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Chromatin Immunoprecipitation Techniques in Neuropsychiatric Research

  • Andrew A. Bartlett
  • Richard G. HunterEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2011)

Abstract

Neuropsychiatric disorders are highly prevalent (e.g., affecting children 2–8 years old at a rate of 14%). Many of these disorders are highly heritable such as major depressive disorder and schizophrenia. Despite this, genome-wide association has failed to identify gene(s) significantly associated with diagnostic status suggesting a strong role for environmental factors and the epigenome. From a molecular standpoint, the study of DNA-protein interactions yields fruitful information regarding the regulation of cellular processes above the level of the nucleotide sequence. Understanding chromatin dynamics may continue to explain individual variation to environmental perturbation and subsequent behavioral response. Chromatin immunoprecipitation (ChIP) techniques have allowed for probing of epigenetic effectors at specific regions of the genome. The following article reviews the current techniques and considerations when incorporation ChIP into neuropsychiatric models.

Key words

Neuropsychiatric disorders Chromatin immunoprecipitation DNA-protein Epigenetic 

Notes

Acknowledgments

The authors would like to thank both Brian B Griffiths and Amanda MK Madden for technical assistance as well as the University of Massachusetts Boston for startup funding (RGH).

References

  1. 1.
    CDC (2018) Data & statistics. Children’s mental health. NCBDDD, CDC, Atlanta, GA. https://www.cdc.gov/childrensmentalhealth/data.html. Accessed 15 Mar 2018.Google Scholar
  2. 2.
    Gejman P, Sanders A, Duan J (2010) The role of genetics in the etiology of Schizophrenia. Psychiatr Clin North Am 33:35–66CrossRefGoogle Scholar
  3. 3.
    Lohoff FW (2010) Overview of the genetics of major depressive disorder. Curr Psychiatry Rep 12:539–546CrossRefGoogle Scholar
  4. 4.
    Bartlett AA, Singh R, Hunter RG (2017) Anxiety and epigenetics. Adv Exp Med Biol 978:145–166CrossRefGoogle Scholar
  5. 5.
    Collins AL, Kim Y, Sklar P, International Schizophrenia Consortium, O’Donovan MC, Sullivan PF (2012) Hypothesis-driven candidate genes for schizophrenia compared to genome-wide association results. Psychol Med 42:607–616CrossRefGoogle Scholar
  6. 6.
    CONVERGE consortium (2015) Sparse whole-genome sequencing identifies two loci for major depressive disorder. Nature 523:588–591CrossRefGoogle Scholar
  7. 7.
    Need AC, Ge D, Weale ME, Maia J, Feng S, Heinzen EL, Shianna KV, Yoon W, Kasperaviciūte D, Gennarelli M, Strittmatter WJ, Bonvicini C, Rossi G, Jayathilake K, Cola PA, McEvoy JP, Keefe RSE, Fisher EMC, St Jean PL, Giegling I, Hartmann AM, Möller H-J, Ruppert A, Fraser G, Crombie C, Middleton LT, St Clair D, Roses AD, Muglia P, Francks C, Rujescu D, Meltzer HY, Goldstein DB (2009) A genome-wide investigation of SNPs and CNVs in schizophrenia. PLoS Genet 5:e1000373CrossRefGoogle Scholar
  8. 8.
    Solomon MJ, Larsen PL, Varshavsky A (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937–947CrossRefGoogle Scholar
  9. 9.
    LaPlant Q, Nestler EJ (2011) CRACKing the histone code: cocaine’s effects on chromatin structure and function. Horm Behav 59:321–330CrossRefGoogle Scholar
  10. 10.
    Maze I, Covington HE, Dietz DM, LaPlant Q, Renthal W, Russo SJ, Mechanic M, Mouzon E, Neve RL, Haggarty SJ, Ren Y, Sampath SC, Hurd YL, Greengard P, Tarakhovsky A, Schaefer A, Nestler EJ (2010) Essential role of the histone methyltransferase G9a in cocaine-induced plasticity. Science 327:213–216CrossRefGoogle Scholar
  11. 11.
    Renthal W, Kumar A, Xiao G, Wilkinson M, Covington HE, Maze I, Sikder D, Robison AJ, LaPlant Q, Dietz DM, Russo SJ, Vialou V, Chakravarty S, Kodadek TJ, Stack A, Kabbaj M, Nestler EJ (2009) Genome wide analysis of chromatin regulation by cocaine reveals a novel role for sirtuins. Neuron 62:335–348CrossRefGoogle Scholar
  12. 12.
    Levenson JM, O’Riordan KJ, Brown KD, Trinh MA, Molfese DL, Sweatt JD (2004) Regulation of histone acetylation during memory formation in the hippocampus. J Biol Chem 279:40545–40559CrossRefGoogle Scholar
  13. 13.
    Lubin FD, Roth TL, Sweatt JD (2008) Epigenetic regulation of BDNF gene transcription in the consolidation of fear memory. J Neurosci 28:10576–10586CrossRefGoogle Scholar
  14. 14.
    Miller CA, Sweatt JD (2007) Covalent modification of DNA regulates memory formation. Neuron 53:857–869CrossRefGoogle Scholar
  15. 15.
    Hunter RG, McCarthy KJ, Milne TA, Pfaff DW, McEwen BS (2009) Regulation of hippocampal H3 histone methylation by acute and chronic stress. Proc Natl Acad Sci U S A 106:20912–20917CrossRefGoogle Scholar
  16. 16.
    Hunter RG, Murakami G, Dewell S, Seligsohn M, Baker MER, Datson NA, McEwen BS, Pfaff DW (2012) Acute stress and hippocampal histone H3 lysine 9 trimethylation, a retrotransposon silencing response. Proc Natl Acad Sci U S A 109:17657–17662CrossRefGoogle Scholar
  17. 17.
    Polman JAE, Kloet D, Ronald E, Datson NA (2013) Two populations of glucocorticoid receptor-binding sites in the male rat hippocampal genome. Endocrinology 154:1832–1844CrossRefGoogle Scholar
  18. 18.
    Mifsud KR, Reul JMHM (2016) Acute stress enhances heterodimerization and binding of corticosteroid receptors at glucocorticoid target genes in the hippocampus. Proc Natl Acad Sci U S A 113:11336–11341CrossRefGoogle Scholar
  19. 19.
    Feng J, Liu T, Qin B, Zhang Y, Liu XS (2012) Identifying ChIP-seq enrichment using MACS. Nat Protoc 7:1728.  https://doi.org/10.1038/nprot.2012.101CrossRefPubMedGoogle Scholar
  20. 20.
    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:R137CrossRefGoogle Scholar
  21. 21.
    Bartlett AA, Hunter RG (2018) Transposons, stress and the functions of the deep genome. Front Neuroendocrinol 49:170.  https://doi.org/10.1016/j.yfrne.2018.03.002CrossRefPubMedGoogle Scholar
  22. 22.
    Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung M-S, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SCR, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD (2011) An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18:91–93CrossRefGoogle Scholar
  23. 23.
    Wardle FC, Tan H (2015) A ChIP on the shoulder? Chromatin immunoprecipitation and validation strategies for ChIP antibodies. F1000Res 4:235.  https://doi.org/10.12688/f1000research.6719.1CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Polman JAE, Welten JE, Bosch DS, de Jonge RT, Balog J, van der Maarel SM, de Kloet ER, Datson NA (2012) A genome-wide signature of glucocorticoid receptor binding in neuronal PC12 cells. BMC Neurosci 13:118CrossRefGoogle Scholar
  25. 25.
    Haring M, Offermann S, Danker T, Horst I, Peterhansel C, Stam M (2007) Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods 3:11CrossRefGoogle Scholar
  26. 26.
    Gasper WC, Marinov GK, Pauli-Behn F, Scott MT, Newberry K, DeSalvo G, Ou S, Myers RM, Vielmetter J, Wold BJ (2014) Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies. Sci Rep 4:5152.  https://doi.org/10.1038/srep05152CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Arora S, Ayyar BV, O’Kennedy R (2014) Affinity chromatography for antibody purification. In: Labrou NE (ed) Protein downstream processing: design, development and application of high and low-resolution methods, Methods in molecular biology. Humana Press, Totowa, NJ. https://www.researchgate.net/publication/261171028_Affinity_Chromatography_for_Antibody_Purification. Accessed 15 Mar 2018.Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of PsychologyUniversity of Massachusetts, BostonBostonUSA
  2. 2.Laboratory of NeuroendocrinologyThe Rockefeller UniversityNew YorkUSA

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