Molecular Functions of Conserved Developmentally-Regulated GTP-Binding Protein Drg1 in Translation
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PROVIDER: PRJNA645425 | ENA |
REPOSITORIES: ENA
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Project description:Developmentally-regulated GTP-binding (Drg) proteins are important for embryonic development, cell growth, proliferation, and differentiation. Despite their highly conserved nature, the functions of Drg proteins in translation are unknown. Here, we performed a wide analysis of ribosome dynamic in S.cerevisiae Rbg1, Rbg2 and Slh1 depleted cells using 5Pseq (Pelechano et al. 2015 PMID 26046441), which allows the study of ribosome dynamics by sequencing the 5' phoshporylated mRNA co-translational degradation itermediates. We demonstrate the yeast Drg ortholog, Rbg1, alleviates ribosome pausing at Arginine/Lysine-rich regions in mRNAs, and mainly targets genes related to ribonucleoprotein complex biogenesis and non-coding RNA processing pathways.
2020-07-11 | GSE154212 | GEO
Project description:Developmentally regulated requirement for the conserved transcription factor Grainy head in determining chromatin accessibility
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Project description:A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit comparable translation levels and dynamics to annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions. 37 ribosome footprint samples from mouse BMDCs across a time course of LPS stimulation and in the presence or absence of translation inhibitors cycloheximide, harringtonine, or lactimidomycin. A mock (non-LPS stimulated) time course is also included, collected in the presence of cycloheximide. Two replicates are available for the LPS timecourse under CHX treatment.
2015-12-03 | E-GEOD-74139 | biostudies-arrayexpress
Project description:A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit comparable translation levels and dynamics to annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions.
2015-12-03 | GSE74139 | GEO
Project description:This project examined if sex differences in K48 polyubiquitination in the amygdala were developmentally regulated. This used basolateral amygdala (BLA) samples collected from 4 and 9 week old male and female Sprague-Dawley rats.
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Project description:Initiation factor 2 (eIF2) delivering the initiator methionine transfer RNA (Met-tRNAiMet) to the ribosome is a conserved key step in translation initiation. Argonaute (Ago) proteins were initially identified as eukaryotic translation initiation factor 2C,2 (EIF2C2). In the past 2 decades, Argonaute were extensively studied as a core component of RNA induced gene silencing, although various model raised the exact mechanism of Ago in translation repression remains elusive. Here we found Ago protein directly bind Met- tRNAiMet independent of miRNA binding, which interfere the formation of the ternary complex eIF2–GTP–Met- tRNAiMet. Ago proteins can solely inhibit protein synthesis via competing tRNAiMet with eIF2. Our findings elucidate a physical link between Ago and tRNAiMet and provide mechanistic insight into translation repression by Ago proteins.
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Project description:Nocte is an RNA binding protein but its functions in Drosophila eye development is unknown. We found that knockdown of nocte by RNAi in Drosophila eyes leads to small and rough eye phenotypes. We detected nocte's functions at mRNA levels by doing RNA-seq with purified polyA mRNA. We detected nocte's functions in mRNA translation by doing Ribo-seq and total RNA-seq to calculate the translation efficiencies.
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Project description:Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of human genes, we identified 5 Hox gene paralogs initiated by AUG codons in conserved suboptimal context as well as 13 Hox genes that contain evolutionarily conserved upstream open reading frames (uORFs) that initiate at AUG codons in poor sequence context. We analyzed published CAGE-seq data and generated CAGE-seq data from mRNAs from mouse somites. These data demonstrate that the 5’ leaders of Hox mRNAs of interest contain conserved uORFs, are much shorter than reported, and lack previously proposed IRES elements. We show that the conserved uORFs inhibit Hox reporter expression and that altering the stringency of start codon selection by overexpressing eIF1 or eIF5 modulates the expression of Hox reporters. We also show that modifying ribosome homeostasis by depleting a large ribosomal subunit protein or treating cells with sublethal concentrations of puromycin leads to lower stringency of start codon selection. Thus, altering global translation can confer gene-specific effects through altered start codon selection stringency.
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