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Resources and Methods for the Analysis of MicroRNA Function in Drosophila

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Drosophila

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2540))

Abstract

Since the widespread discovery of microRNAs (miRNAs) 20 years ago, the Drosophila melanogaster model system has made important contributions to understanding the biology of this class of noncoding RNAs. These contributions are based on the amenability of this model system not only for biochemical analysis but molecular, genetic, and cell biological analyses as well. Nevertheless, while the Drosophila genome is now known to encode 258 miRNA precursors, the function of only a small minority of these have been well characterized. In this review, we summarize the current resources and methods that are available to study miRNA function in Drosophila with a particular focus on the large-scale resources that enable systematic analysis. Application of these methods will accelerate the discovery of ways that miRNAs are embedded into genetic networks that control basic features of metazoan cells.

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References

  1. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294(5543):853–858. https://doi.org/10.1126/science.1064921

    Article  CAS  PubMed  Google Scholar 

  2. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294(5543):862–864. https://doi.org/10.1126/science.1065329

    Article  CAS  PubMed  Google Scholar 

  3. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294(5543):858–862. https://doi.org/10.1126/science.1065062

    Article  CAS  PubMed  Google Scholar 

  4. Agarwal V, Subtelny AO, Thiru P, Ulitsky I, Bartel DP (2018) Predicting microRNA targeting efficacy in Drosophila. Genome Biol 19(1):152. https://doi.org/10.1186/s13059-018-1504-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) miRBase: from microRNA sequences to function. Nucleic Acids Res 47(D1):D155–D162. https://doi.org/10.1093/nar/gky1141

    Article  CAS  PubMed  Google Scholar 

  6. Luhur A, Chawla G, Wu YC, Li J, Sokol NS (2014) Drosha-independent DGCR8/Pasha pathway regulates neuronal morphogenesis. Proc Natl Acad Sci 111(4):1421–1426. https://doi.org/10.1073/pnas.1318445111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Yang J-S, Eric (2011) Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol Cell 43(6):892–903. https://doi.org/10.1016/j.molcel.2011.07.024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chen YW, Song S, Weng R, Verma P, Kugler JM, Buescher M, Rouam S, Cohen SM (2014) Systematic study of Drosophila microRNA functions using a collection of targeted knockout mutations. Dev Cell 31(6):784–800. https://doi.org/10.1016/j.devcel.2014.11.029

    Article  CAS  PubMed  Google Scholar 

  9. Picao-Osorio J, Lago-Baldaia I, Patraquim P, Alonso CR (2017) Pervasive behavioral effects of MicroRNA regulation in Drosophila. Genetics 206(3):1535–1548. https://doi.org/10.1534/genetics.116.195776

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Atilano ML, Glittenberg M, Monteiro A, Copley RR, Ligoxygakis P (2017) MicroRNAs that contribute to coordinating the immune response in Drosophila melanogaster. Genetics 207(1):163–178. https://doi.org/10.1534/genetics.116.196584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Iftikhar H, Johnson NL, Marlatt ML, Carney GE (2019) The role of miRNAs in Drosophila melanogaster male courtship behavior. Genetics 211(3):925–942. https://doi.org/10.1534/genetics.118.301901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Fulga TA, McNeill EM, Binari R, Yelick J, Blanche A, Booker M, Steinkraus BR, Schnall-Levin M, Zhao Y, Deluca T, Bejarano F, Han Z, Lai EC, Wall DP, Perrimon N, Van Vactor D (2015) A transgenic resource for conditional competitive inhibition of conserved Drosophila microRNAs. Nat Commun 6(1):7279. https://doi.org/10.1038/ncomms8279

    Article  CAS  PubMed  Google Scholar 

  13. McGuire SE, Le PT, Osborn AJ, Matsumoto K, Davis RL (2003) Spatiotemporal rescue of memory dysfunction in Drosophila. Science 302(5651):1765–1768. https://doi.org/10.1126/science.1089035

    Article  CAS  PubMed  Google Scholar 

  14. Donelson NC, Dixit R, Pichardo-Casas I, Chiu EY, Ohman RT, Slawson JB, Klein M, Fulga TA, Van Vactor D, Griffith LC (2020) MicroRNAs regulate multiple aspects of locomotor behavior in Drosophila. G3 (Bethesda) 10(1):43–55. https://doi.org/10.1534/g3.119.400793

    Article  CAS  Google Scholar 

  15. Goodwin PR, Meng A, Moore J, Hobin M, Fulga TA, Van Vactor D, Griffith LC (2018) MicroRNAs regulate sleep and sleep homeostasis in Drosophila. Cell Rep 23(13):3776–3786. https://doi.org/10.1016/j.celrep.2018.05.078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. You S, Fulga TA, Van Vactor D, Jackson FR (2018) Regulation of circadian behavior by astroglial MicroRNAs in Drosophila. Genetics 208(3):1195–1207. https://doi.org/10.1534/genetics.117.300342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Bejarano F, Bortolamiol-Becet D, Dai Q, Sun K, Saj A, Chou YT, Raleigh DR, Kim K, Ni JQ, Duan H, Yang JS, Fulga TA, Van Vactor D, Perrimon N, Lai EC (2012) A genome-wide transgenic resource for conditional expression of Drosophila microRNAs. Development 139(15):2821–2831. https://doi.org/10.1242/dev.079939

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Schertel C, Rutishauser T, Forstemann K, Basler K (2012) Functional characterization of Drosophila microRNAs by a novel in vivo library. Genetics 192(4):1543–1552. https://doi.org/10.1534/genetics.112.145383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Szuplewski S, Kugler JM, Lim SF, Verma P, Chen YW, Cohen SM (2012) MicroRNA transgene overexpression complements deficiency-based modifier screens in Drosophila. Genetics 190(2):617–626. https://doi.org/10.1534/genetics.111.136689

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Redmond W, Allen D, Elledge MC, Arellanes R, Redmond L, Yeahquo J, Zhang S, Youngblood M, Reiner A, Seo J (2019) Screening of microRNAs controlling body fat in Drosophila melanogaster and identification of miR-969 and its target, Gr47b. PLoS One 14(7):e0219707. https://doi.org/10.1371/journal.pone.0219707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Bhat S, Jones WD (2016) An accelerated miRNA-based screen implicates Atf-3 in Drosophila odorant receptor expression. Sci Rep 6:20109. https://doi.org/10.1038/srep20109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Mazaud D, Kottler B, Goncalves-Pimentel C, Proelss S, Tuchler N, Deneubourg C, Yuasa Y, Diebold C, Jungbluth H, Lai EC, Hirth F, Giangrande A, Fanto M (2019) Transcriptional regulation of the glutamate/GABA/glutamine cycle in adult glia controls motor activity and seizures in Drosophila. J Neurosci 39(27):5269–5283. https://doi.org/10.1523/JNEUROSCI.1833-18.2019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Bejarano F, Chang CH, Sun K, Hagen JW, Deng WM, Lai EC (2021) A comprehensive in vivo screen for anti-apoptotic miRNAs indicates broad capacities for oncogenic synergy. Dev Biol 475:10–20. https://doi.org/10.1016/j.ydbio.2021.02.010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233. https://doi.org/10.1016/j.cell.2009.01.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, Graveley BR, Lai EC (2012) Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep 1(3):277–289. https://doi.org/10.1016/j.celrep.2012.01.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Easow G, Teleman AA, Cohen SM (2007) Isolation of microRNA targets by miRNP immunopurification. RNA 13(8):1198–1204. https://doi.org/10.1261/rna.563707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kadener S, Menet JS, Sugino K, Horwich MD, Weissbein U, Nawathean P, Vagin VV, Zamore PD, Nelson SB, Rosbash M (2009) A role for microRNAs in the Drosophila circadian clock. Genes Dev 23(18):2179–2191. https://doi.org/10.1101/gad.1819509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460(7254):479–486. https://doi.org/10.1038/nature08170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141(1):129–141. https://doi.org/10.1016/j.cell.2010.03.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhang C, Darnell RB (2011) Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 29(7):607–614. https://doi.org/10.1038/nbt.1873

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB (2014) Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc 9(2):263–293. https://doi.org/10.1038/nprot.2014.012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Wessels HH, Lebedeva S, Hirsekorn A, Wurmus R, Akalin A, Mukherjee N, Ohler U (2019) Global identification of functional microRNA-mRNA interactions in Drosophila. Nat Commun 10(1):1626. https://doi.org/10.1038/s41467-019-09586-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Coronnello C, Benos PV (2013) ComiR: combinatorial microRNA target prediction tool. Nucleic Acids Res 41(Web Server issue):W159–W164. https://doi.org/10.1093/nar/gkt379

    Article  PubMed  PubMed Central  Google Scholar 

  34. Brummer A, Hausser J (2014) MicroRNA binding sites in the coding region of mRNAs: extending the repertoire of post-transcriptional gene regulation. Bioessays 36(6):617–626. https://doi.org/10.1002/bies.201300104

    Article  CAS  PubMed  Google Scholar 

  35. Bertolazzi G, Benos PV, Tumminello M, Coronnello C (2020) An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs. BMC Bioinformatics 21(Suppl 8):201. https://doi.org/10.1186/s12859-020-3519-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27(1):91–105. https://doi.org/10.1016/j.molcel.2007.06.017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Marco A (2018) SeedVicious: analysis of microRNA target and near-target sites. PLoS One 13(4):e0195532. https://doi.org/10.1371/journal.pone.0195532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Chen K, Rajewsky N (2006) Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 38(12):1452–1456. https://doi.org/10.1038/ng1910

    Article  CAS  PubMed  Google Scholar 

  39. Saunders MA, Liang H, Li WH (2007) Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A 104(9):3300–3305. https://doi.org/10.1073/pnas.0611347104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Marco A (2015) Selection against maternal microRNA target sites in maternal transcripts. G3 (Bethesda) 5(10):2199–2207. https://doi.org/10.1534/g3.115.019497

    Article  CAS  Google Scholar 

  41. Clifton BD, Librado P, Yeh SD, Solares ES, Real DA, Jayasekera SU, Zhang W, Shi M, Park RV, Magie RD, Ma HC, Xia XQ, Marco A, Rozas J, Ranz JM (2017) Rapid functional and sequence differentiation of a tandemly repeated species-specific multigene family in Drosophila. Mol Biol Evol 34(1):51–65. https://doi.org/10.1093/molbev/msw212

    Article  CAS  PubMed  Google Scholar 

  42. Aboobaker AA, Tomancak P, Patel N, Rubin GM, Lai EC (2005) Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci U S A 102(50):18017–18022. https://doi.org/10.1073/pnas.0508823102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7):1401–1414. https://doi.org/10.1016/j.cell.2007.04.040

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, Walhout AJ (2008) Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res 18(12):2005–2015. https://doi.org/10.1101/gr.083055.108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH (2005) MicroRNA expression in zebrafish embryonic development. Science 309(5732):310–311. https://doi.org/10.1126/science.1114519

    Article  CAS  PubMed  Google Scholar 

  46. Chawla G, Luhur A, Sokol N (2016) Analysis of MicroRNA function in Drosophila. Methods Mol Biol 1478:79–94. https://doi.org/10.1007/978-1-4939-6371-3_4

    Article  CAS  PubMed  Google Scholar 

  47. Biemar F, Zinzen R, Ronshaugen M, Sementchenko V, Manak JR, Levine MS (2005) Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc Natl Acad Sci U S A 102(44):15907–15911. https://doi.org/10.1073/pnas.0507817102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Kwon C, Han Z, Olson EN, Srivastava D (2005) MicroRNA1 influences cardiac differentiation in Drosophila and regulates Notch signaling. Proc Natl Acad Sci U S A 102(52):18986–18991. https://doi.org/10.1073/pnas.0509535102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Sokol NS, Ambros V (2005) Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes Dev 19(19):2343–2354. https://doi.org/10.1101/gad.1356105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Weng R, Cohen SM (2012) Drosophila miR-124 regulates neuroblast proliferation through its target anachronism. Development 139(8):1427–1434. https://doi.org/10.1242/dev.075143

    Article  CAS  PubMed  Google Scholar 

  51. Teleman AA, Maitra S, Cohen SM (2006) Drosophila lacking microRNA miR-278 are defective in energy homeostasis. Genes Dev 20(4):417–422. https://doi.org/10.1101/gad.374406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Chawla G, Sokol NS (2012) Hormonal activation of let-7-C microRNAs via EcR is required for adult Drosophila melanogaster morphology and function. Development 139(10):1788–1797. https://doi.org/10.1242/dev.077743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Wu YC, Lee KS, Song Y, Gehrke S, Lu B (2017) The bantam microRNA acts through Numb to exert cell growth control and feedback regulation of Notch in tumor-forming stem cells in the Drosophila brain. PLoS Genet 13(5):e1006785. https://doi.org/10.1371/journal.pgen.1006785

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Duan H, de Navas LF, Hu F, Sun K, Mavromatakis YE, Viets K, Zhou C, Kavaler J, Johnston RJ, Tomlinson A, Lai EC (2018) The mir-279/996 cluster represses receptor tyrosine kinase signaling to determine cell fates in the Drosophila eye. Development 145(7). https://doi.org/10.1242/dev.159053

  55. Mukherjee S, Paricio N, Sokol NS (2021) A stress-responsive miRNA regulates BMP signaling to maintain tissue homeostasis. Proc Natl Acad Sci U S A 118(21). https://doi.org/10.1073/pnas.2022583118

  56. Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113(1):25–36. https://doi.org/10.1016/s0092-8674(03)00231-9

    Article  CAS  PubMed  Google Scholar 

  57. Lai EC, Tam B, Rubin GM (2005) Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev 19(9):1067–1080. https://doi.org/10.1101/gad.1291905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Forstemann K, Tomari Y, Du T, Vagin VV, Denli AM, Bratu DP, Klattenhoff C, Theurkauf WE, Zamore PD (2005) Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol 3(7):e236. https://doi.org/10.1371/journal.pbio.0030236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Kitatani Y, Tezuka A, Hasegawa E, Yanagi S, Togashi K, Tsuji M, Kondo S, Parrish JZ, Emoto K (2020) Drosophila miR-87 promotes dendrite regeneration by targeting the transcriptional repressor Tramtrack69. PLoS Genet 16(8):e1008942. https://doi.org/10.1371/journal.pgen.1008942

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Epstein Y, Perry N, Volin M, Zohar-Fux M, Braun R, Porat-Kuperstein L, Toledano H (2017) miR-9a modulates maintenance and ageing of Drosophila germline stem cells by limiting N-cadherin expression. Nat Commun 8(1):600. https://doi.org/10.1038/s41467-017-00485-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Toledano H, D'Alterio C, Loza-Coll M, Jones DL (2012) Dual fluorescence detection of protein and RNA in Drosophila tissues. Nat Protoc 7(10):1808–1817. https://doi.org/10.1038/nprot.2012.105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Kosman D, Mizutani CM, Lemons D, Cox WG, McGinnis W, Bier E (2004) Multiplex detection of RNA expression in Drosophila embryos. Science 305(5685):846. https://doi.org/10.1126/science.1099247

    Article  CAS  PubMed  Google Scholar 

  63. Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T, Hammond SM (2006) Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev 20(16):2202–2207. https://doi.org/10.1101/gad.1444406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Soni K, Choudhary A, Patowary A, Singh AR, Bhatia S, Sivasubbu S, Chandrasekaran S, Pillai B (2013) miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio. Nucleic Acids Res 41(8):4470–4480. https://doi.org/10.1093/nar/gkt139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Kucherenko MM, Barth J, Fiala A, Shcherbata HR (2012) Steroid-induced microRNA let-7 acts as a spatio-temporal code for neuronal cell fate in the developing Drosophila brain. EMBO J 31(24):4511–4523. https://doi.org/10.1038/emboj.2012.298

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Toledano H, D'Alterio C, Czech B, Levine E, Jones DL (2012) The let-7-Imp axis regulates ageing of the Drosophila testis stem-cell niche. Nature 485(7400):605–610. https://doi.org/10.1038/nature11061

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Katti P, Thimmaya D, Madan A, Nongthomba U (2017) Overexpression of miRNA-9 generates muscle hypercontraction through translational repression of Troponin-T in Drosophila melanogaster indirect flight muscles. G3 (Bethesda) 7(10):3521–3531. https://doi.org/10.1534/g3.117.300232

    Article  CAS  PubMed Central  Google Scholar 

  68. Kucherenko MM, Shcherbata HR (2018) Stress-dependent miR-980 regulation of Rbfox1/A2bp1 promotes ribonucleoprotein granule formation and cell survival. Nat Commun 9(1):312. https://doi.org/10.1038/s41467-017-02757-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Li D, Liu Y, Pei C, Zhang P, Pan L, Xiao J, Meng S, Yuan Z, Bi X (2017) miR-285-Yki/Mask double-negative feedback loop mediates blood-brain barrier integrity in Drosophila. Proc Natl Acad Sci U S A 114(12):E2365–E2374. https://doi.org/10.1073/pnas.1613233114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Minogue AL, Arur S (2019) In situ hybridization for detecting mature MicroRNAs in vivo at single-cell resolution. Curr Protoc Mol Biol 127(1):e93. https://doi.org/10.1002/cpmb.93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Trcek T, Lionnet T, Shroff H, Lehmann R (2017) mRNA quantification using single-molecule FISH in Drosophila embryos. Nat Protoc 12(7):1326–1348. https://doi.org/10.1038/nprot.2017.030

    Article  CAS  PubMed  Google Scholar 

  72. Tsanov N, Samacoits A, Chouaib R, Traboulsi AM, Gostan T, Weber C, Zimmer C, Zibara K, Walter T, Peter M, Bertrand E, Mueller F (2016) smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Res 44(22):e165. https://doi.org/10.1093/nar/gkw784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Gallicchio L, Griffiths-Jones S, Ronshaugen M (2021) miR-9a regulates levels of both rhomboid mRNA and protein in the early Drosophila melanogaster embryo. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.07.12.452096

  74. Hucker SM, Fehlmann T, Werno C, Weidele K, Luke F, Schlenska-Lange A, Klein CA, Keller A, Kirsch S (2021) Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells. Nat Commun 12(1):4316. https://doi.org/10.1038/s41467-021-24611-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Lau NC, Robine N, Martin R, Chung WJ, Niki Y, Berezikov E, Lai EC (2009) Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line. Genome Res 19(10):1776–1785. https://doi.org/10.1101/gr.094896.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Wen J, Mohammed J, Bortolamiol-Becet D, Tsai H, Robine N, Westholm JO, Ladewig E, Dai Q, Okamura K, Flynt AS, Zhang D, Andrews J, Cherbas L, Kaufman TC, Cherbas P, Siepel A, Lai EC (2014) Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines. Genome Res 24(7):1236–1250. https://doi.org/10.1101/gr.161554.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Clark JP, Rahman R, Yang N, Yang LH, Lau NC (2017) Drosophila PAF1 modulates PIWI/piRNA silencing capacity. Curr Biol 27(17):2718–2726 e2714. https://doi.org/10.1016/j.cub.2017.07.052

  78. Post C, Clark JP, Sytnikova YA, Chirn GW, Lau NC (2014) The capacity of target silencing by Drosophila PIWI and piRNAs. RNA 20(12):1977–1986. https://doi.org/10.1261/rna.046300.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Menzel P, McCorkindale AL, Stefanov SR, Zinzen RP, Meyer IM (2019) Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis. RNA Biol 16(1):69–81. https://doi.org/10.1080/15476286.2018.1558907

    Article  PubMed  PubMed Central  Google Scholar 

  80. Abruzzi K, Chen X, Nagoshi E, Zadina A, Rosbash M (2015) RNA-seq profiling of small numbers of Drosophila neurons. Methods Enzymol 551:369–386. https://doi.org/10.1016/bs.mie.2014.10.025

    Article  CAS  PubMed  Google Scholar 

  81. Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L (2018) Cell-type specific sequencing of microRNAs from complex animal tissues. Nat Methods 15(4):283–289. https://doi.org/10.1038/nmeth.4610

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Luan H, Diao F, Scott RL, White BH (2020) The Drosophila split Gal4 system for neural circuit mapping. Front Neural Circuits 14:603397. https://doi.org/10.3389/fncir.2020.603397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Ariyapala IS, Holsopple JM, Popodi EM, Hartwick DG, Kahsai L, Cook KR, Sokol NS (2020) Identification of split-GAL4 drivers and enhancers that allow regional cell type manipulations of the Drosophila melanogaster intestine. Genetics 216(4):891–903. https://doi.org/10.1534/genetics.120.303625

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Buddika K, Xu J, Ariyapala IS, Sokol NS (2021) I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells. Development 148(1). https://doi.org/10.1242/dev.196568

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Authors and Affiliations

  1. Department of Biology, Indiana University, Bloomington, IN, USA

    Sromana Mukherjee & Nicholas Sokol

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  1. Sromana Mukherjee
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  2. Nicholas Sokol
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Correspondence to Nicholas Sokol .

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  1. Institute of Genetics, Technische Universität Dresden, Dresden, Germany

    Christian Dahmann

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Mukherjee, S., Sokol, N. (2022). Resources and Methods for the Analysis of MicroRNA Function in Drosophila. In: Dahmann, C. (eds) Drosophila. Methods in Molecular Biology, vol 2540. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2541-5_3

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  • DOI: https://doi.org/10.1007/978-1-0716-2541-5_3

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