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1000 Titel
  • Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes
1000 Autor/in
  1. Schindler, Stefanie |
  2. Szafranski, Karol |
  3. Hiller, Michael |
  4. Ali, Gul Shad) |
  5. Palusa, Saiprasad G. |
  6. Backofen, Rolf |
  7. Reddy, Anireddy S. N. |
  8. Platzer, Matthias |
1000 Erscheinungsjahr 2008
1000 Art der Datei
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2008-04-10
1000 Erschienen in
1000 Quellenangabe
  • 9: 159
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2008
1000 Lizenz
1000 Verlagsversion
  • http://dx.doi.org/10.1186/1471-2164-9-159 |
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375911/ |
1000 Ergänzendes Material
  • http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-159#Declarations |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • BACKGROUND: Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes. RESULTS: In a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes. CONCLUSION: NAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.
1000 Fachgruppe
  1. Medizin |
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://frl.publisso.de/adhoc/creator/U2NoaW5kbGVyLCBTdGVmYW5pZQ==|https://frl.publisso.de/adhoc/creator/U3phZnJhbnNraSwgS2Fyb2w=|https://frl.publisso.de/adhoc/creator/SGlsbGVyLCBNaWNoYWVs|https://frl.publisso.de/adhoc/creator/QWxpLCBHdWwgU2hhZCk=|https://frl.publisso.de/adhoc/creator/UGFsdXNhLCBTYWlwcmFzYWQgRy4=|https://frl.publisso.de/adhoc/creator/QmFja29mZW4sIFJvbGY=|https://frl.publisso.de/adhoc/creator/UmVkZHksIEFuaXJlZGR5IFMuIE4u|http://orcid.org/0000-0003-0596-8582
1000 Förderer
  1. German Ministry of Education and Research |
  2. Deutsche Forschungsgemeinschaft |
  3. Department of Energy |
1000 Fördernummer
  1. 0313652D
  2. SFB604-02
  3. DE-FG02-04ER15556
1000 Förderprogramm
  1. -
  2. -
  3. -
1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer German Ministry of Education and Research |
    1000 Förderprogramm -
    1000 Fördernummer 0313652D
  2. 1000 joinedFunding-child
    1000 Förderer Deutsche Forschungsgemeinschaft |
    1000 Förderprogramm -
    1000 Fördernummer SFB604-02
  3. 1000 joinedFunding-child
    1000 Förderer Department of Energy |
    1000 Förderprogramm -
    1000 Fördernummer DE-FG02-04ER15556
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6402765.rdf
1000 Erstellt am 2017-06-02T12:04:35.245+0200
1000 Erstellt von 21
1000 beschreibt frl:6402765
1000 Bearbeitet von 218
1000 Zuletzt bearbeitet Mon Apr 30 13:43:31 CEST 2018
1000 Objekt bearb. Mon Apr 30 13:43:30 CEST 2018
1000 Vgl. frl:6402765
1000 Oai Id
  1. oai:frl.publisso.de:frl:6402765 |
1000 Sichtbarkeit Metadaten public
1000 Sichtbarkeit Daten public
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