Profiling Open Chromatin Structure in the Ovarian Somatic Cells Using ATAC-seq

  • Kensaku Murano
  • Yuka W. Iwasaki
  • Haruhiko SiomiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1680)


The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was recently established as a method to profile open chromatin, which overcomes the sample size limitations of the alternative methods DNase/MNase-seq. To investigate the role of Piwi in heterochromatin formation around transposable element loci, we have used ATAC-seq to examine chromatin accessibility at target transposable elements in a Drosophila cultured cell line, ovarian somatic cells (OSCs). In this chapter, we describe our method to profile open chromatin structure in OSCs using ATAC-seq.

Key words

ATAC-seq Chromatin accessibility Heterochromatin Small RNA Transposons Drosophila OSC 



This work was supported by grants from the Kato Memorial Bioscience Foundation to K.M., and Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) to Y.W.I. and H.S.


  1. 1.
    Bell O, Tiwari VK, Thoma NH, Schubeler D (2011) Determinants and dynamics of genome accessibility. Nat Rev Genet 12(8):554–564. doi: 10.1038/nrg3017 CrossRefPubMedGoogle Scholar
  2. 2.
    Gross DS, Garrard WT (1988) Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57:159–197. doi: 10.1146/ CrossRefPubMedGoogle Scholar
  3. 3.
    Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA (2012) The accessible chromatin landscape of the human genome. Nature 489(7414):75–82. doi: 10.1038/nature11232 CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10(12):1213–1218. doi: 10.1038/nmeth.2688 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Iwasaki YW, Murano K, Ishizu H, Shibuya A, Iyoda Y, Siomi MC, Siomi H, Saito K (2016) Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons. Mol Cell 63(3):408–419. doi: 10.1016/j.molcel.2016.06.008 CrossRefPubMedGoogle Scholar
  6. 6.
    Iwasaki YW, Siomi MC, Siomi H (2015) PIWI-interacting RNA: its biogenesis and functions. Annu Rev Biochem 84:405–433. doi: 10.1146/annurev-biochem-060614-034258 CrossRefPubMedGoogle Scholar
  7. 7.
    Siomi MC, Sato K, Pezic D, Aravin AA (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12(4):246–258. doi: 10.1038/nrm3089 CrossRefPubMedGoogle Scholar
  8. 8.
    Saito K (2014) RNAi and overexpression of genes in ovarian somatic cells. Methods Mol Biol 1093:25–33. doi: 10.1007/978-1-62703-694-8_3 CrossRefPubMedGoogle Scholar
  9. 9.
    Saito K, Inagaki S, Mituyama T, Kawamura Y, Ono Y, Sakota E, Kotani H, Asai K, Siomi H, Siomi MC (2009) A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila. Nature 461(7268):1296–1299. doi: 10.1038/nature08501 CrossRefPubMedGoogle Scholar
  10. 10.
    Ohtani H, Iwasaki YW, Shibuya A, Siomi H, Siomi MC, Saito K (2013) DmGTSF1 is necessary for Piwi-piRISC-mediated transcriptional transposon silencing in the Drosophila ovary. Genes Dev 27(15):1656–1661. doi: 10.1101/gad.221515.113 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Sienski G, Donertas D, Brennecke J (2012) Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151(5):964–980. doi: 10.1016/j.cell.2012.10.040 CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    FastQC: a quality control tool for high throughput sequence data.
  13. 13.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. doi: 10.1038/nmeth.1923 CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
  15. 15.
    Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9(9):R137. doi: 10.1186/gb-2008-9-9-r137 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D (2002) The human genome browser at UCSC. Genome Res 12(6):996–1006. doi: 10.1101/gr.229102. Article published online before print in May 2002CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12. doi: CrossRefGoogle Scholar
  18. 18.
  19. 19.
    Shin H, Liu T, Manrai AK, Liu XS (2009) CEAS: cis-regulatory element annotation system. Bioinformatics 25(19):2605–2606. doi: 10.1093/bioinformatics/btp479 CrossRefPubMedGoogle Scholar
  20. 20.
    Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57. doi: 10.1038/nprot.2008.211 CrossRefPubMedGoogle Scholar
  21. 21.
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29. doi: 10.1038/75556 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Kensaku Murano
    • 1
  • Yuka W. Iwasaki
    • 1
  • Haruhiko Siomi
    • 1
    Email author
  1. 1.Department of Molecular BiologyKeio University School of MedicineTokyoJapan

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