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Field-specific reportingPlease select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection.

Life sciences Behavioural & social sciences Ecological, evolutionary & environmental sciences

For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf

Life sciences study designAll studies must disclose on these points even when the disclosure is negative.

Sample size No statistical analyses were used in this study. To describe the different phenomena studied in this manuscript, we selected a number of

samples enough to cover the biological variability observed. These sample sizes are in line with similar studies in the field.

Data exclusions No data was excluded from our analyses.

Replication All experiments were repeated at least three times. All attempts at replication were successful.

Randomization All brains and flies analyzed in this study were randomly selected.

Blinding The investigators were blinded to group allocation during data collection and analysis.

Reporting for specific materials, systems and methodsWe require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material,

system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.

Materials & experimental systems

n/a Involved in the study

Antibodies

Eukaryotic cell lines

Palaeontology and archaeology

Animals and other organisms

Human research participants

Clinical data

Dual use research of concern

Methods

n/a Involved in the study

ChIP-seq

Flow cytometry

MRI-based neuroimaging

Antibodies

Antibodies used Primaries

anti-Bruchpilot: DSHB, Cat# nc82, dilution 1:50

rat anti-Deadpan: Abcam, Cat# ab195173, dilution 1:100

mouse anti-HA: Roche, Cat# 11 666 606 001, dilution 1:500

rabbit anti-V5: Abcam, Cat# ab9137, dilution 1:500

rat anti-RFP: Chromotek, Cat# 5f8, dilution 1:500

rabbit anti-DsRed: Clontech,Cat# 632496 , dilution 1:500

rat anti-GFP: Nacalai Tesque, Cat# 04404-84, dilution 1:500

Secondaries

DyLight 405 AffiniPure Goat Anti-Mouse IgG: Jackson ImmunoResearch, Cat# 115-475-003, dilution 1:1000

Alexa Fluor® 647-AffiniPure Goat Anti-Mouse IgG: Jackson ImmunoResearch, Cat# 115-605-003, dilution 1:1000

Alexa 488-conjugated goat anti-Rat IgG: Thermo Fisher Scientific, Cat# A-11006, dilution 1:1000

Alexa 488-conjugated goat anti-Rabbit IgG: Thermo Fisher Scientific, Cat# A27034, dilution 1:1000

Alexa 568-conjugated goat anti-Rabbit: Thermo Fisher Scientific, Cat# A-11011, dilution 1:1000

Alexa 568 goat anti-Rat IgG: Thermo Fisher Scientific, Cat# A-11077, dilution 1:1000

Alexa 647 goat anti-Mouse IgG: Thermo Fisher Scientific, Cat# A28181, dilution 1:1000

Validation rat anti-Deadpan: Sato K et al. Partial proteasomal degradation of Lola triggers the male-to-female switch of a dimorphic courtship

circuit. Nat Commun 10:166 (2019). Mirkovic M et al. Induced aneuploidy in neural stem cells triggers a delayed stress response and

impairs adult life span in flies. PLoS Biol 17:e3000016 (2019).

mouse anti-HA: Roche: Wilson,l.A.,Niman,H.L.,Houghten,R.A.,Cherenson,A.R., Connolly, M.L. and Lerner, R.A. (1984) Cell 37: 767–78.

Field,J.,Nikawa,J.l.,Broek,D.,MacDonald,B.,Rodgers,L., Wilson, l.A., Lemer, R.A. and Wigler, M. (1988) Mol. Cell. Biol. 8: 2159–2165.

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Vanderspek,J.,Hemand,A.,Dautry-Varsat,A.,Boquet,P.and Murphy, J.R. (1994) Leukemia 8 (Suppl 1): 5144-5148. Soldati,T.and

Perriand,J.-C.(1991) Cell 66:277-289.

rabbit anti-V5: Fossat N et al. C to U RNA editing mediated by APOBEC1 requires RNA-binding protein RBM47. EMBO Rep : (2014).

Wiradjaja F et al. Regulation of PDGFC signalling and extracellular matrix composition by FREM1 in mice. Dis Model Mech 6:1426-33

(2013).

rat anti-RFP: A. Rottach, E. Kremmer, D. Nowak, P. Boisguerin, R. Volkmer, M. C. Cardoso, H. Leonhardt, U. Rothbauer (2008):

Generation and characterization of a rat monoclonal antibody specific for PCNA, Hybridoma (Larchmt). Tonnesen, J. Parish, C. L.

Sorensen, A. T. Andersson, A. Lundberg, C. Deisseroth, K. Arenas, E. Lindvall, O. Kokaia, M. (2011): Functional integration of grafted

neural stem cell-derived dopaminergic neurons monitored by optogenetics in an in vitro Parkinson model. PLoS One. 6: e17560.

rabbit anti-DsRed: Nicolai LJJ et al., 2010. PNAS 107(47) 20553-20558.

rat anti-GFP: Yonehara, K. Nature. 469(7330):407-10 (2011), Abe, K. et al. Biol Reprod 85(5):1013-24 (2011), Hide, T. et al. Stem Cells.

29(4):590-9 (2011)

Eukaryotic cell lines

Policy information about cell lines

Cell line source(s) S2-DGRC: Made from Oregon R embryos on the verge of hatching. This isolate was a gift from Cheeptip Benyajati to the

Cherbas lab, ca. 1980.

Authentication Cell line was directly ordered from DGRC and was not otherwise authenticated

Mycoplasma contamination Cell line was not tested for mycoplasma contamination

Commonly misidentified lines(See ICLAC register)

No commonly misidentified cell lines were used in this study.

Animals and other organisms

Policy information about studies involving animals; ARRIVE guidelines recommended for reporting animal research

Laboratory animals Drosophila melanogaster: Sex: males and females. Age: 0 hours ALH to adults.

Danio rerio: casper background (White et al., Cell Stem Cell, 2008). Sex: males and females. Age: 0 dpf to 2 years old.

Wild animals This study did not involved any wild animals.

Field-collected samples This study did not involved samples collected from the field.

Ethics oversight Drosophila melanogaster: no ethical approval was required.

Danio rerio: All experiments were conducted according to the NIH guidelines for animal research and were

approved by the Institutional Animal Care and Use Committee of Janelia Research Campus.

Note that full information on the approval of the study protocol must also be provided in the manuscript.