# A neural m6A/Ythdf pathway is required for learning and memory in Drosophila

**Authors:** Lijuan Kan, Stanislav Ott, Brian Joseph, Eun Sil Park, Wei Dai, Ralph E. Kleiner, Adam Claridge-Chang, Eric C. Lai

PMC · DOI: 10.1038/s41467-021-21537-1 · Nature Communications · 2021-03-05

## TL;DR

This study shows that a specific RNA modification pathway is crucial for learning and memory in fruit flies.

## Contribution

The study identifies the m6A/Ythdf pathway's role in Drosophila learning and provides detailed molecular and behavioral analyses.

## Key findings

- m6A/Ythdf pathway is essential for associative learning in Drosophila mushroom bodies.
- Mettl3-dependent m6A sites are enriched in 5’ UTRs and linked to translational activation.
- m6A modification does not affect RNA stability but influences translational efficiency.

## Abstract

Epitranscriptomic modifications can impact behavior. Here, we used Drosophila melanogaster to study N6-methyladenosine (m6A), the most abundant modification of mRNA. Proteomic and functional analyses confirm its nuclear (Ythdc1) and cytoplasmic (Ythdf) YTH domain proteins as major m6A binders. Assays of short term memory in m6A mutants reveal neural-autonomous requirements of m6A writers working via Ythdf, but not Ythdc1. Furthermore, m6A/Ythdf operate specifically via the mushroom body, the center for associative learning. We map m6A from wild-type and Mettl3 mutant heads, allowing robust discrimination of Mettl3-dependent m6A sites that are highly enriched in 5’ UTRs. Genomic analyses indicate that Drosophila m6A is preferentially deposited on genes with low translational efficiency and that m6A does not affect RNA stability. Nevertheless, functional tests indicate a role for m6A/Ythdf in translational activation. Altogether, our molecular genetic analyses and tissue-specific m6A maps reveal selective behavioral and regulatory defects for the Drosophila Mettl3/Ythdf pathway.

Epitranscriptomic modifications can regulate learning and memory. Here, the authors provide proteomic and functional analysis of N6-methyladenosine (m6A)-binding proteins in D. melanogaster and unveil behavioral and regulatory defects for m6A/Ythdf mutants.

## Linked entities

- **Genes:** METTL3 (methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit) [NCBI Gene 56339], YTHDC1 (YTH N6-methyladenosine RNA binding protein C1) [NCBI Gene 91746], Ythdf (YTH N6-methyladenosine RNA binding protein) [NCBI Gene 42995]
- **Proteins:** YTHDC1 (YTH N6-methyladenosine RNA binding protein C1), Ythdf (YTH N6-methyladenosine RNA binding protein)
- **Species:** Drosophila melanogaster (taxon 7227)

## Full-text entities

- **Genes:** Atpalpha (Na pump alpha subunit) [NCBI Gene 48971] {aka (Na[+]/k[+])-ATPase, ATP-alpha, ATPBagr, ATPa, ATPalpha1, Atp}, CAPRIN1 [NCBI Gene 100733092], Syx1A (Syntaxin 1A) [NCBI Gene 42854] {aka CG10716, CG18615, CG31136, CG5448, CT30033, Dm Syx1}, METTL14 (methyltransferase 14, N6-adenosine-methyltransferase non-catalytic subunit) [NCBI Gene 57721] {aka hMETTL14}, Mettl14 (methyltransferase 14, N6-adenosine-methyltransferase subunit) [NCBI Gene 210529] {aka G430022H21Rik, mKIAA1627}, METTL3 (methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit) [NCBI Gene 56339] {aka IME4, M6A, MT-A70, Spo8, hMETTL3}, YTHDC1 [NCBI Gene 100722788], fl(2)d (female lethal d) [NCBI Gene 36527] {aka CG6315, Dmel\CG6315, Fl(2d), v(2)k16105}, Lrpprc (leucine-rich PPR-motif containing) [NCBI Gene 72416] {aka 3110001K13Rik, Gp130, Lrp130, Lsfc}, fne (found in neurons) [NCBI Gene 32245] {aka BEST:HL02010, BcDNA:HL02010, BcDNA:RE25290, CG4396, CR32646, Dmel\CG4396}, FTO (FTO alpha-ketoglutarate dependent dioxygenase) [NCBI Gene 79068] {aka ALKBH9, BMIQ14, GDFD, IFEX9}, pros (prospero) [NCBI Gene 41363] {aka 0244/09, 0320/10, 0441/16, 0451/09, 0563/18, 0585/13}, YTHDF1 (YTH N6-methyladenosine RNA binding protein F1) [NCBI Gene 54915] {aka C20orf21, DF1}, DNaseII (Deoxyribonuclease II) [NCBI Gene 48228] {aka CG7780, DNase, DNase 1, DNase II, DNase-1, DNase1}, Ythdf2 (YTH N6-methyladenosine RNA binding protein 2) [NCBI Gene 213541] {aka 9430020E02Rik, HGRG8, NY-REN-2}, alphaTub67C (alpha-Tubulin at 67C) [NCBI Gene 39130] {aka 4t, 67C, ALPHA 67C, CG8308, D.m.ALPHA-67C, DTA2}, futsch (futsch) [NCBI Gene 5740544] {aka 22C10, 22C10/FUTSCH, 22C20, 22c10, CG14772, CG3064}, Camk2a (calcium/calmodulin-dependent protein kinase II alpha) [NCBI Gene 12322] {aka CaMKII, mKIAA0968}, Mettl3 (methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit) [NCBI Gene 56335] {aka 2310024F18Rik, M6A, Spo8}, Ythdc2 (YTH domain containing 2) [NCBI Gene 240255] {aka 3010002F02Rik, mYTHDC2}, neb (nebbish) [NCBI Gene 35293] {aka 38B.10, 38B.12, CG10718, Dm0332, DmKlp38B, DmNeb}, eIF3H [NCBI Gene 100719471], Non2 (Novel nucleolar protein 2) [NCBI Gene 38341] {aka CG1240, Dmel\CG1240}, fwe (flower) [NCBI Gene 39720] {aka CG6151, Dmel\CG6151, anon-WO0118547.242, dFwe, drFlower}, Sxl (Sex lethal) [NCBI Gene 3772180] {aka CG14425, CG18350, CG33070, CG43770, Dm-Sxl, DmSxl}, nrv3 (nervana 3) [NCBI Gene 35408] {aka CG8663, Dmel\CG8663, JYbeta1, nervana3}, Tpm1 (tropomyosin 1, alpha) [NCBI Gene 22003] {aka TM2, TPM1kappa, Tm3, Tmpa, Tpm-1, alpha-TM}, Eif3a (eukaryotic translation initiation factor 3, subunit A) [NCBI Gene 13669] {aka A830012B05Rik, Csma, Eif3, Eif3s10, mKIAA0139}, gish (gilgamesh) [NCBI Gene 49701] {aka CG6963, CK1, CK1-gamma, CK1[[gamma]], CK1gamma, CKI-related}, elav (embryonic lethal abnormal vision) [NCBI Gene 31000] {aka 44C11, 9F8A9, CG4262, Dmel\CG4262, EC7, EG:65F1.2}, pum (pumilio) [NCBI Gene 41094] {aka CG9755, CG9763, Dmel\CG9755, EP(3)0883, PKL, anon-WO0172774.19}, Ythdc1 (YTH domain containing 1) [NCBI Gene 231386] {aka A730098D12Rik, mKIAA1966}, Prosap (prosap) [NCBI Gene 50225] {aka BcDNA:GH23107, CG13354, CG30483, CG8122, D-ProSAP, Dmel\CG30483}, Mettl3 [NCBI Gene 100712853], Mettl14 (Methyltransferase like 14) [NCBI Gene 34138] {aka CG7818, Dmel\CG7818, dKAR4, dMettl14}, Ythdc1 (YTH domain containing 1) [NCBI Gene 38420] {aka BcDNA:GH01918, CG12076, Dmel\CG12076, YT521, YT521-B, Ythdc}, Mettl3 (Methyltransferase like 3) [NCBI Gene 42844] {aka CG5933, Dm ime4, Dmel\CG5933, IME4, Ime4, MTA70}, Ythdf (YTH N6-methyladenosine RNA binding protein) [NCBI Gene 42995] {aka CG6422, Dmel\CG6422}
- **Diseases:** defects (MESH:D000013), CIMs (MESH:D018365), STM (MESH:D000088562), MB (MESH:D009145), Cancer (MESH:D009369), STM impairment (MESH:D008569), behavioral abnormalities (MESH:D001523), behavioral deficits (MESH:D019958), I (MESH:D006969), H (MESH:D000848), shock (MESH:D012769)
- **Chemicals:** NaCl (MESH:D012965), Nucleotide (MESH:D009711), PBS (MESH:D007854), diazirine (MESH:D003978), H2O (MESH:D014867), OCT (MESH:C051883), nucleoside (MESH:D009705), TRIzol (MESH:C411644), formic acid (MESH:C030544), 4-thiouridine (MESH:D013891), 3-octanol (-), formaldehyde (MESH:D005557), Puromycin (MESH:D011691), Triton X-100 (MESH:D017830), KCl (MESH:D011189), salt (MESH:D012492), ribonucleoside (MESH:D012263), MgCl2 (MESH:D015636), HEPES (MESH:D006531), uridine (MESH:D014529), MCH (MESH:D016210), acetonitrile (MESH:C032159), m6A (MESH:C005955), Poly(A) (MESH:D011061), polyacrylamide (MESH:C016679), HCl (MESH:D006851), bromophenol blue (MESH:D001978), A (MESH:D001151), agarose (MESH:D012685), TBS (MESH:D013725), ZnCl2 (MESH:C016837), urea (MESH:D014508), Actinomycin-D (MESH:D003609), indium tin oxide (MESH:C109984), MB (MESH:D008751), IP (MESH:C041508), adenosine (MESH:D000241), calcium phosphate (MESH:C020243), EDTA (MESH:D004492), SDS (MESH:D012967), NP-40 (MESH:C010615), tryptophan (MESH:D014364), dextrose (MESH:D005947), N6-methyladenosine (MESH:C010223), Effectene (MESH:C498175), ice (MESH:D007053), DTT (MESH:D004229), Tween-20 (MESH:D011136), glycerol (MESH:D005990), agar (MESH:D000362), DAPI (MESH:C007293)
- **Species:** Diptera (flies, order) [taxon 7147], Drosophila melanogaster (fruit fly, species) [taxon 7227], Mus musculus (house mouse, species) [taxon 10090], Cavia porcellus (domestic guinea pig, species) [taxon 10141], Caenorhabditis elegans (species) [taxon 6239], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Homo sapiens (human, species) [taxon 9606], Sus scrofa (pig, species) [taxon 9823], C. elegans [taxon 328850]
- **Mutations:** S1419S, C) at 0, 8820401A into T, L338A, C-to-T, tryptophan/leucine, W459A, M0289S
- **Cell lines:** BSC461 — Rattus norvegicus (Rat), Spontaneously immortalized cell line (CVCL_M116), Ythdf-3A — Homo sapiens (Human), Chronic myelogenous leukemia, BCR-ABL1 positive, Cancer cell line (CVCL_XV21), S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232), MB247 — Homo sapiens (Human), Tongue squamous cell carcinoma, Cancer cell line (CVCL_VJ49), Ythdc1-3A — Homo sapiens (Human), Chronic myelogenous leukemia, BCR-ABL1 positive, Cancer cell line (CVCL_XV18), HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), S2R+ — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z831), BL- — Homo sapiens (Human), Melanoma, Cancer cell line (CVCL_U802)

## Full text

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## Figures

7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC7935873/full.md

## References

107 references — full list in the complete paper: https://tomesphere.com/paper/PMC7935873/full.md

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Source: https://tomesphere.com/paper/PMC7935873