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Chromatin Immunoprecipitation Experiments from Drosophila Ovaries

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Drosophila Oogenesis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2626))

Abstract

Chromatin is composed of DNA and its associated proteins, and has an essential role in all cellular processes, including those taking place during Drosophila oogenesis. In order to understand the molecular basis of chromatin-based processes, such as transcription, it is essential to be able to study how and when different proteins, such as transcription factors, histones and RNA polymerases, interact with chromatin. One of the most popular methods to study this is chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Here, we describe a ChIP-seq protocol that has been optimized for Drosophila ovaries, focusing on sample preparation through preliminary data processing.

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References

  1. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316(5830):1497–1502. https://doi.org/10.1126/science.1141319

    Article  CAS  Google Scholar 

  2. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471(7339):480–485. https://doi.org/10.1038/nature09725

    Article  CAS  Google Scholar 

  3. Mendenhall EM, Bernstein BE (2008) Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev 18(2):109–115. https://doi.org/10.1016/j.gde.2008.01.010

    Article  CAS  Google Scholar 

  4. Bonn S, Zinzen RP, Perez-Gonzalez A, Riddell A, Gavin AC, Furlong EE (2012) Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat Protoc 7(5):978–994. https://doi.org/10.1038/nprot.2012.049

    Article  CAS  Google Scholar 

  5. Guertin MJ, Lis JT (2010) Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet 6(9):e1001114. https://doi.org/10.1371/journal.pgen.1001114

    Article  CAS  Google Scholar 

  6. Ghavi-Helm Y, Zhao B, Furlong EE (2016) Chromatin immunoprecipitation for analyzing transcription factor binding and histone modifications in Drosophila. Methods Mol Biol 1478:263–277. https://doi.org/10.1007/978-1-4939-6371-3_16

    Article  CAS  Google Scholar 

  7. Loubiere V, Delest A, Schuettengruber B, Martinez AM, Cavalli G (2017) Chromatin immunoprecipitation experiments from whole Drosophila embryos or larval imaginal discs. Bio Protoc 7(11):e2327. https://doi.org/10.21769/BioProtoc.2327

    Article  Google Scholar 

  8. Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Negre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP (2014) Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Res 24(7):1224–1235. https://doi.org/10.1101/gr.168807.113

    Article  CAS  Google Scholar 

  9. mod EC, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, HK MA, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, DM MA, Stein LD, White KP, Kellis M (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330(6012):1787–1797. https://doi.org/10.1126/science.1198374

    Article  CAS  Google Scholar 

  10. Spradling A (1993) Developmental genetics of oogenesis. The Development of Drosophila Melanogaster

    Google Scholar 

  11. Rust K, Byrnes LE, Yu KS, Park JS, Sneddon JB, Tward AD, Nystul TG (2020) A single-cell atlas and lineage analysis of the adult Drosophila ovary. Nat Commun 11(1):5628. https://doi.org/10.1038/s41467-020-19361-0

    Article  CAS  Google Scholar 

  12. Jia D, Huang YC, Deng WM (2015) Analysis of cell cycle switches in Drosophila oogenesis. Methods Mol Biol 1328:207–216. https://doi.org/10.1007/978-1-4939-2851-4_15

    Article  CAS  Google Scholar 

  13. Royzman I, Orr-Weaver TL (1998) S phase and differential DNA replication during Drosophila oogenesis. Genes Cells 3(12):767–776. https://doi.org/10.1046/j.1365-2443.1998.00232.x

    Article  CAS  Google Scholar 

  14. Orr-Weaver TL (1991) Drosophila chorion genes: cracking the eggshell’s secrets. BioEssays 13(3):97–105. https://doi.org/10.1002/bies.950130302

    Article  CAS  Google Scholar 

  15. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680. https://doi.org/10.1038/nrg2641

    Article  CAS  Google Scholar 

  16. Sokolova M, Turunen M, Mortusewicz O, Kivioja T, Herr P, Vaharautio A, Bjorklund M, Taipale M, Helleday T, Taipale J (2017) Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion. Cell Cycle 16(2):189–199. https://doi.org/10.1080/15384101.2016.1261765

    Article  CAS  Google Scholar 

  17. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH, mod EC (2009) Unlocking the secrets of the genome. Nature 459(7249):927–930. https://doi.org/10.1038/459927a

    Article  CAS  Google Scholar 

  18. ENCODE. https://www.encodeproject.org/

  19. Bardet AF, He Q, Zeitlinger J, Stark A (2011) A computational pipeline for comparative ChIP-seq analyses. Nat Protoc 7(1):45–61. https://doi.org/10.1038/nprot.2011.420

    Article  CAS  Google Scholar 

  20. Lerdrup M, Johansen JV, Agrawal-Singh S, Hansen K (2016) An interactive environment for agile analysis and visualization of ChIP-sequencing data. Nat Struct Mol Biol 23(4):349–357. https://doi.org/10.1038/nsmb.3180

    Article  CAS  Google Scholar 

  21. Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Gruning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D (2018) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 46(W1):W537–W544. https://doi.org/10.1093/nar/gky379

    Article  CAS  Google Scholar 

  22. Sokolova M, Moore HM, Prajapati B, Dopie J, Merilainen L, Honkanen M, Matos RC, Poukkula M, Hietakangas V, Vartiainen MK (2018) Nuclear actin is required for transcription during Drosophila oogenesis. iScience 9:63–70. https://doi.org/10.1016/j.isci.2018.10.010

    Article  CAS  Google Scholar 

  23. Andrews S FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  24. Burrows-Wheeler Alignment Tool http://bio-bwa.sourceforge.net/bwa.shtml#13

  25. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923

    Article  CAS  Google Scholar 

  26. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26. https://doi.org/10.1038/nbt.1754

    Article  CAS  Google Scholar 

  27. Thompson L, Randolph K, Norvell A (2015) Basic techniques in Drosophila ovary preparation. Methods Mol Biol 1328:21–28. https://doi.org/10.1007/978-1-4939-2851-4_2

    Article  CAS  Google Scholar 

  28. Ramirez F, Ryan DP, Gruning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dundar F, Manke T (2016) deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 44(W1):W160–W165. https://doi.org/10.1093/nar/gkw257

    Article  CAS  Google Scholar 

  29. Le Rolle V, Hernandez AI, Richard PY, Donal E, Carrault G (2008) Model-based analysis of myocardial strain data acquired by tissue Doppler imaging. Artif Intell Med 44(3):201–219. https://doi.org/10.1016/j.artmed.2008.06.001

    Article  Google Scholar 

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Acknowledgments

Work in the Vartiainen lab was supported by the Academy of Finland, Sigrid Juselius, Jane and Aatos Erkko as well as Finnish Cancer foundations.

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Authors and Affiliations

  1. Institute of Biotechnology, University of Helsinki, Helsinki, Finland

    Maria Sokolova & Maria K. Vartiainen

Authors
  1. Maria Sokolova
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  2. Maria K. Vartiainen
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Correspondence to Maria K. Vartiainen .

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Editors and Affiliations

  1. Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA

    Michelle S. Giedt

  2. Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA

    Tina L. Tootle

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Sokolova, M., Vartiainen, M.K. (2023). Chromatin Immunoprecipitation Experiments from Drosophila Ovaries. In: Giedt, M.S., Tootle, T.L. (eds) Drosophila Oogenesis. Methods in Molecular Biology, vol 2626. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2970-3_18

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  • DOI: https://doi.org/10.1007/978-1-0716-2970-3_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2969-7

  • Online ISBN: 978-1-0716-2970-3

  • eBook Packages: Springer Protocols

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