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Series GSE168595 Query DataSets for GSE168595
Status Public on Aug 10, 2021
Title Codon usage and protein length-dependent feedback from translation elongation to translation initiation and kinetics
Organism Neurospora crassa
Experiment type Expression profiling by high throughput sequencing
Summary In yeast and mammals, activated GCN2 can phosphorylate its substrate eIF2α, which is a part of the eIF2-GTP-Met-tRNAiMet ternary complex. The eIF2α phosphorylation blocks the ternary complex formation and therefore inhibits translation initiation. Meanwhile, GCN2 activation associates with ribosomes and some translation elongation factors such as eEF1A. In Neurospora crassa, the homolog of GCN2 is CPC-3. Ribosome profiling and accompanying RNA-seq experiments in this project were used to explore the effects of CPC-3 on translation kinetics. Here we show that poor codon usage of mRNAs with long CDS preferentially causes CPC-3 activation, which in turn suppresses the translation initiation and elongation in both codon usage and CDS length dependent manner.
 
Overall design The ribosome protected fragment (RPF) profiles and transcription profiles of Δcpc-3 and wild-type strains of Neurospora crassa were generated by high-throughput sequencing
 
Contributor(s) Lyu X, Liu Y
Citation(s) 34417614
Submission date Mar 09, 2021
Last update date Sep 29, 2021
Contact name xueliang lyu
E-mail(s) lvxueliang0715@aliyun.com
Organization name UT Southwestern Medical Center
Department Physiology
Lab Yi Liu
Street address 6001 Forest Park Road
City Dallas
State/province Texas
ZIP/Postal code 75235
Country USA
 
Platforms (2)
GPL16164 Illumina HiSeq 2000 (Neurospora crassa)
GPL29831 DNBSEQ-G400 (Neurospora crassa)
Samples (33)
GSM5150307 Ribo-WT-1wt_1
GSM5150308 Ribo-WT-1wt_2
GSM5150309 Ribo-WT-1wt_3
Relations
BioProject PRJNA708348
SRA SRP310013

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Supplementary file Size Download File type/resource
GSE168595_RAW.tar 7.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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