[PMC free article] [PubMed] [Google Scholar] 9. dynamic phenotypes of eukaryotic cells. Through technological improvements DNMT1 in high-throughput sequencing and proteomics, it is now possible to follow gene expression from transcription to protein turnover (1C5). One of the remaining fundamental difficulties in modern biology CaMKII-IN-1 includes the unraveling of the full diversity of proteoforms (i.e. the different molecular forms of proteins) (6,7) expressed from single genes. An increasing line of evidence suggests that mRNA translation may both be a rapid means of gene expression control (8C10) as well as a major source of proteoforms (11C14). However, genes undergoing translational control (8,15) and regulation of proteoform expression (16C18) remain poorly investigated. Alternative translation initiation mechanisms allow to select between multiple start codons and open reading frames (ORFs) within a single mRNA molecule. Here, the scanning ribosomes may omit less efficient upstream start codons (e.g. non-AUG start codons and start codons embedded in a suboptimal nucleotide context) to initiate translation downstream in a process referred to as leaky scanning (8,19). Reinitiation, another alternative translation initiation mechanism (8,19,20), may occur when post-termination ribosomes are retained on the mRNA molecule after completing translation of an upstream ORF (uORF) and reused to CaMKII-IN-1 support translation of a proximal downstream ORF. A particular role in alternative translation was postulated for short ORFs situated in the mRNA 5? leaders (uORFs) or upstream and partially overlapping the main protein-coding sequence (CDS) (upstream-overlapping ORFs or u-oORFs). Due to the directionality of ribosomal scanning, these short ORFs may regulate protein translation (21,22) or even impact on the selection of alternative translation sites giving rise to alternative protein N-termini and thus N-terminal proteoforms (16C18). The importance of u(-o)ORFs was supported by sequencing of ribosome associated mRNA regions (ribosome profiling, or ribo-seq) (5,23) which provided evidence for the ubiquitous translation from non-AUG start sites situated outside annotated protein-coding regions. Prevalence of regulatory features in 5? leaders was further highlighted by translation complex profile sequencing (TCP-seq), a ribo-seq derived method, which specifically tracks the footprints of small ribosomal subunits during the scanning process (4). uORFs were characterized in a variety of organisms and conditions (9,10,24C26), and their impact on the translation efficiency of proteins was found to be conserved among orthologous genes (24,25). Considering the directionality of scanning, ribosome profiling experiments revealed that ribosomes distribute asymmetrically across ORFs, as they readily accumulate at translation initiation and termination sites (5), an effect which may be enlarged due to pretreatment with translation elongation inhibitors (5,27), overall warranting caution when interpreting uORF expression levels. Importantly however, further studies reveled that ribosome footprints of 5? leaders generally resemble those of coding sequences, suggesting genuine translation of these regions (23). Translation initiation is a determining control step in translation (28). In consequence, translational control is mainly facilitated by eukaryotic translation initiation factors (eIFs) which may readily respond to (extra)cellular conditions by changing the global rates of protein synthesis at the ribosome. To reduce the high energy cost of protein production, translational control through reinitiation can be triggered by eIF2 phosphorylation in response to nutrient deprivation and accumulation of unfolded proteins (15). On the other hand, eIF1 was shown to orchestrate leaky scanning by stabilizing open, scanning-competent conformation of the ribosome (29) and thereby regulate translation initiation rates at suboptimal translation initiation start sites (30,31). Besides, eIF1 protein levels and its phosphorylation have been linked to reprogrammed translation of uORFs (32,33) and responses CaMKII-IN-1 to stress stimuli, including arsenite (33); glucose or oxygen deprivation (10). Although eIF1 plays a central role in translation initiation (34), a genome-wide assessment of its role in translational regulation is lacking. By combining tailored proteomic strategies with ribosome profiling and mRNA sequencing we here identified the biological targets of the translation control exerted by eIF1. MATERIALS AND METHODS Cell culture The human colon cancer cell line HCT116 was kindly provided by the Johns Hopkins Sidney Kimmel Comprehensive Cancer Center CaMKII-IN-1 (Baltimore, USA). The HAP1 wild type and CRISPR/Cas9 engineered knockout cell lines were obtained from Horizon Genomics GmbH, Vienna. In particular, a single eIF1B knockout clone and two eIF1 knockout clones were.