Genomics

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Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_4]


ABSTRACT: Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. These distinct ribosome conformational states revealed by ribosome profiling are seen in all eukaryotes tested including fungi, worms and mammals. This high-resolution ribosome profiling approach reveals the anticipated Rck2-dependent inhibition of translocation through eEF2 phosphorylation during hyperosmotic stress. These same approaches reveal a strong translation elongation arrest during oxidative stress where the ribosomes are trapped in a pre-translocation state, but in this case the translational arrest is independent of Rck2-driven eEF2 phosphorylation. These results provide new insights and approaches for defining the molecular events that impact translation elongation throughout biology. Overall design: 24 biological samples are included for ribosome footprinting samples. These include HeLa, MB-MDA-231 and yeast cells and C. elegans embryos.

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Colin Wu 

PROVIDER: GSE115161 | GEO | 2019-01-27

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE115161_CHXANS_21ntRPF_occupancy.csv.gz Csv
GSE115161_CHXTIG_21ntRPF_occupancy2.csv.gz Csv
GSE115161_Mammalian_21ntRPF_occupancy.csv.gz Csv
GSE115161_RAW.tar Raw
filelist.txt Txt
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