Abstract:
:Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Fuchs A,Riegler S,Ayatollahi Z,Cavallari N,Giono LE,Nimeth BA,Mutanwad KV,Schweighofer A,Lucyshyn D,Barta A,Petrillo E,Kalyna Mdoi
10.1093/nar/gkaa1260subject
Has Abstractpub_date
2021-01-25 00:00:00pages
1133-1151issue
2eissn
0305-1048issn
1362-4962pii
6066634journal_volume
49pub_type
杂志文章abstract::Earlier we have shown that exogenous expression of HIPPI, a molecular partner of Huntingtin interacting protein HIP-1, induces apoptosis and increases expression of caspases-1, -8 and -10 in HeLa and Neuro2A cells. The C-terminal pseudo death effector domain of HIPPI (pDED-HIPPI) specifically interacts with the putati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1011
更新日期:2010-01-01 00:00:00
abstract::Nuclei isolated from cultured mouse and rat cell lines initiated pre-rRNA chains at the correct site and with the correct nucleotide specificity (A for mouse, G for rat). Nucleic acid filter hybridization and S1 nuclease mapping were used to analyze the RNA products initiated with nucleoside (beta-S)triphosphates. Ini...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.21.8115
更新日期:1984-11-12 00:00:00
abstract::Genome-wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA-pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1060
更新日期:2008-04-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg126
更新日期:2003-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.4.1070
更新日期:1998-02-15 00:00:00
abstract::The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh123
更新日期:2004-01-01 00:00:00
abstract::Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp468
更新日期:2009-08-01 00:00:00
abstract::Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.14.4279
更新日期:1982-07-24 00:00:00
abstract::In Saccharomyces cerevisiae, RNA polymerase II assembly is probably initiated by the formation of the RPB3-RPB11 heterodimer. RPB3 is encoded by a single copy gene in the yeast, mouse and human genomes. The RPB11 gene is also unique in yeast and mouse, but in humans a gene family has been identified that potentially e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki672
更新日期:2005-06-24 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl783
更新日期:2007-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn918
更新日期:2009-02-01 00:00:00
abstract::We have determined the DNA sequence surrounding the transcription terminator following rpoC, the gene that codes for the beta' subunit of RNA polymerase in E. coli K12. The 2044 bp sequence obtained contains the distal 335 codons of rpoC followed by a 212 bp non-coding region and a second open reading frame (ORFa) of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.24.6827
更新日期:1981-12-21 00:00:00
abstract::Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesion...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky386
更新日期:2018-06-20 00:00:00
abstract::Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding differentially expressed genes in different samples or tissues rather than finding co-expressed genes. To fill this gap, we have deve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki480
更新日期:2005-07-01 00:00:00
abstract::A human telomere ends in a single-stranded 3' tail, composed of repeats of T2AG3. G-quadruplexes (GQs) formed from four consecutive repeats have been shown to possess high-structural and mechanical diversity. In principle, a GQ can form from any four repeats that are not necessarily consecutive. To understand the dyna...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz906
更新日期:2019-12-02 00:00:00
abstract::Superhelical PM2 DNA can be photochemically modified by u.v. irradiation. The variation of S20,w with dose shows the following characteristics. There is a linear increase from 28 to 31s produced by a low dose of u.v. irradiation (4,000 ergs/mm2). A plateau in S20,w occurs between 4,000 and 10,000 ergs/mm2. The S20,w t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.5.1243
更新日期:1977-01-01 00:00:00
abstract::Unlike most yeast ribosomal protein genes studied so far the genes coding for S24 and L46 are adjacent on the genome. Sequence analysis showed that the two genes are transcribed divergently, their initiation codons being 630 bp apart. Taking the respective ATG translation start sites as reference points, the 5'- end o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.3.701
更新日期:1985-02-11 00:00:00
abstract::The identification of genes with specific patterns of change (e.g. down-regulated and methylated) as phenotype drivers or samples with similar profiles for a given gene set as drivers of clinical outcome, requires the integration of several genomic data types for which an 'integrate by intersection' (IBI) approach is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1503
更新日期:2016-04-20 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv816
更新日期:2015-10-15 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2017-06-02 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.19.3805
更新日期:1995-10-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx515
更新日期:2017-09-06 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5363
更新日期:1991-10-11 00:00:00
abstract::Recent effective use of TAL Effectors (TALEs) has provided an important approach to the design and synthesis of sequence-specific DNA-binding proteins. However, it is still a challenging task to design and manufacture effective TALE modulators because of the limited knowledge of TALE-DNA interactions. Here we synthesi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku535
更新日期:2014-08-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa023
更新日期:2020-03-18 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.18.4283
更新日期:1980-09-25 00:00:00
abstract::The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq834
更新日期:2011-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky802
更新日期:2018-11-16 00:00:00
abstract::The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.2801
更新日期:1978-08-01 00:00:00
abstract::Intrinsic energetic and solvation factors contributing to the unusual structural and biochemical properties of N3'-phosphoramidate DNA analogs have been re-examined using a combination of quantum mechanical and molecular dynamics methods. Evaluation of the impact of the N3'-H substitution was performed via comparison ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.15.3219
更新日期:2001-08-01 00:00:00