Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of <i>Dscam</i> exon 9 variable exons

Ustaoglu, Pinar; Haussmann, Irmgard U.; HongZhi, Liao; Torres-Méndez, Antonio; Arnold, Roland; Irimia, Manuel; Soller, Matthias

doi:10.1261/rna.071316.119

Cited by 17 publications

(17 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, genetic variants of Dscam have been linked to insecticide resistance in Drosophila 43 . Dscam alternative splicing has been studied in exon-clusters 4, 6 and 9, which harbour an array of mutually exclusive variable exons and exon selection can be mediated by the splicing regulator Srrm234 in Drosophila 44–48 .…”

Section: Introductionmentioning

confidence: 99%

Acute thiamethoxam toxicity in honeybees is not enhanced by common fungicide and herbicide and lacks stress-induced changes in mRNA splicing

Décio

Ustaoglu

Roat

et al. 2019

Sci Rep

Self Cite

View full text Add to dashboard Cite

Securing food supply for a growing population is a major challenge and heavily relies on the use of agrochemicals to maximize crop yield. It is increasingly recognized, that some neonicotinoid insecticides have a negative impact on non-target organisms, including important pollinators such as the European honeybee Apis mellifera. Toxicity of neonicotinoids may be enhanced through simultaneous exposure with additional pesticides, which could help explain, in part, the global decline of honeybee colonies. Here we examined whether exposure effects of the neonicotinoid thiamethoxam on bee viability are enhanced by the commonly used fungicide carbendazim and the herbicide glyphosate. We also analysed alternative splicing changes upon pesticide exposure in the honeybee. In particular, we examined transcripts of three genes: (i) the stress sensor gene X box binding protein-1 (Xbp1), (ii) the Down Syndrome Cell Adhesion Molecule (Dscam) gene and iii) the embryonic lethal/abnormal visual system (elav) gene, which are important for neuronal function. Our results showed that acute thiamethoxam exposure is not enhanced by carbendazim, nor glyphosate. Toxicity of the compounds did not trigger stress-induced, alternative splicing in the analysed mRNAs, thereby leaving dormant a cellular response pathway to these man-made environmental perturbations.

show abstract

Section: Introductionmentioning

confidence: 99%

Acute thiamethoxam toxicity in honeybees is not enhanced by common fungicide and herbicide and lacks stress-induced changes in mRNA splicing

Décio

Ustaoglu

Roat

et al. 2019

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…In exon cluster 9, we found a specific downstream docking site, which can base pair with the selector sequences downstream of each exon 9 (Hong, Shi, Xu, & Jin, 2020). These results described above strongly argue against the idea about the absence of long-range base-pairings in Dscam1 exon 4 and 9 clusters (Haussmann et al, 2019;Ustaoglu et al, 2019). Moreover, we discovered conserved dual docking sites within Dscam exon 4 and 9 clusters in hymenopteran species, which could pair with the selectors to form upstream and downstream RNA pairings (Yue et al, 2016).…”

Section: Competing Rna Secondary Structures In Alternative Splicingmentioning

confidence: 59%

RNA structures in alternative splicing and back‐splicing

Meng

Jin

2020

WIREs RNA

View full text Add to dashboard Cite

Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back-and trans-splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and backsplicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and backsplicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases.

show abstract

“…Overall, the docking site of Dscam1 exons 4 and 9 is clade or species specific and less conserved to exon 6. Therefore, less apparent docking sites make some researchers question the mechanism model of competitive RNA secondary structure regulating the alternative splicing of exons 4 and 9 clusters ( Haussmann et al, 2019 ; Ustaoglu et al, 2019 ). In this study, through sequence alignment, we identified the clade- or species-specific docking sites of Coleoptera Dscam1 exon 4 and exon 9 clusters, but the docking site-selector base pairings are conserved in the secondary structure level, which provided more evidence for Dscam1 exon 4 and 9 clusters of competitive RNA secondary structure to regulate mutually exclusive alternative splicing.…”

Section: Discussionmentioning

confidence: 99%

“…Bidirectional competitive RNA secondary structure regulated the inclusion of variable exons in the exon 4 cluster of Hymenopteran Dscam1 and the exon 9 clusters of Lepidopteran and Hymenopteran Dscam1 ( Yue et al, 2016 ). However, some other researchers questioned the regulatory mechanisms by which long-range competitive RNA secondary structure regulates the splicing of exons 4 and 9 due to the lack of apparent conserved intron elements ( Haussmann et al, 2019 ; Ustaoglu et al, 2019 ). Recently, a unique evolutionary midge-specific docking site has been found in the exon 6 cluster, which regulates the process of alternative splicing via base pairing ( Hong et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Complex RNA Secondary Structures Mediate Mutually Exclusive Splicing of Coleoptera Dscam1

Dong

Zhu

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

Mutually exclusive splicing is an important mechanism for expanding protein diversity. An extreme example is the Down syndrome cell adhesion molecular (Dscam1) gene of insects, containing four clusters of variable exons (exons 4, 6, 9, and 17), which potentially generates tens of thousands of protein isoforms through mutually exclusive splicing, of which regulatory mechanisms are still elusive. Here, we systematically analyzed the variable exon 4, 6, and 9 clusters of Dscam1 in Coleoptera species. Through comparative genomics and RNA secondary structure prediction, we found apparent evidence that the evolutionarily conserved RNA base pairing mediates mutually exclusive splicing in the Dscam1 exon 4 cluster. In contrast to the fly exon 6, most exon 6 selector sequences in Coleoptera species are partially located in the variable exon region. Besides, bidirectional RNA–RNA interactions are predicted to regulate the mutually exclusive splicing of variable exon 9 of Dscam1. Although the docking sites in exon 4 and 9 clusters are clade specific, the docking sites-selector base pairing is conserved in secondary structure level. In short, our result provided a mechanistic framework for the application of long-range RNA base pairings in regulating the mutually exclusive splicing of Coleoptera Dscam1.

show abstract

Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons

Cited by 17 publications

References 64 publications

Acute thiamethoxam toxicity in honeybees is not enhanced by common fungicide and herbicide and lacks stress-induced changes in mRNA splicing

Acute thiamethoxam toxicity in honeybees is not enhanced by common fungicide and herbicide and lacks stress-induced changes in mRNA splicing

RNA structures in alternative splicing and back‐splicing

Complex RNA Secondary Structures Mediate Mutually Exclusive Splicing of Coleoptera Dscam1

Contact Info

Product

Resources

About