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Plant Chromatin Dynamics pp 167–181Cite as

Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1675))

Abstract

Nucleosomes are the basic repeating units of eukaryotic chromatin. They play important roles in chromatin compaction and gene regulation. Therefore, it is important to profile the in vivo locations of nucleosomes in the genome. Here we illustrate how to profile nucleosome occupancy at genome-wide scale using micrococcal nuclease (MNase) digestion combined with high throughput Illumina sequencing (MNase-seq). Nucleosome-associated DNA is relatively insensitive to digestion by micrococcal nuclease (MNase). Upon mild MNase treatment, the undigested nucleosomal DNA can be purified and sequenced allowing a precise localization of in vivo nucleosomes at a genome-wide level.

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References

  1. Noll M (1974) Subunit structure of chromatin. Nature 251(5472):249–251. doi:10.1038/251249a0

    Article  CAS  PubMed  Google Scholar 

  2. Clapier CR, Cairns BR (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem 78:273–304. doi:10.1146/annurev.biochem.77.062706.153223

    Article  CAS  PubMed  Google Scholar 

  3. Zentner GE, Henikoff S (2014) High-resolution digital profiling of the epigenome. Nat Rev Genet 15(12):814–827. doi:10.1038/nrg3798

    Article  CAS  PubMed  Google Scholar 

  4. Axel R (1975) Cleavage of DNA in nuclei and chromatin with Staphylococcal nuclease. Biochemistry 14(13):2921–2925. doi:10.1021/Bi00684a020

    Article  CAS  PubMed  Google Scholar 

  5. Sulkowski E, Laskowski M (1962) Mechanism of action of micrococcal nuclease on deoxyribonucleic acid. J Biol Chem 237(8):2620

    CAS  PubMed  Google Scholar 

  6. Becker J, Yau C, Hancock JM, Holmes CC (2013) NucleoFinder: a statistical approach for the detection of nucleosome positions. Bioinformatics 29(6):711–716. doi:10.1093/bioinformatics/bts719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W (2013) DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res 23(2):341–351. doi:10.1101/gr.142067.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Polishko A, Bunnik EM, Le Roch KG, Lonardi S (2014) PuFFIN – a parameter-free method to build nucleosome maps from paired-end reads. BMC Bioinformatics 15. doi:10.1186/1471-2105-15-S9-S11

  9. Woo SS, Zhang XK, Sauteraud R, Robert F, Gottardo R (2013) PING 2.0: an R/bioconductor package for nucleosome positioning using next-generation sequencing data. Bioinformatics 29(16):2049–2050. doi:10.1093/bioinformatics/btt348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Zhang XY, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5(5):1026–1035. doi:10.1371/journal.pbio.0050129

    CAS  Google Scholar 

  11. Carone BR, Hung JH, Hainer SJ, Chou MT, Carone DM, Weng ZP, Fazzio TG, Rando OJ (2014) High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Dev Cell 30(1):11–22. doi:10.1016/j.devcel.2014.05.024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chung HR, Dunkel I, Heise F, Linke C, Krobitsch S, Ehrenhofer-Murray AE, Sperling SR, Vingron M (2010) The effect of micrococcal nuclease digestion on nucleosome positioning data. PLoS One 5(12):e15754. doi:10.1371/journal.pone.0015754

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25. doi:10.1186/Gb-2009-10-3-R25

    Article  PubMed  PubMed Central  Google Scholar 

  14. Li RQ, Yu C, Li YR, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966–1967. doi:10.1093/bioinformatics/btp336

    Article  CAS  PubMed  Google Scholar 

  15. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760. doi:10.1093/bioinformatics/btp324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Babraham Bioinformatics FASTQC: a quality control tool for high througput sequencing data. http://wwwbioinformaticsbabrahamacuk/projects/fastqc/

    Google Scholar 

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Author information

Authors and Affiliations

  1. Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

    Alice Pajoro & Gerco C. Angenent

  2. Department of Computational Molecular Biology, Max-Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany

    Jose M. Muiño

  3. Business Unit Bioscience, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

    Gerco C. Angenent

  4. Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany

    Kerstin Kaufmann

Authors
  1. Alice Pajoro
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  2. Jose M. Muiño
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  3. Gerco C. Angenent
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  4. Kerstin Kaufmann
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Corresponding author

Correspondence to Alice Pajoro .

Editor information

Editors and Affiliations

  1. Department of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands

    Marian Bemer

  2. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

    Célia Baroux

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Pajoro, A., Muiño, J.M., Angenent, G.C., Kaufmann, K. (2018). Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis. In: Bemer, M., Baroux, C. (eds) Plant Chromatin Dynamics. Methods in Molecular Biology, vol 1675. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7318-7_11

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  • DOI: https://doi.org/10.1007/978-1-4939-7318-7_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7317-0

  • Online ISBN: 978-1-4939-7318-7

  • eBook Packages: Springer Protocols

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