Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes

Schindler, Stefanie; Szafranski, Karol; Hiller, Michael; Gul Shad Ali; Palusa, Saiprasad G.; Backofen, Rolf; Platzer, Matthias; Reddy, Anireddy S. N.
January 2008
BMC Genomics;2008, Vol. 9, Special section p1
Academic Journal
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.


Related Articles

  • Characterization of paralogous protein families in rice. Haining Lin; Shu Ouyang; Egan, Amy; Nobuta, Kan; Haas, Brian J.; Wei Zhu; Xun Gu; Silva, Joana C.; Meyers, Blake C.; Buell, C. Robin // BMC Plant Biology;2008, Vol. 8, Special section p1 

    Background: High gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 Mb genome that has undergone segmental duplication of a substantial portion of its genome. This, coupled with...

  • Determining the transcriptional regulation pattern of PgTIP1 in transgenic Arabidopsis thaliana by constructing gene coexpression networks. Haiying Chen; Lu Ying; Jing Jin; Qi Li; Weiming Cai // Advances in Bioscience & Biotechnology;Dec2010, Vol. 1 Issue 5, p384 

    The seed size, seed mass, and growth rate of transgenic Arabidopsis plants containing PgTIP1, a ginseng tonoplast aquaporin gene, are significantly higher than those of wild-type Arabidopsis plants. Whole genome expression and bioinformatics analysis, including analysis of co-expression networks...

  • A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences. Trick, Martin; Foo Cheung; Drou, Nizar; Fraser, Fiona; Lobenhofer, Edward K.; Hurban, Patrick; Magusin, Andreas; Town, Christopher D.; Bancroft, Ian // BMC Plant Biology;2009, Vol. 9, Special section p1 

    Background: The Brassica species include an important group of crops and provide opportunities for studying the evolutionary consequences of polyploidy. They are related to Arabidopsis thaliana, for which the first complete plant genome sequence was obtained and their genomes show extensive,...

  • Genome wide gene expression in artificially synthesized amphidiploids of Arabidopsis. Fujimoto, Ryo; Taylor, Jennifer; Sasaki, Taku; Kawanabe, Takahiro; Dennis, Elizabeth // Plant Molecular Biology;Nov2011, Vol. 77 Issue 4/5, p419 

    The merging of two different genomes occurs during the formation of amphidiploids, and the merged regulatory networks have the potential to generate a new gene expression pattern. We examined the genome-wide gene expression of two newly synthesized amphidiploids between Arabidopsis thaliana and...

  • Impact of AtNHX1, a vacuolar Na+/H+ antiporter, upon gene expression during short- and long-term salt stress in Arabidopsis thaliana. Sottosanto, Jordan B.; Saranga, Yehoshua; Blumwald, Eduardo // BMC Plant Biology;2007, Vol. 7, p1 

    Background: AtNHX1, the most abundant vacuolar Na+/H+ antiporter in Arabidopsis thaliana, mediates the transport of Na+ and K+ into the vacuole, influencing plant development and contributing to salt tolerance. In this report, microarray expression profiles of wild type plants, a T-DNA insertion...

  • HR4 Gene Is Induced in the Arabidopsis-Trichoderma atroviride Beneficial Interaction. Sáenz-Mata, Jorge; Jiménez-Bremont, Juan Francisco // International Journal of Molecular Sciences;Jul2012, Vol. 13 Issue 7, p9110 

    Plants are constantly exposed to microbes, for this reason they have evolved sophisticated strategies to perceive and identify biotic interactions. Thus, plants have large collections of so-called resistance (R) proteins that recognize specific microbe factors as signals of invasion. One of...

  • Regulation of Sucrose Non-Fermenting Related Kinase 1 Genes in Arabidopsis thaliana. Williams, Sarah Phoebe; Rangarajan, Padma; Donahue, Janet L.; Hess, Jenna E.; Gillaspy, Glenda E. // Frontiers in Plant Science;Jun2014, Vol. 5, preceding p1 

    The Sucrose non-Fermenting Related Kinase 1 (SnRK1) proteins have been linked to regulation of energy and stress signaling in eukaryotes. In plants, there is a small SnRK1 gene family. While the SnRK1.1 gene has been well studied, the role other SnRK1 isoforms play in energy or stress signaling...

  • Arabidopsis thaliana gene expression microarray services. LaBrie, Sam; Turner, Lauré; Evertsz, Elizabeth; Hopkins, Chris; Shah, Sejal; Watson, Drew; Guegler, Karl // Nature Genetics;Nov99 Supplement, Vol. 23, p56 

    Presents an abstract for the article on a gene expression biochip for the analysis of the plant functional genomic system Arabidopsis thaliana.

  • A Genomic Region Upstream of Arabidopsis thaliana PELPK1 Promotes Transcription in Aleurone Tissues and in Response to Pseudomonas syringae or Pythium irregulare. Rashid, Abdur; Hobson, Neil; Deyholos, Michael // Plant Molecular Biology Reporter;Aug2013, Vol. 31 Issue 4, p1025 

    PELPK1 (At5g09530) is an Arabidopsis thaliana gene that encodes a putative intrinsically disordered protein, which, when overexpressed, accelerates germination. We cloned a 1,085-bp genomic fragment from upstream of PELPK1 and tested its ability to direct gene expression in a transcriptional...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics