Pervasive Behavioral Effects of MicroRNA Regulation in<i>Drosophila</i>

Picao-Osorio, Joao; Lago-Baldaia, Inês; Patraquim, Pedro; Alonso, Claudio R.

doi:10.1534/genetics.116.195776

Cited by 30 publications

(32 citation statements)

References 69 publications

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“…Similar to other model organisms 14 , only few fly miRNA deletions exert lethal phenotypes or strong morphological abnormalities. However, many miRNA have been found have subtle effects 15,16 , which become more pronounced when the organism is challenged. It remains difficult to describe direct organismic miRNA effects via individual targets in a quantitative manner.…”

Section: Introductionmentioning

confidence: 99%

Global identification of functional microRNA::mRNA interactions in Drosophila

Wessels

Lebedeva

Hirsekorn

et al. 2018

Preprint

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23MicroRNAs (miRNAs) are key mediators of post-transcriptional gene 24 expression silencing. Although Drosophila has been of critical importance for miRNA 25 discovery, biogenesis and function, there has been no comprehensive experimental 26 annotation of functional miRNA target sites. To close this gap, we generated the first 27 in vivo map of miRNA::mRNA interactions in Drosophila melanogaster, making use 28 of crosslinked nucleotides in Argonaute (AGO) crosslinking and immunoprecipitation 29 (CLIP) experiments that enable an unambiguous assignment of miRNAs to AGO 30 binding sites at much higher signal-to-noise ratio than computational predictions 31 alone. 32Absolute quantification of cellular miRNA levels showed the miRNA pool in 33Drosophila cell lines to be more diverse than previously reported. Benchmarking two 34 different CLIP approaches, we identified a similar predictive potential to 35 unambiguously assign thousands of miRNA::mRNA pairs from AGO1 interaction 36 data at unprecedented depth. Quantitative RNA-Seq and subcodon-resolution 37 ribosomal footprinting data upon AGO1 depletion enabled the determination of 38 miRNA-mediated effects on target expression and translation. We thus provide the 39 first comprehensive resource of miRNA target sites as well as their quantitative 40 functional impact in Drosophila. 41 42 43 65 have greatly enhanced our understanding about miRNA function, while our 66 understanding of fly miRNA function is lagging behind. In Drosophila, a recent 67 comparative study of small RNAs across 25 cell lines suggested that the miRNA 68 landscape in non-ovary cell lines showed little diversity and low complexity in terms 69 of relative expression levels of individual miRNAs, which would argue against fly cell 70 lines as a good model to study miRNA function 12 . 71 4 Although knowledge of mature miRNA sequences alone have enabled to 72 identify physiologically relevant targets 5,17 , computational methods have greatly 73 contributed to successful miRNA target prediction, especially after recognition of the 74 miRNA seed region (nt 2-7) 18-21 . To date, there is a plethora of computational 75 miRNA target predictions tools, including popular approaches such as TargetScan, 76 MIRZA and mirSVR 2,22,23 , which leverage conservation, target sequence context 77 feature information or RNA::RNA hybridization energies and other features to 78 improve prediction accuracy. Purely computational tools predict miRNA targets sites 79 across entire 3'UTRs, neglecting cell type specific miRNA expression level and target 80 site availability, which can lead to numerous and tightly spaced predictions. In vivo 81 AGO binding information generated from Crosslinking and Immunoprecipitation 82 (CLIP) followed by sequencing (CLIP-seq or HITSCLIP) methods has been used to 83 greatly decrease the search space from whole 3'UTRs to about 30-40nt per AGO 84 footprint 24 . AGO footprints do not directly reveal the identity of the miRNA engaged, 85 and in many cases, multiple possible miRNA seed matches overl...

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Section: Introductionmentioning

confidence: 99%

Global identification of functional microRNA::mRNA interactions in Drosophila

Wessels

Lebedeva

Hirsekorn

et al. 2018

Preprint

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“…Similar to our screens of adult locomotion, a large fraction (44 of 128; 34%) of our miR-SP lines induced a significant effect on one or more locomotor parameters in L2 stage larva ( Figure 5). This percentage of hits was approximately equal to the frequency of miRNA hits in an early larval deficiency screen selective to self-righting behavior (Picao-Osorio et al 2017), confirming that many miRNAs play some role in establishing normal motor circuitry, but that many of the effects may not be selective to particular motor responses. Despite the large number of hits, we found larval phenotypes to exhibit a greater degree parameter selectivity than the neurally-driven miR-SPs assayed in early adulthood.…”

Section: Mirna Regulation Of Larval Locomotionmentioning

confidence: 74%

“…These studies argue that miRNAs provide a potentially important level of regulation in motor circuits, but the use of null mutants and chronic global manipulations did not allow investigators to disambiguate developmental and functional roles or to understand the tissue-specificity of miRNA actions. Recently, using a very specific assay for early larval self-righting behavior to screen many deletion alleles, a surprisingly large number miRNA were shown to modulate various aspects of this simple patterned motor response (Picao-Osorio et al 2017). Interestingly, multiple miRNA hits in this focused screen appear to converge on the developmental patterning gene Abdominal-B (Abd-B), a HOX-class transcription factor (Picao-Osorio et al 2017), suggesting that developmental events are a major target of translational regulation.…”

Section: Microrna Motor Behavior Drosophila Melanogastermentioning

confidence: 99%

MicroRNAs Regulate Multiple Aspects of Locomotor Behavior inDrosophila

Donelson

Dixit

Pichardo‐Casas

et al. 2020

G3 Genes|Genomes|Genetics

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Locomotion is an ancient and fundamental output of the nervous system required for animals to perform many other complex behaviors. Although the formation of motor circuits is known to be under developmental control of transcriptional mechanisms that define the fates and connectivity of the many neurons, glia and muscle constituents of these circuits, relatively little is known about the role of post-transcriptional regulation of locomotor behavior. MicroRNAs have emerged as a potentially rich source of modulators for neural development and function. In order to define the microRNAs required for normal locomotion in Drosophila melanogaster, we utilized a set of transgenic Gal4-dependent competitive inhibitors (microRNA sponges, or miR-SPs) to functionally assess ca. 140 high-confidence Drosophila microRNAs using automated quantitative movement tracking systems followed by multiparametric analysis. Using ubiquitous expression of miR-SP constructs, we identified a large number of microRNAs that modulate aspects of normal baseline adult locomotion. Addition of temperature-dependent Gal80 to identify microRNAs that act during adulthood revealed that the majority of these microRNAs play developmental roles. Comparison of ubiquitous and neural-specific miR-SP expression suggests that most of these microRNAs function within the nervous system. Parallel analyses of spontaneous locomotion in adults and in larvae also reveal that very few of the microRNAs required in the adult overlap with those that control the behavior of larval motor circuits. These screens suggest that a rich regulatory landscape underlies the formation and function of motor circuits and that many of these mechanisms are stage and/or parameter-specific.

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“…Larval SR behaviour was assayed as previously described (Picao-Osorio et al, 2015;Picao-Osorio et al, 2017) . For adult SR behaviour tests, flies were grown in non-crowed conditions at 25ºC.…”

Section: Self-righting Testsmentioning

confidence: 99%

“…Our previous work showed that miR-iab4 affects larval movement through regulation of one of its molecular targets, the Hox gene Ultrabithorax (Ubx), whose level of expression in a set of metameric motor neurons is critical for normal SR behaviour (Picao-Osorio et al, 2015). To explore the generality of the effects of miRNA regulation on larval SR movement we recently conducted a genetic screen that revealed that at least 40% of all miRNAs expressed in young Drosophila larva can affect SR demonstrating an unprecedented and widespread role of miRNA regulation in the control of postural adjustments and locomotor behaviour (Picao-Osorio et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

A single microRNA-Hox gene module controls complex movement in morphologically-distinct developmental forms ofDrosophila

Issa

Picao-Osorio

Rito

et al. 2019

Preprint

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Movement is the main output of the nervous system. It emerges during development to become a highly coordinated physiological process essential to the survival and adaptation of the organism to the environment. Similar movements can be observed in morphologically-distinct developmental stages of an organism, but it is currently unclear whether these movements have a common or diverse molecular basis. Here we explore this problem in Drosophila focusing on the roles played by the microRNA (miRNA) locus miR-iab4/8 which was previously shown to be essential for the fruit fly larva to correct its orientation if turned upside down (self-righting) (Picao-Osorio et al., 2015). Our study shows that miR-iab4 is required for normal self-righting across all three Drosophila larval stages. Unexpectedly, we also discover that this miRNA is essential for normal self-righting behaviour in the Drosophila adult, an organism with radically different morphological and neural constitution. Through the combination of gene-expression, optical imaging and quantitative behavioural approaches we provide evidence that miR-iab4 exerts its effects on adult self-righting behaviour through repression of the Hox gene Ultrabithorax (Ubx) (Morgan, 1923;Sánchez-Herrero et al., 1985) in a specific set of motor neurons that innervate the adult Drosophila leg. Our results show that this miRNA-Hox module affects the function, rather than the morphology of motor neurons and indicate that postdevelopmental changes in Hox gene expression can modulate behavioural outputs in the adult.Altogether our work reveals that a common miRNA-Hox genetic module can control complex movement in morphologically-distinct organisms and describes a novel post-developmental role of the Hox genes in adult neural function.

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Pervasive Behavioral Effects of MicroRNA Regulation inDrosophila

Abstract: Picao-Osorio et al. reveal pervasive effects of microRNA regulation on complex locomotor behaviors in Drosophila larvae: over 40% of microRNAs display...

Cited by 30 publications

References 69 publications

Global identification of functional microRNA::mRNA interactions in Drosophila

Global identification of functional microRNA::mRNA interactions in Drosophila

MicroRNAs Regulate Multiple Aspects of Locomotor Behavior inDrosophila

A single microRNA-Hox gene module controls complex movement in morphologically-distinct developmental forms ofDrosophila

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