[an error occurred while processing this directive]
Research Article

Screening of Drosophila melanogaster RNA m6A modification pathway factors

Expand
  • State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China

Received date: 2024-12-03

  Revised date: 2025-01-25

  Online published: 2025-03-03

Supported by

National Natural Science Foundation of China(31970786);National Natural Science Foundation of China(32270868)

Abstract

N6-methyladenosine (m6A), one of the most prevalent mRNA modifications, plays crucial roles during animal and plant development and in various physiological and pathological processes. Previous studies have characterized m6A methyltransferase complexes, demethylases, and m6A-binding proteins, but as a relatively new epitranscriptomic pathway, it is likely that new m6A components remain to be discovered. To explore the effects of m6A modification on tissues and organs, the m6A reader Ythdc1 was overexpressed in Drosophila melanogaster eye imaginal discs. Our results showed that overexpression of Ythdc1 leads to ectopic expression of Sxl in males, the rough eye in both males and females, and the activation of JNK signaling and apoptotic pathway. In order to screen m6A modifiers using the rough eye phenotype, a stable Drosophila strain overexpressing Ythdc1 was further constructed. By screening of more than 1,500 RNAi lines, several repressors and enhancers that may be involved in m6A modification were successfully identified. These genes are less studied in m6A pathway, and therefore we further verified them and conducted preliminary mechanistic analyses on them. In summary, this study identified multiple potential factors of the m6A modification pathway, expanded our understanding of the m6A modification network, and provided ideas and directions for exploring new regulatory mechanisms of this important pathway.

Cite this article

Shuyang Gao, Houguang Lu, Yanhua Wang, Dong Yan . Screening of Drosophila melanogaster RNA m6A modification pathway factors[J]. Hereditas(Beijing), 2025 , 47(4) : 476 -488 . DOI: 10.16288/j.yczz.24-341

References

[1] Zaccara S, Ries RJ, Jaffrey SR. Reading, writing and erasing mRNA methylation. Nat Rev Mol Cell Biol, 2019, 20(10): 608-624.
[2] Zhao BS, Roundtree IA, He C. Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol, 2017, 18(1): 31-42.
[3] Yang Y, Hsu PJ, Chen YS, Yang YG. Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism. Cell Res, 2018, 28(6): 616-624.
[4] Bokar JA, Rath-Shambaugh ME, Ludwiczak R, Narayan P, Rottman F. Characterization and partial purification of mRNA N6-adenosine methyltransferase from HeLa cell nuclei. Internal mRNA methylation requires a multisubunit complex. J Biol Chem, 1994, 269(26): 17697-17704.
[5] Bokar JA, Shambaugh ME, Polayes D, Matera AG, Rottman FM. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA, 1997, 3(11): 1233-1247.
[6] Ortega A, Niksic M, Bachi A, Wilm M, Sánchez L, Hastie N, Valcárcel J. Biochemical function of female-lethal (2)D/Wilms' tumor suppressor-1-associated proteins in alternative pre-mRNA splicing. J Biol Chem, 2003, 278(5): 3040-3047.
[7] Schöller E, Weichmann F, Treiber T, Ringle S, Treiber N, Flatley A, Feederle R, Bruckmann A, Meister G. Interactions, localization, and phosphorylation of the m6A generating Mettl3-Mettl14-Wtap complex. RNA, 2018, 24(4): 499-512.
[8] Yue YN, Liu J, Cui XL, Cao J, Luo GZ, Zhang ZZ, Cheng T, Gao MS, Shu X, Ma HH, Wang FQ, Wang XX, Shen B, Wang YZ, Feng XH, He C, Liu JZ. Vrima mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation. Cell Discov, 2018, 4: 10.
[9] Patil DP, Chen CK, Pickering BF, Chow A, Jackson C, Guttman M, Jaffrey SR. m6A RNA methylation promotes Xist-mediated transcriptional repression. Nature, 2016, 537(7620): 369-373.
[10] Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d. Genes Dev, 2018, 32(5-6): 415-429.
[11] Wen J, Lv RT, Ma HH, Shen HJ, He CX, Wang JH, Jiao FF, Liu H, Yang PY, Tan L, Lan F, Shi YG, He C, Shi Y, Diao JB. Zc3h13 regulates nuclear RNA m6A methylation and mouse embryonic stem cell self-renewal. Mol Cell, 2018, 69(6): 1028-1038.e6.
[12] Růžička K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, Eeckhout D, El-Showk S, Li HY, Zhong SL, De Jaeger G, Mongan NP, Hejátko J, Helariutta Y, Fray RG. Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol, 2017, 215(1): 157-172.
[13] Wang YH, Zhang LF, Ren H, Ma LJ, Guo J, Mao DC, Lu ZW, Lu LJ, Yan D. Role of Hakai in m6A modification pathway in Drosophila. Nat Commun, 2021, 12(1): 2159.
[14] Jia GF, Fu Y, Zhao X, Dai Q, Zheng GQ, Yang Y, Yi CQ, Lindahl T, Pan T, Yang YG, He C. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol, 2011, 7(12): 885-887.
[15] Zhao X, Yang Y, Sun BF, Shi Y, Yang X, Xiao W, Hao YJ, Ping XL, Chen YS, Wang WJ, Jin KX, Wang X, Huang CM, Fu Y, Ge XM, Song SH, Jeong HS, Yanagisawa H, Niu YM, Jia GF, Wu W, Tong WM, Okamoto A, He C, Rendtlew Danielsen JM, Wang XJ, Yang YG. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res, 2014, 24(12): 1403-1419.
[16] Zheng GQ, Dahl JA, Niu YM, Fedorcsak P, Huang CM, Li CJ, Vågbø CB, Shi Y, Wang WL, Song SH, Lu ZK, Bosmans RPG, Dai Q, Hao YJ, Yang X, Zhao WM, Tong WM, Wang XJ, Bogdan F, Furu K, Fu Y, Jia GF, Zhao X, Liu J, Krokan HE, Klungland A, Yang YG, He C. Alkb5h is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell, 2013, 49(1): 18-29.
[17] Tang C, Klukovich R, Peng HY, Wang ZQ, Yu T, Zhang Y, Zheng HL, Klungland A, Yan W. Alkb5h-dependent m6A demethylation controls splicing and stability of long 3′-UTR mRNAs in male germ cells. Proc Natl Acad Sci USA, 2018, 115(2): E325-E333.
[18] Dai ZK, Asgari S. Alkbh8 as a potential N(6)- methyladenosine (m6A) eraser in insects. Insect Mol Biol, 2023, 32(5): 461-468.
[19] Xiao W, Adhikari S, Dahal U, Chen YS, Hao YJ, Sun BF, Sun HY, Li A, Ping XL, Lai WY, Wang X, Ma HL, Huang CM, Yang Y, Huang N, Jiang GB, Wang HL, Zhou Q, Wang XJ, Zhao YL, Yang YG. Nuclear m6A reader Ythdc1 regulates mRNA splicing. Mol Cell, 2016, 61(4): 507-519.
[20] Kretschmer J, Rao H, Hackert P, Sloan KE, Höbartner C, Bohnsack MT. The m6A reader protein Ythdc2 interacts with the small ribosomal subunit and the 5′-3′ exoribonuclease XRN1. RNA, 2018, 24(10): 1339-1350.
[21] Wang X, Zhao BS, Roundtree IA, Lu ZK, Han DL, Ma HH, Weng XC, Chen K, Shi HL, He C. N(6)-methyladenosine modulates messenger RNA translation efficiency. Cell, 2015, 161(6): 1388-1399.
[22] Wang X, Lu ZK, Gomez A, Hon GC, Yue YN, Han DL, Fu Y, Parisien M, Dai Q, Jia GF, Ren B, Pan T, He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature, 2014, 505(7481): 117-120.
[23] Du H, Zhao Y, He JQ, Zhang Y, Xi HR, Liu MF, Ma JB, Wu LG. Ythdf2 destabilizes m6A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex. Nat Commun, 2016, 7: 12626.
[24] Li A, Chen YS, Ping XL, Yang X, Xiao W, Yang Y, Sun HY, Zhu Q, Baidya P, Wang X, Bhattarai DP, Zhao YL, Sun BF, Yang YG. Cytoplasmic m6A reader Ythdf3 promotes mRNA translation. Cell Res, 2017, 27(3): 444-447.
[25] Shi HL, Wang X, Lu ZK, Zhao BS, Ma HH, Hsu PJ, Liu C, He C. Ythdf3 facilitates translation and decay of N(6)- methyladenosine-modified RNA. Cell Res, 2017, 27(3): 315-328.
[26] Tian M, Maniatis T. A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell, 1993, 74(1): 105-114.
[27] Billeter JC, Rideout EJ, Dornan AJ, Goodwin SF. Control of male sexual behavior in Drosophila by the sex determination pathway. Curr Biol, 2006, 16(17): R766-R776.
[28] Guo J, Tang HW, Li J, Perrimon N, Yan D. Xio is a component of the Drosophila sex determination pathway and RNA N(6)-methyladenosine methyltransferase complex. Proc Natl Acad Sci USA, 2018, 115(14): 3674-3679.
[29] Lence T, Akhtar J, Bayer M, Schmid K, Spindler L, Ho CH, Kreim N, Andrade-Navarro MA, Poeck B, Helm M, Roignant JY. m6A modulates neuronal functions and sex determination in Drosophila. Nature, 2016, 540(7632): 242-247.
[30] He PC, He C. m6A RNA methylation: from mechanisms to therapeutic potential. EMBO J, 2021, 40(3): e105977.
[31] Zhao BS, Wang X, Beadell AV, Lu ZK, Shi HL, Kuuspalu A, Ho RK, He C. m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature, 2017, 542(7642): 475-478.
[32] Zhang CX, Chen YS, Sun BF, Wang L, Yang Y, Ma DY, Lv JH, Heng J, Ding YY, Xue YY, Lu XY, Xiao W, Yang YG, Liu F. m6A modulates haematopoietic stem and progenitor cell specification. Nature, 2017, 549(7671): 273-276.
[33] Arribas-Hernández L, Bressendorff S, Hansen MH, Poulsen C, Erdmann S, Brodersen P. An m(6)A-YTH module controls developmental timing and morphogenesis in Arabidopsis. Plant Cell, 2018, 30(5): 952-967.
[34] Yu Q, Liu S, Yu L, Xiao Y, Zhang SS, Wang XP, Xu YY, Yu H, Li YL, Yang JB, Tang J, Duan HC, Wei LH, Zhang HY, Wei JB, Tang Q, Wang CL, Zhang WT, Wang Y, Song PZ, Lu Q, Zhang W, Dong SQ, Song BA, He C, Jia GF. RNA demethylation increases the yield and biomass of rice and potato plants in field trials. Nat Biotechnol, 2021, 39(12): 1581-1588.
[35] Ma XJ, Huang JH, Yang LX, Yang Y, Li WZ, Xue L. Nopo modulates egr-induced JNK-independent cell death in Drosophila. Cell Res, 2012, 22(2): 425-431.
[36] Li Y, Liu DY, Wang HC, Zhang XJ, Lu BW, Li SX. The Ire1/Xbp1 axis restores ER and tissue homeostasis perturbed by excess notch in Drosophila. Dev Biol, 2024, 507: 11-19.
[37] Kan LJ, Ott S, Joseph B, Park ES, Dai W, Kleiner RE, Claridge-Chang A, Lai EC. A neural m6A/Ythdf pathway is required for learning and memory in Drosophila. Nat Commun, 2021, 12(1): 1458.
[38] Mao YP, Rauskolb C, Cho E, Hu WL, Hayter H, Minihan G, Katz FN, Irvine KD. Dachs: an unconventional myosin that functions downstream of Fat to regulate growth, affinity and gene expression in Drosophila. Development, 2006, 133(13): 2539-2551.
[39] Vrabioiu AM, Struhl G. Fat/Dachsous signaling promotes Drosophila wing growth by regulating the conformational state of the NDR kinase warts. Dev Cell, 2015, 35(6): 737-749.
[40] Misra JR, Irvine KD. Vamana couples fat signaling to the Hippo pathway. Dev Cell, 2016, 39(2): 254-266.
[41] Kwon Y, Vinayagam A, Sun XY, Dephoure N, Gygi SP, Hong PY, Perrimon N. The Hippo signaling pathway interactome. Science, 2013, 342(6159): 737-740.
[42] Imbert G, Saudou F, Yvert G, Devys D, Trottier Y, Garnier JM, Weber C, Mandel JL, Cancel G, Abbas N, Dürr A, Didierjean O, Stevanin G, Agid Y, Brice A. Cloning of the gene for spinocerebellar ataxia 2 reveals a locus with high sensitivity to expanded CAG/glutamine repeats. Nat Genet, 1996, 14(3): 285-291.
[43] Pulst SM, Nechiporuk A, Nechiporuk T, Gispert S, Chen XN, Lopes-Cendes I, Pearlman S, Starkman S, Orozco- Diaz G, Lunkes A, DeJong P, Rouleau GA, Auburger G, Korenberg JR, Figueroa C, Sahba S. Moderate expansion of a normally biallelic trinucleotide repeat in spinocerebellar ataxia type 2. Nat Genet, 1996, 14(3): 269-276.
[44] Elden AC, Kim HJ, Hart MP, Chen-Plotkin AS, Johnson BS, Fang XD, Armakola M, Geser F, Greene R, Lu MM, Padmanabhan A, Clay-Falcone D, McCluskey L, Elman L, Juhr D, Gruber PJ, Rüb U, Auburger G, Trojanowski JQ, Lee VMY, Van Deerlin VM, Bonini NM, Gitler AD. Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALS. Nature, 2010, 466(7310): 1069-1075.
[45] Lim C, Allada R. Ataxin-2 activates period translation to sustain circadian rhythms in Drosophila. Science, 2013, 340(6134): 875-879.
[46] Zhang Y, Ling JL, Yuan CY, Dubruille R, Emery P. A role for Drosophila Atx2 in activation of per translation and circadian behavior. Science, 2013, 340(6134): 879-882.
[47] McCann C, Holohan EE, Das S, Dervan A, Larkin A, Lee JA, Rodrigues V, Parker R, Ramaswami M. The Ataxin-2 protein is required for microRNA function and synapse- specific long-term olfactory habituation. Proc Natl Acad Sci USA, 2011, 108(36): E655-E662.
[48] Ciosk R, DePalma M, Priess JR. Atx-2, the C. elegans ortholog of ataxin-2, functions in translational regulation in the germline. Development, 2004, 131(19): 4831-4841.
[49] Xiong XS, Hou L, Park YP, Molinie B, GTEx Consortium, Gregory RI, Kellis M. Genetic drivers of m6A methylation in human brain, lung, heart and muscle. Nat Genet, 2021, 53(8): 1156-1165.
[50] Layalle S, They L, Ourghani S, Raoul C, Soustelle L. Amyotrophic lateral sclerosis genes in Drosophila melanogaster. Int J Mol Sci, 2021, 22(2): 904.
Outlines

/