Evidence map›Paper›PMID 28625553›Full record

ArticleMolecular cell2017

Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide.

Zhen Shi, Kotaro Fujii, Kyle M Kovary, Naomi R Genuth, Hannes L Röst, Mary N Teruel, Maria Barna

Open access · bronzeAbstract read
In one paragraph

Article in Molecular cell, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 397 papers.

0numbers the graph read from it
0cells of the map it votes in
397citing papers in PubMed
30.1field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

397 citing papers in PubMed, 668 citations in OpenAlex.

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  4. Dynamic evolution and hierarchical regulation of rDNA in polyploid oat.The Plant journal : for cell and molecular biology · 2026
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  14. RiboScreenBiomedicines · 2026
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  20. Perturbation of mitochondrial CaStress biology · 2026
    Article

337 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors at 1 institution in 1 country.

Zhen ShiDepartment of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Kotaro FujiiDepartment of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Kyle M KovaryDepartment of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
Naomi R GenuthDepartment of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
Hannes L RöstDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Mary N TeruelDepartment of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
Maria BarnaDepartment of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address: mbarna@stanford.edu.
Stanford University · US

Funding

Translational Oncology Research Program (Project-005)P30CA124435 · NCI · STANFORD UNIVERSITY · PI Vittorio Sebastiano · 2007 to 2026
$71.4M
TRAINING & OUTREACH COREP50GM107615 · NIGMS · STANFORD UNIVERSITY · PI FERRELL, JAMES E. · 2013 to 2017
$10.9M
Specialized Translational Control of Stem Cell Differentiation and Embryonic DevelopmentR01HD086634 · NICHD · STANFORD UNIVERSITY · PI BARNA, MARIA · 2016 to 2025
$5.5M
Specialized ribosomes in control of gene expression and embryonic developmentDP2OD008509 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BARNA, MARIA · 2011 to 2011
$2.3M
Controlling tissue size by noise and feedbackR01DK106241 · NIDDK · WEILL MEDICAL COLL OF CORNELL UNIV · PI TERUEL, MARY N · 2015 to 2018
$1.4M
Controlling the rate of adipocyte differentiation: Experiments and theoryR01DK101743 · NIDDK · WEILL MEDICAL COLL OF CORNELL UNIV · PI TERUEL, MARY N · 2015 to 2017
$1.1M
Characterizing the ribosome code controlling gene expression and cell fate specificationR21HD086730 · NICHD · STANFORD UNIVERSITY · PI BARNA, MARIA · 2016 to 2017
$431k
NCI NIH HHS P30 CA124435NICHD NIH HHS R01 HD086634NICHD NIH HHS R21 HD086730NIDDK NIH HHS R01 DK101743NIDDK NIH HHS R01 DK106241NIGMS NIH HHS P50 GM107615NIH HHS DP2 OD008509
6 · The paper itself

Abstract

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) exists and 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 differential selectivity for translating subpools of transcripts, including those controlling metabolism, cell cycle, and development. As an example, mRNAs enriched in binding to RPL10A/uL1-containing ribosomes are shown to require RPL10A/uL1 for their efficient translation. Within several of these transcripts, 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.

Indexed as

Protein BiosynthesisAnimalsCell LineDrosophila melanogasterDrosophila ProteinsEmbryonic Stem CellsGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksInternal Ribosome Entry SitesProtein Interaction MapsRibosomal ProteinsRibosomesRNA InterferenceRNA, MessengerTranscriptomeDrosophila ProteinsInternal Ribosome Entry SitesRibosomal ProteinsRNA, Messenger5′ UTR regulatory elementsgene regulationinternal ribosome entry site elementsIRES elementsribosome heterogeneityselected reaction monitoringSRMtranslational control

Identifiers

PMID28625553
PMCPMC5548184
OpenAlexW2625763766

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.