Translation initiation site profiling reveals widespread synthesis of non-AUG-initiated protein isoforms in yeast
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PROVIDER: PRJNA631930 | ENA |
REPOSITORIES: ENA
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Project description:Genomic analyses in budding yeast have helped to define the foundational principles of eukaryotic gene expression, but have systematically excluded specific classes of potential coding regions, including those with non-AUG start codons. Without methods to define coding regions empirically, the prevalence of these non-canonical coding regions has been impossible to assess. Here, we applied an experimental approach to globally annotate translation initiation sites in yeast and identified a class of 149 genes that encode N-terminally extended alternate protein isoforms that result from translation initiation at non-AUG codons upstream of the annotated AUG start codon. These alternate isoforms are produced in concert with canonical isoforms and are translated with a high degree of specificity, resulting from initiation at only a small subset of possible start codons in 5’ leader regions. Their translation is enriched during meiosis, and is induced by low eIF5A levels, which are observed in this context. These findings reveal widespread production of non-canonical protein isoforms and, more generally, show unexpected complexity to the rules by which the budding yeast genome is decoded.
2020-07-24 | GSE150375 | GEO
Project description:Genomic analyses in budding yeast have helped define the foundational principles of eukaryotic gene expression. However, in the absence of empirical methods for defining coding regions, these analyses have historically excluded specific classes of possible coding regions, such as those initiating at non-AUG start codons. Here, we applied an experimental approach to globally annotate translation initiation sites in yeast and identified 149 genes with alternative N-terminally extended protein isoforms initiating from near-cognate codons upstream of annotated AUG start codons. These isoforms are produced in concert with canonical isoforms and translated with high specificity, resulting from initiation at only a small subset of possible start codons. The non-AUG initiation driving their production is enriched during meiosis and induced by low eIF5A, which is seen in this context. These findings reveal widespread production of non-canonical protein isoforms and unexpected complexity to the rules by which even a simple eukaryotic genome is decoded.
| S-EPMC7508262 | biostudies-literature
Project description:To investigate the differences of transcriptional activities between AUG-initiated c-Myc and CUG-initiated c-Myc , we performed a transcriptomic analysis using high throoughput RNA sequencing (RNA-seq).
2018-08-04 | GSE118113 | GEO
Project description:Aberrant translation initiation at non-AUG start codons is associated with multiple cancers and neurodegenerative diseases. Nevertheless, how non-AUG translation is regulated differently from canonical translation is poorly understood. We thus used start codon-selective reporters and ribosome profiling to characterize how translation from non-AUG start codons responds to protein synthesis inhibitors in human cells. These analyses surprisingly revealed that translation of non-AUG reporters and the endogenous GUG-encoded DAP5 (eIF4G2/p97) mRNA are resistant to cycloheximide (CHX), a translation inhibitor which slows but does not completely abrogate elongation. Our data suggest that slowly elongating ribosomes cause queuing of scanning pre-initiation complexes (PIC), preferentially enhancing otherwise poor recognition of non-AUG start codons. Consistent with this model, limiting PIC formation or scanning sensitizes non-AUG translation to CHX. Moreover, PIC queuing can cause translation from an AUG codon in a poor context to become less sensitive to CHX. We further find that non-AUG translation is resistant to other inhibitors that target ribosomes within the coding sequence, but not those targeting newly initiated ribosomes. In total, these data indicate that ribosome queuing enables mRNAs with poor initiation context, namely those from non-AUG start codons, to be resistant to pharmacological inhibitors.
2019-06-05 | GSE125086 | GEO
Project description:Next generation sequencing facilities quantitative analysis of KMST6 cells expressing AUG-initiated c-Myc and CUG-initiated c-Myc.
| PRJNA484493 | ENA
Project description:Negative elongation factor (NELF), a four-subunit protein complex in metazoan, plays an important role in regulating promoter-proximal pausing of RNA polymerase II (RNAPII). Genetic studies demonstrate that the B subunit of mouse NELF (NELF-B) is critical for embryonic development and homeostasis in adult tissue. We report here that both human and mouse NELF-B proteins are translated from a non-AUG codon upstream of the annotated AUG. This non-AUG codon sequence is conserved in mammalian NELF-B but not NELF-B orthologs of lower metazoan. The full-length and a truncated NELF-B that starts at the first AUG codon interact with the other three NELF subunits with comparable efficiency. Furthermore, these two forms of NELF-B have a similar impact on the transcriptomics and proliferation of mouse embryonic fibroblasts. These results strongly suggest that additional amino acid sequence upstream of the annotated AUG is dispensable for the essential function of NELF in supporting cell growth in vitro. While the majority of mouse adult tissues surveyed exclusively express the full-length NELF-B protein, mouse kidney only contains a truncated NELF-B protein with the same apparent size as the AUG-initiated version. This result raises the distinct possibility that translational initiation of mouse NELF-B is regulated in a tissue-dependent manner. triplicates for ATG-Nelf-B, triplicates for FL-Nelf-B
2014-10-11 | E-GEOD-62248 | biostudies-arrayexpress
Project description:We present RNA-Seq data for mice with mutated TERP (TERP-AUG and TERP-del7) and for mice from control groups (TERP-wt-AUG and TERP-del7-wt). TERP-AUG mutation leads to increased translation of TERP, and TERP-del7 mutation leads to the formation of nonfunctional TERP.
2023-03-31 | GSE228285 | GEO
Project description:Negative elongation factor (NELF), a four-subunit protein complex in metazoan, plays an important role in regulating promoter-proximal pausing of RNA polymerase II (RNAPII). Genetic studies demonstrate that the B subunit of mouse NELF (NELF-B) is critical for embryonic development and homeostasis in adult tissue. We report here that both human and mouse NELF-B proteins are translated from a non-AUG codon upstream of the annotated AUG. This non-AUG codon sequence is conserved in mammalian NELF-B but not NELF-B orthologs of lower metazoan. The full-length and a truncated NELF-B that starts at the first AUG codon interact with the other three NELF subunits with comparable efficiency. Furthermore, these two forms of NELF-B have a similar impact on the transcriptomics and proliferation of mouse embryonic fibroblasts. These results strongly suggest that additional amino acid sequence upstream of the annotated AUG is dispensable for the essential function of NELF in supporting cell growth in vitro. While the majority of mouse adult tissues surveyed exclusively express the full-length NELF-B protein, mouse kidney only contains a truncated NELF-B protein with the same apparent size as the AUG-initiated version. This result raises the distinct possibility that translational initiation of mouse NELF-B is regulated in a tissue-dependent manner.
2014-10-11 | GSE62248 | GEO
Project description:In response to environmental changes, cells flexibly and rapidly alter gene expression, through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is upregulated through upstream open reading frames (uORFs) that comprise only AUG and stop codons, in response to a shortage of boric acid in the environment. However, the molecular details of how the minimum uORF controls the translation of the downstream main ORF, in a boric acid concentration-dependent manner, have remained unclear. Here, combining ribosome profiling, TCP-Seq, structural analysis with cryo-electron microscopy, and biochemical assays, we showed that the 80S ribosome (80S) assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 (eRF1) on the 80S on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.
2023-09-19 | GSE223755 | GEO
Project description:Widespread control of alternative 3’UTR isoforms via transcription termination in archaea
| PRJEB14292 | ENA