GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE73357 Query DataSets for GSE73357
Status Public on Jun 15, 2017
Title Heterogeneous ribosomes exist and selectively translate distinct subpools of mRNAs in stem cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether ribosome heterogeneity at the level of core ribosomal proteins (RPs) enables ribosomes to preferentially translate specific mRNAs genome-wide. Here, we measured the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or depleted from select subsets of ribosomes within embryonic stem cells. We find that heterogeneity in RP composition endows ribosomes with different selectivity for translating subpools of transcripts including those controlling metabolism, the cell cycle, and development. As a paradigm example, we show that mRNAs enriched in binding to RPL10A/uL1-containing ribosomes require RPL10A/uL1 for their efficient translation. Within several of these transcripts, we find this level of regulation is mediated, at least in part, by internal ribosome entry sites. Together, these results reveal a critical functional link between ribosome heterogeneity and the post-transcriptional circuitry of gene expression.
Overall design To identify the transcripts specifically translated by ribosomes demarcated by RPL10A or RPS25, we enriched for RPL10A or RPS25-containing ribosomes by immunoprecipitation (IP), and performed RPL10A-Ribo-Seq and RPS25-Ribo-Seq (2 replicates each), with the control being total Ribo-Seq (2 replicates each). To further assess the translation efficiencies of mRNAs upon Rpl10a knockdown at genome-wide scale, we performed RNA-Seq (2 replicates each) of purified RNAs from combined medium and heavy polysome fractions containing the most actively translating ribosomes (>=4 ribosomes along a mRNA molecule), and from all other fractions containing the free ribonucleoproteins (RNPs), 40S/60S ribosomal free subunits, 80S/monosomes as well as light polysomes (2-3 ribosomes per mRNA molecule).
Contributor(s) Shi Z, Fujii K, Kovary K, Genuth N, Röst H, Teruel M, Barna M
Citation(s) 28625553
NIH grant(s)
Grant ID Grant title Affiliation Name
R21 HD086730 Characterizing the ribosome code controlling gene expression and cell fate specification STANFORD UNIVERSITY Maria Barna
Submission date Sep 23, 2015
Last update date May 15, 2019
Contact name Zhen Shi
Organization name Stanford
Street address 279 Campus Drive
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (20)
GSM1891620 Total Ribo-Seq (3xFLAG-Rpl10a cells)_rep1
GSM1891621 Total Ribo-Seq (3xFLAG-Rpl10a cells)_rep2
GSM1891622 RPL10A-Ribo-Seq (3xFLAG-Rpl10a cells)_rep1
BioProject PRJNA297039
SRA SRP064202

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE73357_RAW.tar 970.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap