Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. (Q35860653)

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17 January 2020

title

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis (English)

1 reference

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alternative mRNA splicing, via spliceosome

17 January 2020

main subject

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1

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17 January 2020

Yamile Marquez

5

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17 January 2020

Huy Q Dinh

11

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17 January 2020

Andrea Barta

12

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17 January 2020

author name string

Craig G Simpson

2

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17 January 2020

Naeem H Syed

3

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17 January 2020

Dominika Lewandowska

4

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17 January 2020

Branislav Kusenda

6

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17 January 2020

Jacqueline Marshall

7

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17 January 2020

John Fuller

8

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17 January 2020

Linda Cardle

9

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17 January 2020

Jim McNicol

10

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17 January 2020

John W S Brown

13

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17 January 2020

language of work or name

English

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publication date

29 November 2011

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17 January 2020

published in

Nucleic Acids Research

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17 January 2020

volume

40

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17 January 2020

page(s)

2454-2469

1 reference

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17 January 2020

issue

6

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Creative Commons Attribution-NonCommercial 3.0 Unported

17 January 2020

copyright license

start time

11 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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11 July 2018

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Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping

11 July 2018

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Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors

11 July 2018

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Genome-wide mapping of alternative splicing in Arabidopsis thaliana

11 July 2018

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High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans

11 July 2018

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Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

11 July 2018

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Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus.

11 July 2018

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SR proteins in vertical integration of gene expression from transcription to RNA processing to translation

11 July 2018

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Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila

11 July 2018

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

11 July 2018

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Execution of nonsense-mediated mRNA decay: what defines a substrate?

11 July 2018

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The spliceosome: design principles of a dynamic RNP machine

11 July 2018

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Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis

11 July 2018

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Kill the messenger: mRNA decay and plant development

11 July 2018

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Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.

11 July 2018

1 reference

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Alternative isoform regulation in human tissue transcriptomes

11 July 2018

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Widespread impact of nonsense-mediated mRNA decay on the yeast intronome

11 July 2018

1 reference

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Genome-wide analyses of alternative splicing in plants: opportunities and challenges.

11 July 2018

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11 July 2018

The meaning of nonsense

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Alternative splicing regulation during C. elegans development: splicing factors as regulated targets

11 July 2018

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Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay

11 July 2018

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Messenger RNA regulation: to translate or to degrade

11 July 2018

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Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function

11 July 2018

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mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons.

11 July 2018

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Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay

11 July 2018

1 reference

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The nonsense-mediated decay RNA surveillance pathway

11 July 2018

1 reference

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Stability of plant mRNAs depends on the length of the 3'-untranslated region.

11 July 2018

1 reference

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Both introns and long 3'-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins

11 July 2018

1 reference

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Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection

11 July 2018

1 reference

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Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Understanding alternative splicing: towards a cellular code

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Function of alternative splicing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

The evolving roles of alternative splicing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

An unappreciated role for RNA surveillance

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Mechanisms of alternative pre-messenger RNA splicing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Control of eukaryotic protein synthesis by upstream open reading frames in the 5'-untranslated region of an mRNA

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Alternative splicing: increasing diversity in the proteomic world

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Upstream open reading frames as regulators of mRNA translation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Alternative pre-mRNA splicing: the logic of combinatorial control

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

A regulatory mechanism that detects premature nonsense codons in T-cell receptor transcripts in vivo is reversed by protein synthesis inhibitors in vitro

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense-mediated mRNA decay pathway

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

The RNA binding protein ELF9 directly reduces SUPPRESSOR OF OVEREXPRESSION OF CO1 transcript levels in arabidopsis, possibly via nonsense-mediated mRNA decay.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

The cytosolic protein response as a subcomponent of the wider heat shock response in Arabidopsis.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Arabidopsis SMG7 protein is required for exit from meiosis.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Nonsense-mediated mRNA decay (NMD) silences the accumulation of aberrant trypsin proteinase inhibitor mRNA in Nicotiana attenuata.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

Intron retention is a major phenomenon in alternative splicing in Arabidopsis.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315328

A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKR932

Structural and compositional features of untranslated regions of eukaryotic mRNAs

21 January 2018

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Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKR932

Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts

21 January 2018

1 reference

12 December 2020

Optimal spliced alignment of homologous cDNA to a genomic DNA template

1 reference

12 December 2020

UPF3 suppresses aberrant spliced mRNA in Arabidopsis

1 reference

12 December 2020

The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis

1 reference

12 December 2020

Context analysis of termination codons in mRNA that are recognized by plant NMD

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKR932

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22127866%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22127866%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

1 reference