(Q41903505)

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Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner.

scientific article published on 23 January 2015

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28 February 2020

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner (English)

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28 February 2020

Arabidopsis thaliana

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12

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28 February 2020

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Isao Ebina

1

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28 February 2020

Mariko Takemoto-Tsutsumi

2

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28 February 2020

Shun Watanabe

3

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28 February 2020

Hiroaki Koyama

4

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28 February 2020

Yayoi Endo

5

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28 February 2020

Kaori Kimata

6

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28 February 2020

Takuya Igarashi

7

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28 February 2020

Karin Murakami

8

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28 February 2020

Rin Kudo

9

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28 February 2020

Arisa Ohsumi

10

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28 February 2020

Abdul Latif Noh

11

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28 February 2020

Satoshi Naito

13

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28 February 2020

Hitoshi Onouchi

14

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28 February 2020

publication date

23 January 2015

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28 February 2020

Nucleic Acids Research

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28 February 2020

43

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28 February 2020

3

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28 February 2020

1562-1576

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28 February 2020

copyright license

Creative Commons Attribution-NonCommercial 4.0 International

7 November 2016

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April 2022 Public Data File from Crossref

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0 references

Ribosomes in a stacked array: elucidation of the step in translation elongation at which they are stalled during S-adenosyl-L-methionine-induced translation arrest of CGS1 mRNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Regulation of plant translation by upstream open reading frames.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Interactions of the TnaC nascent peptide with rRNA in the exit tunnel enable the ribosome to respond to free tryptophan

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Arrest peptides: cis-acting modulators of translation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Arabidopsis CBL-interacting protein kinase (CIPK6) is involved in plant response to salt/osmotic stress and ABA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Conserved Peptide Upstream Open Reading Frames are Associated with Regulatory Genes in Angiosperms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

The arginine attenuator peptide interferes with the ribosome peptidyl transferase center

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Arginine changes the conformation of the arginine attenuator peptide relative to the ribosome tunnel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Known and novel post-transcriptional regulatory sequences are conserved across plant families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Crucial elements that maintain the interactions between the regulatory TnaC peptide and the ribosome exit tunnel responsible for Trp inhibition of ribosome function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone deubiquitinase complexes in plant gene repression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Calcium-dependent modulation and plasma membrane targeting of the AKT2 potassium channel by the CBL4/CIPK6 calcium sensor/protein kinase complex.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Nascent polypeptide sequences that influence ribosome function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Phosphorylation of eIF2 facilitates ribosomal bypass of an inhibitory upstream ORF to enhance CHOP translation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Structural insight into nascent polypeptide chain-mediated translational stalling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

A ribosome-nascent chain sensor of membrane protein biogenesis in Bacillus subtilis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Sucrose control of translation mediated by an upstream open reading frame-encoded peptide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

The plasticity of a translation arrest motif yields insights into nascent polypeptide recognition inside the ribosome tunnel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Programmed drug-dependent ribosome stalling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Effects on translation pausing of alterations in protein and RNA components of the ribosome exit tunnel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

The RCC1 superfamily: from genes, to function, to disease.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Comparative genomic analysis of novel conserved peptide upstream open reading frames in Drosophila melanogaster and other dipteran species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Posttranscriptional regulation by the upstream open reading frame of the phosphoethanolamine N-methyltransferase gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

The dwarf phenotype of the Arabidopsis acl5 mutant is suppressed by a mutation in an upstream ORF of a bHLH gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

mRNA sequence features that contribute to translational regulation in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

A nascent polypeptide domain that can regulate translation elongation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Reinitiation and recycling are distinct processes occurring downstream of translation termination in yeast.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

S-adenosyl-L-methionine is an effector in the posttranscriptional autoregulation of the cystathionine gamma-synthase gene in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Scoring residue conservation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

The ribosomal exit tunnel functions as a discriminating gate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Regulatory nascent peptides in the ribosomal tunnel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Physical evidence for distinct mechanisms of translational control by upstream open reading frames

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Inhibition of CHOP translation by a peptide encoded by an open reading frame localized in the chop 5'UTR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

The mechanism of tryptophan induction of tryptophanase operon expression: tryptophan inhibits release factor-mediated cleavage of TnaC-peptidyl-tRNA(Pro).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Secretion monitor, SecM, undergoes self-translation arrest in the cytosol

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Upstream open reading frames as regulators of mRNA translation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

A highly conserved mechanism of regulated ribosome stalling mediated by fungal arginine attenuator peptides that appears independent of the charging status of arginyl-tRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Ribosome stalling is responsible for arginine-specific translational attenuation in Neurospora crassa

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Recognition of AUG and alternative initiator codons is augmented by G in position +4 but is not generally affected by the nucleotides in positions +5 and +6.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Ribosome regulation by the nascent peptide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Coding sequence-dependent ribosomal arrest at termination of translation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Controlled proteolysis of nascent polypeptides in rat liver cell fractions. I. Location of the polypeptides within ribosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Partial resistance of nascent polypeptide chains to proteolytic digestion due to ribosomal shielding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

Site-directed mutagenesis by overlap extension using the polymerase chain reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

5 June 2018

BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

An inhibitory effect of the sequence-conserved upstream open-reading frame on the translation of the main open-reading frame of HsfB1 transcripts in Arabidopsis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

Molecular mechanism of drug-dependent ribosome stalling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

A dual upstream open reading frame-based autoregulatory circuit controlling polyamine-responsive translation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

Identification of a short highly conserved amino acid sequence as the functional region required for posttranscriptional autoregulation of the cystathionine gamma-synthase gene in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

Synchronous Arabidopsis suspension cultures for analysis of cell-cycle gene activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4330380

18 August 2018

Assaying chimeric genes in plants: The GUS gene fusion system

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV018

21 January 2018

Multisite ribosomal stalling: a unique mode of regulatory nascent chain action revealed for MifM

1 reference

https://pubmed.ncbi.nlm.nih.gov/25618853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evidence for autoregulation of cystathionine gamma-synthase mRNA stability in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/25618853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Polyamine-responsive ribosomal arrest at the stop codon of an upstream open reading frame of the AdoMetDC1 gene triggers nonsense-mediated mRNA decay in Arabidopsis thaliana

1 reference

https://pubmed.ncbi.nlm.nih.gov/25618853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effect of the sequence context of the AUG initiation codon on the rate of translation in dicotyledonous and monocotyledonous plant cells

1 reference

https://pubmed.ncbi.nlm.nih.gov/25618853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKV018

1 reference

Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25618853%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25618853%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25618853%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

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