Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism

Seo, Pil Joon; Kim, Mi Jung; Ryu, Jaeyong; Jeong, Euigyung; Park, Chung‐Mo

doi:10.1038/ncomms1303

Cited by 148 publications

(174 citation statements)

References 28 publications

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“…Additionally, AS has also been functionally implicated in nutrient metabolism. For example, the Arabidopsis TF gene IDD14 generates two splicing variants to competitively form nonfunctional heterodimers to regulate starch metabolism (Seo et al, 2011). In our RNA-seq data of maize embryo and endosperm, 50.7% of multiexonic genes were found to undergo AS, which is higher than that in Arabidopsis and rice (Filichkin et al, 2010;Lu et al, 2010).…”

Section: Embryo and Endosperm Exhibit Differential As Patternsmentioning

confidence: 76%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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Transcriptome analysis of early-developing maize (Zea mays) seed was conducted using Illumina sequencing. We mapped 11,074,508 and 11,495,788 paired-end reads from endosperm and embryo, respectively, at 9 d after pollination to define gene structure and alternative splicing events as well as transcriptional regulators of gene expression to quantify transcript abundance in both embryo and endosperm. We identified a large number of novel transcribed regions that did not fall within maize annotated regions, and many of the novel transcribed regions were tissue-specifically expressed. We found that 50.7% (8,556 of 16,878) of multiexonic genes were alternatively spliced, and some transcript isoforms were specifically expressed either in endosperm or in embryo. In addition, a total of 46 trans-splicing events, with nine intrachromosomal events and 37 interchromosomal events, were found in our data set. Many metabolic activities were specifically assigned to endosperm and embryo, such as starch biosynthesis in endosperm and lipid biosynthesis in embryo. Finally, a number of transcription factors and imprinting genes were found to be specifically expressed in embryo or endosperm. This data set will aid in understanding how embryo/endosperm development in maize is differentially regulated.Maize (Zea mays) seeds are one of the most important crop materials that provide resources for food, feed, biofuel, and raw material for processing. Maize seed development initiates from double fertilization, in which two of the pollen sperms fuse with an egg cell and a central cell to produce embryo and endosperm, respectively (Randolph, 1936;Chaudhury et al., 2001). The main function of endosperm is to provide nutrient for the developing embryo and germinating embryo.After fertilization, the zygote undergoes an asymmetric division into a small apical cell and a large basal cell, giving rise to the embryo proper and the suspensor, respectively. The radial symmetry of the proembryo is shifted to a bilateral symmetry at the transition stage, which is characterized by protoderm formation. The shoot apical meristem and the root apical meristem can be distinguished at the onset of the coleoptile stage, and then the position of the future coleoptile is marked by a small protuberance. The mature embryo is composed of the embryo axis, which is formed by the plumule with five or six short internodes, and leaf primordia and primary root surrounded by the coleoptile and the coleorhiza, respectively, and the scutellum (Randolph, 1936;Abbe and Stein, 1954;Diboll, 1968;Lammeren, 1986;Vernoud et al., 2005).Maize endosperm follows the nucleus-type endosperm development, where the fertilized central cell undergoes several rounds of synchronous division in the absence of cell wall formation and cytokinesis to produce a syncytium (Lopes and Larkins, 1993;Olsen, 2004). Cellularization allows the formation of the internuclear radial microtubule systems and open-ended alveolation from the periphery of the endosperm toward the central vacuole (Olsen et al., ...

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Section: Embryo and Endosperm Exhibit Differential As Patternsmentioning

confidence: 76%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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“…regulation of the transcription factor activity [64]. The occurrence of AS in transcription factors intimates to another level of relationship between transcription and splicing [63].…”

Section: Functional Ontology Of As Genesmentioning

confidence: 99%

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

et al. 2015

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a b s t r a c tIn this study, using homology mapping of assembled expressed sequence tags against the genomic data, we identified alternative splicing events in barley. Results demonstrated that intron retention is frequently associated with specific abiotic stresses. Network analysis resulted in discovery of some specific sub-networks between miRNAs and transcription factors in genes with high number of alternative splicing, such as cross talk between SPL2, SPL10 and SPL11 regulated by miR156 and miR157 families. To confirm the alternative splicing events, elongation factor protein (MLOC_3412) was selected followed by experimental verification of the predicted splice variants by Semi quantitative Reverse Transcription PCR (qRT-PCR). Our novel integrative approach opens a new avenue for functional annotation of alternative splicing through regulatory-based network discovery.

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“…Both dominant-negative mutations and splice variants of TFs have been extensively studied in animals (15)(16)(17)(18). In plants, there are two very recent reports on two alternative splice forms in Arabidopsis TFs that act as regulators inhibiting their full-size gene product from activating a direct downstream target (19,20). In animals, a dominant negative is often an antagonist of a set of targets or of multiple members of a TF family (17,18).…”

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confidence: 99%

Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa

Lin

Sun

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

134

164

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Secondary Wall-Associated NAC Domain 1s (SND1s) are transcription factors (TFs) known to activate a cascade of TF and pathway genes affecting secondary cell wall biosynthesis (xylogenesis) in Arabidopsis and poplars. Elevated SND1 transcriptional activation leads to ectopic xylogenesis and stunted growth. Nothing is known about the upstream regulators of SND1. Here we report the discovery of a stem-differentiating xylem (SDX)-specific alternative SND1 splice variant, PtrSND1-A2 IR , that acts as a dominant negative of SND1 transcriptional network genes in Populus trichocarpa. PtrSND1-A2 IR derives from PtrSND1-A2, one of the four fully spliced PtrSND1 gene family members (PtrSND1-A1, -A2, -B1, and -B2). Each full-size PtrSND1 activates its own gene, and all four full-size members activate a common MYB gene (PtrMYB021). PtrSND1-A2 IR represses the expression of its PtrSND1 member genes and PtrMYB021. Repression of the autoregulation of a TF family by its only splice variant has not been previously reported in plants. PtrSND1-A2 IR lacks DNA binding and transactivation abilities but retains dimerization capability. PtrSND1-A2 IR is localized exclusively in cytoplasmic foci. In the presence of any full-size PtrSND1 member, PtrSND1-A2 IR is translocated into the nucleus exclusively as a heterodimeric partner with full-size PtrSND1s. Our findings are consistent with a model in which the translocated PtrSND1-A2 IR lacking DNA-binding and transactivating abilities can disrupt the function of full-size PtrSND1s, making them nonproductive through heterodimerization, and thereby modulating the SND1 transcriptional network. PtrSND1-A2 IR may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth.

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Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism

Cited by 148 publications

References 28 publications

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa

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