Kiltschewskij et al. 2020 (PRJNA655417)

General Details

Title Transcriptome-wide analysis of mRNA translation and associated post-transcriptional regulatory mechanisms following neuronal membrane depolarisation
Organism
Number of Samples 12
Release Date 2020/08/05 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP276055
ENA SRP276055
GEO GSE155727
BioProject PRJNA655417

Publication

Title
Authors Kiltschewskij DJ,Cairns MJ
Journal International journal of molecular sciences
Publication Date 2020 Sep 25
Abstract Experience-dependent changes to neural circuitry are shaped by spatially-restricted activity-dependent mRNA translation. Although the complexity of mRNA translation in neuronal cells is widely appreciated, translational profiles associated with neuronal excitation remain largely uncharacterized, and the associated regulatory mechanisms are poorly understood. Here, we employed ribosome profiling, mRNA sequencing and small RNA sequencing to profile transcriptome-wide changes in mRNA translation after whole cell depolarization of differentiated neuroblast cultures, and investigate the contribution of sequence-specific regulatory mechanisms. Immediately after depolarization, a functional partition between transcriptional and translational responses was uncovered, in which many mRNAs were subjected to significant changes in abundance or ribosomal occupancy, but not both. After an extended (2 h) post-stimulus rest phase, however, these changes became synchronized, suggesting that there are different layers of post-transcriptional regulation which are temporally separated but become coordinated over time. Globally, changes in mRNA abundance and translation were found to be associated with a number of intrinsic mRNA features, including mRNA length, GC% and secondary structures; however, the effect of these factors differed between both post-depolarization time-points. Furthermore, small RNA sequencing revealed that miRNAs and tRNA-derived small RNA fragments were subjected to peak changes in expression immediately after stimulation, during which these molecules were predominantly associated with fluctuations in mRNA abundance, consistent with known regulatory mechanisms. These data suggest that excitation-associated neuronal translation is subjected to extensive temporal coordination, with substantial contributions from a number of sequence-dependent regulatory mechanisms.
PMC PMC7582590
PMID 32992958
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR12391503 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391506 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391509 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391512 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391515 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391518 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391521 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391524 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391527 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391530 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391533 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
SRR12391536 PRJNA655417 Homo sapiens Neuronally differentiated SH-SY5Y Ribo-Seq Cycloheximide
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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