The RNA‐binding protein caper is required for sensory neuron development in <i>Drosophila melanogaster</i>

Olesnicky, Eugenia C.; Bono, Jeremy M.; Bell, L. Andrew; Schachtner, Logan T.; Lybecker, Meghan

doi:10.1002/dvdy.24523

Cited by 16 publications

(29 citation statements)

References 61 publications

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“…4). These Caper RNAi results are very similar to the previously described Caper loss-of-function phenotype [17]. For the analysis of ythdc1, we used a previously described loss of function mutant [19] combined with Gal4 477 , UAS-mCD8::GFP as well as a ythdc1 RNAi line.…”

Section: Candidate Testing Identifies Novel Regulators Of MD Neuron Dsupporting

confidence: 81%

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Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling

Aboukilila

Sami

Wang

et al. 2020

Preprint

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Obtaining neuron transcriptomes is challenging; their complex morphology and interconnected microenvironments make it difficult to isolate neurons without potentially altering gene expression. Multidendritic sensory neurons (md neurons) of Drosophila larvae are commonly used to study peripheral nervous system biology, particularly dendrite arborization. We sought to test if EC-tagging, a biosynthetic RNA tagging and purification method that avoids the caveats of physical isolation, would enable discovery of novel regulators of md neuron dendrite arborization. RNAs were biosynthetically tagged by expressing CD:UPRT (a nucleobase-converting fusion enzyme) in md neurons and feeding 5-ethynylcytosine (EC) to larvae. Tagged RNAs were subsequently purified and used for RNA-sequencing. Reference RNA was prepared in a similar manner using 5-ethynyluridine (EUd) to tag RNA in all cells and negative control RNA-seq was performed on “mock tagged” samples to identify non-specifically purified transcripts. Differential expression analysis identified md neuron enriched and depleted transcripts. Three candidate genes encoding RNA-binding proteins (RBPs) were tested for a role in md neuron dendrite arborization. Loss-of-function for the m6A-binding factor Ythdc1 did not cause any dendrite arborization defects while RNAi of the other two candidates, the poly(A) polymerase Hiiragi and the translation regulator Hephaestus, caused significant defects in dendrite arborization. This work provides an expanded view of transcription in md neurons and a technical framework for combining EC-tagging with RNA-seq to profile transcription in cells that may not be amenable to physical isolation.

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Section: Candidate Testing Identifies Novel Regulators Of MD Neuron Dsupporting

confidence: 81%

“…We selected a known md neuron RBP enriched in our dataset, Caper, as a positive control. Caper regulates alternative splicing and is required for proper dendrite arborization of the ddaC class IV da neuron [17]. We crossed UAS-RNAi lines to Gal4 477 , UAS-mCD8::GFP [4].…”

Section: Candidate Testing Identifies Novel Regulators Of MD Neuron Dmentioning

confidence: 99%

Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling

Aboukilila

Sami

Wang

et al. 2020

Preprint

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“…We identified 30 genes involved in RNA splicing that were differentially expressed between day 10 and 40 in photoreceptors (Figure 1a, Supporting Information Table S1). Two‐thirds of these splicing‐related genes were downregulated during aging including splicing factors such as SC35 and Caper that have been previously shown to play a role in alternative splicing in neurons (Gabut, Dejardin, Tazi, & Soret, 2007; Olesnicky, Bono, Bell, Schachtner, & Lybecker, 2017). Based on this analysis, we identified seven splicing‐related genes that showed consistent patterns of decline with age, had relatively strong fold decreases during aging, and had available RNAi fly lines for functional analysis.…”

Section: Resultsmentioning

confidence: 99%

Proper splicing contributes to visual function in the aging Drosophila eye

et al. 2018

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Changes in splicing patterns are a characteristic of the aging transcriptome; however, it is unclear whether these age‐related changes in splicing facilitate the progressive functional decline that defines aging. In Drosophila, visual behavior declines with age and correlates with altered gene expression in photoreceptors, including downregulation of genes encoding splicing factors. Here, we characterized the significance of these age‐regulated splicing‐associated genes in both splicing and visual function. To do this, we identified differential splicing events in either the entire eye or photoreceptors of young and old flies. Intriguingly, aging photoreceptors show differential splicing of a large number of visual function genes. In addition, as shown previously for aging photoreceptors, aging eyes showed increased accumulation of circular RNAs, which result from noncanonical splicing events. To test whether proper splicing was necessary for visual behavior, we knocked down age‐regulated splicing factors in photoreceptors in young flies and examined phototaxis. Notably, many of the age‐regulated splicing factors tested were necessary for proper visual behavior. In addition, knockdown of individual splicing factors resulted in changes in both alternative splicing at age‐spliced genes and increased accumulation of circular RNAs. Together, these data suggest that cumulative decreases in splicing factor expression could contribute to the differential splicing, circular RNA accumulation, and defective visual behavior observed in aging photoreceptors.

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“…AS is especially prevalent in neuronal tissue, and many AS events are specific to neural cell types (Raj and Blencowe 2015). Over recent years, it has become clear that neuronal development is highly influenced by AS, both in mammals (Vuong et al 2016) and flies (Liu and Bossing 2016;Olesnicky et al 2017), even at the single-cell level (Liu and Bossing 2016;Liu et al 2017). More importantly, a growing body of evidence shows that behavioral traits are fine-tuned by AS in many species (Poplawski et al 2016;Tomioka et al 2016;Wang et al 2016).…”

Section: Splicing and The Brainmentioning

confidence: 99%

Rhythmic Behavior Is Controlled by the SRm160 Splicing Factor inDrosophila melanogaster

et al. 2017

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Circadian clocks organize the metabolism, physiology, and behavior of organisms throughout the day-night cycle by controlling daily rhythms in gene expression at the transcriptional and post-transcriptional levels. While many transcription factors underlying circadian oscillations are known, the splicing factors that modulate these rhythms remain largely unexplored. A genome-wide assessment of the alterations of gene expression in a null mutant of the alternative splicing regulator SR-related matrix protein of 160 kDa (SRm160) revealed the extent to which alternative splicing impacts on behavior-related genes. We show that affects gene expression in pacemaker neurons of the brain to ensure proper oscillations of the molecular clock. A reduced level of SRm160 in adult pacemaker neurons impairs circadian rhythms in locomotor behavior, and this phenotype is caused, at least in part, by a marked reduction in () levels. Moreover, rhythmic accumulation of the neuropeptide PIGMENT DISPERSING FACTOR in the dorsal projections of these neurons is abolished after SRm160 depletion. The lack of rhythmicity in SRm160-downregulated flies is reversed by a fully spliced construct, but not by an extra copy of the endogenous locus, showing that positively regulates levels in a splicing-dependent manner. Our findings highlight the significant effect of alternative splicing on the nervous system and particularly on brain function in an model.

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The RNA‐binding protein caper is required for sensory neuron development in Drosophila melanogaster

Cited by 16 publications

References 61 publications

Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling

Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling

Proper splicing contributes to visual function in the aging Drosophila eye

Rhythmic Behavior Is Controlled by the SRm160 Splicing Factor inDrosophila melanogaster

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