A conserved alternative splicing event in plants reveals an ancient exonization of 5S rRNA that regulates TFIIIA

Barbazuk, W. Brad

doi:10.4161/rna.7.4.12684

Cited by 12 publications

(20 citation statements)

References 34 publications

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“…TFIIIA possesses an ExonS event conserved across land plants (Fu et al 2009;Barbazuk 2010). This event was also identified in all species examined in our study.…”

Section: Resultsmentioning

confidence: 65%

“…In addition, TFIIIA is connected to the splicing protein network via RNA-binding protein (AT4G35785). TFIIIA has an ExonS event that is conserved across the land plants (Fu et al 2009;Barbazuk 2010). Similar to the network based on TFs in response to stress, we identified a close connection between the R2R3-MYB class with a splicing protein network via TFIID-1 (AT3G13445), and proline-rich spliceosomeassociated family protein (AT4G21660) (Figure 6).…”

Section: R2r3-myb Is Tightly Connected With a Plant-specific Sr Protementioning

confidence: 64%

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Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella. In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splicefactor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.

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“…TFIIIA possesses an ExonS event conserved across land plants (Fu et al 2009;Barbazuk 2010). This event was also identified in all species examined in our study.…”

Section: Resultsmentioning

confidence: 65%

Section: R2r3-myb Is Tightly Connected With a Plant-specific Sr Protementioning

confidence: 64%

Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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“…Insertions of the first intron from the UBQ10 gene into intronless genes markedly increased mRNA accumulation over 150-fold (Emami et al, 2013). Recently, plant 5S RNA mimic (discussed above), a naturally occurring alternatively spliced suicide exon (Hammond et al, 2009;Barbazuk, 2010), has been used to regulate gene expression at the premRNA splicing level (Hickey et al, 2012). In this case, skipping of a suicide exon produces a functional transcript, whereas inclusion of this exon generates a transcript that is a target for NMD.…”

Section: Potential Biotechnological Applications Of Asmentioning

confidence: 99%

Complexity of the Alternative Splicing Landscape in Plants

et al. 2013

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Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.

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“…The exon-skipping form encodes the full-length TFIIIA that contains nine ZFs (TFIIIA-9ZF); in contrast, the exoninclusion form has a predicted open reading frame encoding a TFIIIA variant that has only seven ZFs and lacks the first two ZFs of the TFIIIA-9ZF (Supplemental Figure 2). Although it had been initially suggested that the exon-inclusion form of the TFIIIA mRNA may be targeted for degradation (Fu et al, 2009;Hammond et al, 2009), the recent finding that TFIIIA-7ZF protein is present in Arabidopsis (Layat et al, 2012) prompts questions about its biological function and its functional parallels with TFIIIA-9ZF, which is a well established transcription factor for 5S rRNA biogenesis and transport in animals and plants (Barbazuk, 2010).…”

Section: Introductionmentioning

confidence: 99%

“…It binds to the internal promoter of 5S rDNA to promote transcription of 5S rRNA and then binds to 5S rRNA to inhibit further transcription as well as to facilitate nuclear export of 5S rRNA for ribosome biogenesis (Klug, 2005). The TFIIIA gene in land plants has evolved a conserved alternative splicing mechanism to generate exon-inclusion and exon-skipping variants (Fu et al, 2009;Hammond et al, 2009;Barbazuk, 2010). The exon-skipping form encodes the full-length TFIIIA that contains nine ZFs (TFIIIA-9ZF); in contrast, the exoninclusion form has a predicted open reading frame encoding a TFIIIA variant that has only seven ZFs and lacks the first two ZFs of the TFIIIA-9ZF (Supplemental Figure 2).…”

Section: Introductionmentioning

confidence: 99%

A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II

Wang

et al. 2015

The Plant Cell

106

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Some DNA-dependent RNA polymerases (DdRPs) possess RNA-dependent RNA polymerase activity, as was first discovered in the replication of Potato spindle tuber viroid (PSTVd) RNA genome in tomato (Solanum lycopersicum). Recent studies revealed that this activity in bacteria and mammals is important for transcriptional and posttranscriptional regulatory mechanisms. Here, we used PSTVd as a model to uncover auxiliary factors essential for RNA-templated transcription by DdRP. PSTVd replication in the nucleoplasm generates (2)-PSTVd intermediates and (+)-PSTVd copies. We found that the Nicotiana benthamiana canonical 9-zinc finger (ZF) Transcription Factor IIIA (TFIIIA-9ZF) as well as its variant TFIIIA-7ZF interacted with (+)-PSTVd, but only TFIIIA-7ZF interacted with (2)-PSTVd. Suppression of TFIIIA-7ZF reduced PSTVd replication, and overexpression of TFIIIA-7ZF enhanced PSTVd replication in planta. Consistent with the locale of PSTVd replication, TFIIIA-7ZF was found in the nucleoplasm and nucleolus, in contrast to the strictly nucleolar localization of TFIIIA-9ZF. Footprinting assays revealed that only TFIIIA-7ZF bound to a region of PSTVd critical for initiating transcription. Furthermore, TFIIIA-7ZF strongly enhanced the in vitro transcription of circular (+)-PSTVd by partially purified Pol II. Together, our results identify TFIIIA-7ZF as a dedicated cellular transcription factor that acts in DdRP-catalyzed RNA-templated transcription, highlighting both the extraordinary evolutionary adaptation of viroids and the potential of DdRPs for a broader role in cellular processes.

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A conserved alternative splicing event in plants reveals an ancient exonization of 5S rRNA that regulates TFIIIA

Abstract: To cite this article: W. Brad Barbazuk (2010) A conserved alternative splicing event in plants reveals an ancient exonization of 5S rRNA that regulates TFIIIA, RNA Biology, 7:4,[397][398][399][400][401][402]

Cited by 12 publications

References 34 publications

Evolutionarily Conserved Alternative Splicing Across Monocots

Evolutionarily Conserved Alternative Splicing Across Monocots

Complexity of the Alternative Splicing Landscape in Plants

A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II

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