Evidence map›Paper›PMID 29386352›Full record

ArticleThe Journal of biological chemistry2018

Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response.

Gary Loughran, Irwin Jungreis, Ioanna Tzani, Michael Power, Ruslan I Dmitriev, Ivaylo P Ivanov, Manolis Kellis, John F Atkins

Open access · hybridAbstract read
In one paragraph

Article in The Journal of biological chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed
4.5field-weighted citation impact, top 4% 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

37 citing papers in PubMed, 80 citations in OpenAlex.

  1. RNAViruses · 2026
    Review
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Distal nucleotides affect the rate of stop codon read-through.Quantitative biology (Beijing, China) · 2023
    Article
  15. Article
  16. Article
  17. Insights into high-risk multiple myeloma from an analysis of the role of PHF19 in cancer.Journal of experimental & clinical cancer research : CR · 2021
    Review
  18. Article
  19. Article
  20. Nonsense suppression therapies in human genetic diseases.Cellular and molecular life sciences : CMLS · 2021
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 2 institutions in 2 countries.

Gary LoughranFrom the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, g.loughran@ucc.ie.
Irwin JungreisComputer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, and.
Ioanna TzaniFrom the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Michael PowerFrom the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Ruslan I DmitrievFrom the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Ivaylo P IvanovFrom the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Manolis KellisComputer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, and.
John F AtkinsFrom the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, j.atkins@ucc.ie.
University College Cork · IEMassachusetts Institute of Technology · US

Funding

GENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3M
Regulatory Morif Discovery in the Human Genome Using Comparative GenomicsR01HG004037 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI KELLIS, MANOLIS · 2007 to 2015
$3.9M
NHGRI NIH HHS R01 HG004037NHGRI NIH HHS U41 HG007234Wellcome Trust
6 · The paper itself

Abstract

Although stop codon readthrough is used extensively by viruses to expand their gene expression, verified instances of mammalian readthrough have only recently been uncovered by systems biology and comparative genomics approaches. Previously, our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon readthrough of several mammalian genes, all of which have been validated experimentally. Four mRNAs display highly efficient stop codon readthrough, and these mRNAs have a UGA stop codon immediately followed by CUAG (UGA_CUAG) that is conserved throughout vertebrates. Extending on the identification of this readthrough motif, we here investigated stop codon readthrough, using tissue culture reporter assays, for all previously untested human genes containing UGA_CUAG. The readthrough efficiency of the annotated stop codon for the sequence encoding vitamin D receptor (VDR) was 6.7%. It was the highest of those tested but all showed notable levels of readthrough. The VDR is a member of the nuclear receptor superfamily of ligand-inducible transcription factors, and it binds its major ligand, calcitriol, via its C-terminal ligand-binding domain. Readthrough of the annotated

Indexed as

Codon, TerminatorProtein BiosynthesisCalcitriolCalcium Channel AgonistsGene Expression RegulationHEK293 CellsHeLa CellsHumansOpen Reading FramesReceptors, CalcitriolRNA, MessengerCalcitriolCalcium Channel AgonistsCodon, TerminatorReceptors, CalcitriolRNA, MessengerVDR protein, humancalcitriolnuclear receptorPhyloCSFreadthroughstop codontranscription factortransfer RNA (tRNA)translation release factorVDRvitamin D

Identifiers

PMID29386352
PMCPMC5868278
OpenAlexW2786236873

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.