Evidence map›Paper›PMID 37889754›Full record

ArticleCell reports2023

Molecular and functional characterization of the Drosophila melanogaster conserved smORFome.

Justin A Bosch, Nathan Keith, Felipe Escobedo, William W Fisher, James Thai LaGraff, Jorden Rabasco, Kenneth H Wan, Richard Weiszmann, Yanhui Hu, Shu Kondo and 3 more

Erratum issuedOpen access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.9field-weighted citation impact, top 24% 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

4 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors at 4 institutions in 2 countries.

Justin A BoschDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Nathan KeithDivision of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Felipe EscobedoDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
William W FisherDivision of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
James Thai LaGraffDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Jorden RabascoDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Kenneth H WanDivision of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Richard WeiszmannDivision of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Yanhui HuDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Shu KondoLaboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
James B BrownDivision of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jbbrown@lbl.gov.
Norbert PerrimonDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: perrimon@genetics.med.harvard.edu.
Susan E CelnikerDivision of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: secelniker@lbl.gov.
Lawrence Berkeley National Laboratory · USHarvard University · USHoward Hughes Medical Institute · USNational Institute of Genetics · JP

Funding

TRAINING GRANT IN GENETICST32GM007748 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI Anne O'Donnell-Luria, Louise Wilkins-Haug · 1985 to 2026
$12.0M
TRiP resources for modeling human diseaseR24OD030002 · OD · HARVARD MEDICAL SCHOOL · PI PERRIMON, NORBERT · 2020 to 2023
$3.2M
Systematic, Genome-Scale Functional Characterization of Conserved smORFsR01HG009352 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI CELNIKER, SUSAN E · 2017 to 2019
$3.0M
Using CRISPR technology to study the function of paralogous genesR24OD026435 · OD · HARVARD MEDICAL SCHOOL · PI BELLEN, HUGO J, PERRIMON, NORBERT · 2018 to 2021
$2.5M
Howard Hughes Medical InstituteNHGRI NIH HHS R01 HG009352NIGMS NIH HHS T32 GM007748NIH HHS R24 OD026435NIH HHS R24 OD030002
6 · The paper itself

Abstract

Short polypeptides encoded by small open reading frames (smORFs) are ubiquitously found in eukaryotic genomes and are important regulators of physiology, development, and mitochondrial processes. Here, we focus on a subset of 298 smORFs that are evolutionarily conserved between Drosophila melanogaster and humans. Many of these smORFs are conserved broadly in the bilaterian lineage, and ∼182 are conserved in plants. We observe remarkably heterogeneous spatial and temporal expression patterns of smORF transcripts-indicating wide-spread tissue-specific and stage-specific mitochondrial architectures. In addition, an analysis of annotated functional domains reveals a predicted enrichment of smORF polypeptides localizing to mitochondria. We conduct an embryonic ribosome profiling experiment and find support for translation of 137 of these smORFs during embryogenesis. We further embark on functional characterization using CRISPR knockout/activation, RNAi knockdown, and cDNA overexpression, revealing diverse phenotypes. This study underscores the importance of identifying smORF function in disease and phenotypic diversity.

Indexed as

Drosophila melanogasterPeptidesAnimalsGenomeHumansOpen Reading FramesPeptidesCP: GenomicsCRISPRDrosophilagene functiongene knockoutpeptideribosome profilingsmORF

Identifiers

PMID37889754
PMCPMC10843857
OpenAlexW4387961256

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.