of transcription and neuronal / neurotransmitter activity. Furthermore, 281 of these genes have both highly conserved AUG uORFs and downstream RBP binding sites and have even greater enrichment in RNA polymerase II related activities, serine / threonine kinase activity, and chromatin modification functions (P < 0.05). Most notably, using publicly available ribosome profiling data we found that uORFs with downstream RBP binding sites have ~1.5-fold higher ribosome occupancy (p = 3.31e-7) than uORFs without such sites. We will discuss ongoing experiments to test human RBPs regulation of uORF activity using tissue culture reporter assays. Overall, these results suggest novel roles for human RBPs in regulating hundreds of uORFs from critical genes.
Keywords: RNA binding proteins (RBPs), upstream open reading frames (uORFs)