Abstract
Recent development of targeted manipulation of histone modification enables us to experimentally and directly test the functional relevance of histone modifications accumulated at specific genomic regions. In particular, dCas9 epigenome editing has been widely used for site-specific manipulation of epigenetic modification. Here, we describe how to apply dCas9 epigenome editing in fish (medaka, Oryzias latipes) embryos and how to analyze induced changes in histone modification.
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References
Nakamura M, Gao Y, Dominguez AA, Qi LS (2021) CRISPR technologies for precise epigenome editing. Nat Cell Biol 23:11–22. https://doi.org/10.1038/s41556-020-00620-7
Heller EA, Cates HM, Peña CJ et al (2014) Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors. Nat Neurosci 17:1720–1727. https://doi.org/10.1038/nn.3871
Aleyasin H, Flanigan ME, Golden SA et al (2018) Cell-type-specific role of ΔFosB in nucleus accumbens in modulating intermale aggression. J Neurosci 38:5913–5924. https://doi.org/10.1523/JNEUROSCI.0296-18.2018
Hamilton PJ, Burek DJ, Lombroso SI et al (2018) Cell-type-specific epigenetic editing at the Fosb gene controls susceptibility to social defeat stress. Neuropsychopharmacology 43:272–284. https://doi.org/10.1038/npp.2017.88
Bustos FJ, Ampuero E, Jury N et al (2017) Epigenetic editing of the Dlg4/PSD95 gene improves cognition in aged and Alzheimer’s disease mice. Brain 140:3252–3268. https://doi.org/10.1093/brain/awx272
Mendenhall EM, Williamson KE, Reyon D et al (2013) Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol 31:1133–1136. https://doi.org/10.1038/nbt.2701
Konermann S, Brigham MD, Trevino AE et al (2013) Optical control of mammalian endogenous transcription and epigenetic states. Nature 500:472–476. https://doi.org/10.1038/nature12466
Hilton IB, D’Ippolito AM, Vockley CM et al (2015) Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol 33:510–517. https://doi.org/10.1038/nbt.3199
Fukushima HS, Takeda H, Nakamura R (2019) Targeted in vivo epigenome editing of H3K27me3. Epigenetics Chromatin 12:17. https://doi.org/10.1186/s13072-019-0263-z
Hwang WY, Fu Y, Reyon D et al (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31:227–229. https://doi.org/10.1038/nbt.2501
Stemmer M, Thumberger T, Del Sol KM et al (2015) CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One 10:e0124633. https://doi.org/10.1371/journal.pone.0124633
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595. https://doi.org/10.1093/bioinformatics/btp698
Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. https://doi.org/10.1093/bioinformatics/btq033
Zhang Y, Liu T, Meyer CA et al (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9:R137. https://doi.org/10.1186/gb-2008-9-9-r137
Qi LS, Larson MH, Gilbert LA et al (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–1183. https://doi.org/10.1016/j.cell.2013.02.022
Barkal AA, Srinivasan S, Hashimoto T et al (2016) Cas9 functionally opens chromatin. PLoS One 11:e0152683. https://doi.org/10.1371/journal.pone.0152683
Polstein LR, Perez-Pinera P, Kocak DD et al (2015) Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res 25:1158–1169. https://doi.org/10.1101/gr.179044.114
Varshney GK, Pei W, LaFave MC et al (2015) High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res 25:1030–1042. https://doi.org/10.1101/gr.186379.114
Hoshijima K, Jurynec MJ, Klatt Shaw D et al (2019) Highly efficient CRISPR-Cas9-based methods for generating deletion mutations and F0 embryos that lack gene function in zebrafish. Dev Cell 51:645–657.e4. https://doi.org/10.1016/j.devcel.2019.10.004
Nakamura R, Tsukahara T, Qu W et al (2014) Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates. Development 141:2568–2580. https://doi.org/10.1242/dev.108548
Tie F, Banerjee R, Stratton CA et al (2009) CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development 136:3131–3141. https://doi.org/10.1242/dev.037127
Yuan W, Xu M, Huang C et al (2011) H3K36 methylation antagonizes PRC2-mediated H3K27 methylation. J Biol Chem 286:7983–7989. https://doi.org/10.1074/jbc.M110.194027
Wu X, Scott DA, Kriz AJ et al (2014) Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32:670–676. https://doi.org/10.1038/nbt.2889
Singh R, Kuscu C, Quinlan A et al (2015) Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res 43:e118–e118. https://doi.org/10.1093/nar/gkv575
Maeder ML, Linder SJ, Cascio VM et al (2013) CRISPR RNA–guided activation of endogenous human genes. Nat Methods 10:977–979. https://doi.org/10.1038/nmeth.2598
Perez-Pinera P, Kocak DD, Vockley CM et al (2013) RNA-guided gene activation by CRISPR-Cas9–based transcription factors. Nat Methods 10:973–976. https://doi.org/10.1038/nmeth.2600
Lin L, Liu Y, Xu F et al (2018) Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience 7. https://doi.org/10.1093/gigascience/giy011
Pflueger C, Tan D, Swain T et al (2018) A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Res 28:1193–1206. https://doi.org/10.1101/gr.233049.117
Acknowledgments
This work was supported by JSPS Grant-in-Aid for JSPS Research Fellow Grant Number JP18J21761 to H.S.F., by Japan Agency for Medical Research and Development (AMED) under Grant Number JP18gm1110007h0001 to H.T., by Japan Society for the Promotion of Science (JSPS) grant number JP21K06013, and by Grant-in-Aid for Scientific Research on Innovative Areas grant number JP21H00245 to R.N.
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Fukushima, H.S., Takeda, H., Nakamura, R. (2023). Targeted Manipulation of Histone Modification in Medaka Embryos. In: Hatada, I., Horii, T. (eds) Epigenomics. Methods in Molecular Biology, vol 2577. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2724-2_20
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DOI: https://doi.org/10.1007/978-1-0716-2724-2_20
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