Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain

Sapiro, Anne L.; Shmueli, Anat; Henry, Gilbert L.; Li, Qin; Shalit, Tali; Yaron, Orly; Paas, Yoav; Li, Jin Billy; Shohat-Ophir, Galit

doi:10.1101/370296

Cited by 15 publications

(26 citation statements)

References 78 publications

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“…To explore the connection between transcriptional programs in NPFR neurons and behavior, we used a recently generated dataset from our lab consisting of RNA sequences from several neuronal populations in the brain, that were obtained by immunoprecipitation of genetically tagged nuclei (INTACT method) 8 . The dataset included 10 neuronal populations known to regulate behavior and physiology: dopaminergic neurons ( TH-Gal4 ), octopaminergic neurons ( Tdc2-Gal4 ), serotonergic neurons ( TRH-Gal4 ), NPF neurons ( NPF-Gal4 ), NPF-receptor neurons ( NPFR-Gal4 ), mushroom bodies ( OK107-Gal4 ), Corazonin neurons ( CRZ-Gal4 ), Dh44 neurons ( CRF orthologue DH44-Gal4 ), fruitless-expressing neurons ( Fru-Gal4 ), and all neurons ( Elav-Gal4 ).…”

Section: Resultsmentioning

confidence: 99%

Transcriptome Analysis of NPFR Neurons Reveals a Connection Between proteome Diversity and Social Behavior

Ryvkin

Bentzur

Shmueli

et al. 2020

Preprint

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Complex social behaviors are mediated by the activity of highly intricate neuronal networks, the function of which is shaped by their transcriptomic and proteomic content. Contemporary advances in neurogenetics, genomics, and tools for automated behavior analysis make it possible to functionally connect the transcriptome profile of candidate neurons to their role in regulating behavior. In this study we used Drosophila melanogaster to explore the molecular signature of neurons expressing receptor for neuropeptide F (NPF), the fly homologue of neuropeptide Y (NPY). By comparing the transcription profile of NPFR neurons to those of nine other populations of neurons, we discovered that NPFR neurons exhibit a unique transcriptome, enriched with receptors for various neuropeptides and neuromodulators, as well as with genes known to regulate behavioral processes, such as learning and memory. By manipulating RNA editing and protein ubiquitination programs specifically in NPFR neurons, we demonstrate that their delicate transcriptome and proteome repertoires are required to suppress male courtship and certain features of social group interaction. Our results highlight the importance of transcriptome and proteome diversity in the regulation of complex behaviors and pave the path for future dissection of the spatiotemporal regulation of genes within highly complex tissues, such as the brain.

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Section: Resultsmentioning

confidence: 99%

Transcriptome Analysis of NPFR Neurons Reveals a Connection Between proteome Diversity and Social Behavior

Ryvkin

Bentzur

Shmueli

et al. 2020

Preprint

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“…While RNA sequence and structure are critical determinants of editing levels, studies querying tissue-specific and developmental-stage-specific editing levels show that the level of editing at the same editing site can vary greatly between individuals and tissues. These changes do not always correlate with ADAR mRNA or protein expression, suggesting a complex regulation of editing events by factors other than ADAR proteins (Sapiro et al, 2019; Tan et al, 2017; Wahlstedt et al, 2009). Recently, an analysis of proteins with an RNA-binding domain profiled by ENCODE suggested that RNA-binding proteins play a role in RNA editing regulation.…”

Section: Introductionmentioning

confidence: 96%

Unbiased identification of trans regulators of ADAR and A-to-I RNA editing

Freund

Sapiro

et al. 2019

Preprint

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13Adenosine-to-Inosine RNA editing is catalyzed by ADAR enzymes that deaminate adenosine to 14 inosine. While many RNA editing sites are known, few trans regulators have been identified. We 15 perform BioID followed by mass-spectrometry to identify trans regulators of ADAR1 and ADAR2 16 in HeLa and M17 neuroblastoma cells. We identify known and novel ADAR-interacting proteins. 17Using ENCODE data we validate and characterize a subset of the novel interactors as global or 18 site-specific RNA editing regulators. Our set of novel trans regulators includes all four members 19 of the DZF-domain-containing family of proteins: ILF3, ILF2, STRBP, and ZFR. We show that 20 these proteins interact with each ADAR and modulate RNA editing levels. We find ILF3 is a 21 global negative regulator of editing. This work demonstrates the broad roles RNA binding 22 proteins play in regulating editing levels and establishes DZF-domain containing proteins as a 23 group of highly influential RNA editing regulators. 24 25 47 the majority of ADAR1-regulated editing sites are found in repeat regions, ADAR2 is primarily 48 responsible for editing adenosines found in non-repeat regions, particularly in the brain (Tan et 49 al., 2017). ADAR2-regulated sites in non-repetitive regions include a number of editing events 50 that alter the protein-coding sequences of neuronal RNAs, including GluR2, which encodes a 51 glutamate receptor in which RNA editing is necessary for its proper function. Further 52 demonstrating its important role in neuronal editing, dysregulation of human ADAR2 is 53 associated with multiple neurological diseases, including amyotrophic lateral sclerosis, 54 astrocytoma and transient forebrain ischemia (Slotkin and Nishikura, 2013; Tran et al., 2019). 55Maintaining RNA editing levels is critical for human health, but how RNA editing levels are 56 regulated at specific editing sites across tissues and development is poorly understood. 58While RNA sequence and structure are critical determinants of editing levels, studies querying 59 tissue-specific and developmental-stage-specific editing levels show that the level of editing at 60 the same editing site can vary greatly between individuals and tissues. These changes do not 61 always correlate with ADAR mRNA or protein expression, suggesting a complex regulation of 62 editing events by factors other than ADAR proteins (Sapiro et al., 2019; Tan et al., 2017; 63 Wahlstedt et al., 2009). Recently, an analysis of proteins with an RNA-binding domain profiled 64 by ENCODE suggested that RNA-binding proteins play a role in RNA editing regulation. Further, 65 in mammals, a small number of trans regulators of editing have been identified through 66 functional experiments (Quinones-Valdez et al., 2019). Some of these trans regulators of editing 67 are site-specific, in that they affect editing levels at only a small subset of editing sites. These 68 include RNA binding proteins such as DHX15, HNRNPA2/B1, RPS14, TDP-43, Drosha and 69 Ro60 (Garncarz et al., 2013; Quinones-Valdez ...

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“…Additional promiscuous RNA editing occurs in long dsRNAs formed by inverted repetitive elements in both mammals and Drosophila; in humans this additional ADAR RNA editing occurs at millions of sites, mostly non-specifically and at low efficiency in Alu dsRNA hairpins embedded in protein-coding transcripts [3][4][5] . Unlike DNA mutations, RNA editing usually changes only some proportion of the transcripts of particular genes, and editing levels at individual sites can be different in different tissues and developmental stages [5][6][7][8] , due to different ADAR expression levels and other tissue-specific factors. Thus, RNA editing is a powerful tool that can over-write and enrich the genomically encoded information during the process of gene expression.…”

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confidence: 99%

Adar RNA editing-dependent and -independent effects are required for brain and innate immune functions in Drosophila

et al. 2020

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ADAR RNA editing enzymes are high-affinity dsRNA-binding proteins that deaminate adenosines to inosines in pre-mRNA hairpins and also exert editing-independent effects. We generated a Drosophila Adar E374A mutant strain encoding a catalytically inactive Adar with CRISPR/Cas9. We demonstrate that Adar adenosine deamination activity is necessary for normal locomotion and prevents age-dependent neurodegeneration. The catalytically inactive protein, when expressed at a higher than physiological level, can rescue neurodegeneration in Adar mutants, suggesting also editing-independent effects. Furthermore, loss of Adar RNA editing activity leads to innate immune induction, indicating that Drosophila Adar, despite being the homolog of mammalian ADAR2, also has functions similar to mammalian ADAR1. The innate immune induction in fly Adar mutants is suppressed by silencing of Dicer-2, which has a RNA helicase domain similar to MDA5 that senses unedited dsRNAs in mammalian Adar1 mutants. Our work demonstrates that the single Adar enzyme in Drosophila unexpectedly has dual functions.

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Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain

Cited by 15 publications

References 78 publications

Transcriptome Analysis of NPFR Neurons Reveals a Connection Between proteome Diversity and Social Behavior

Transcriptome Analysis of NPFR Neurons Reveals a Connection Between proteome Diversity and Social Behavior

Unbiased identification of trans regulators of ADAR and A-to-I RNA editing

Adar RNA editing-dependent and -independent effects are required for brain and innate immune functions in Drosophila

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