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5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells

Abstract

Nucleosomes are the basic unit of chromatin that help the packaging of genetic material while controlling access to the genetic information. The underlying DNA sequence, together with transcription-associated proteins and chromatin remodelling complexes, are important factors that influence the organization of nucleosomes. Here, we show that the naturally occurring DNA modification, 5-formylcytosine (5fC) is linked to tissue-specific nucleosome organization. Our study reveals that 5fC is associated with increased nucleosome occupancy in vitro and in vivo. We demonstrate that 5fC-associated nucleosomes at enhancers in the mammalian hindbrain and heart are linked to elevated gene expression. Our study also reveals the formation of a reversible-covalent Schiff base linkage between lysines of histone proteins and 5fC within nucleosomes in a cellular environment. We define their specific genomic loci in mouse embryonic stem cells and look into the biological consequences of these DNA–histone Schiff base sites. Collectively, our findings show that 5fC is a determinant of nucleosome organization and plays a role in establishing distinct regulatory regions that control transcription.

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Fig. 1: 5fC increases nucleosome occupancy and stability.
Fig. 2: 5fC within a genomic sequence context enhances nucleosome occupancy in vitro.
Fig. 3: 5fC is a determinant of nucleosome organization in vivo that is linked to gene expression.
Fig. 4: 5fC–histone interaction model within a nucleosome.
Fig. 5: 5fC can form a Schiff base with histones in a chromatin context that impacts transcription elongation.

Data availability

Sequencing data are available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession no. E-MTAB-6271. 5fC regions in tissues are available in the GEO database under accession no. GSE77447. 5fC and 5caC regions in mESCs are available under accession no. GSE42250. Histone marks were obtained from ENCODE (https://www.encodeproject.org/) with the following accession numbers: H3K27ac (ENCFF203QTV) and H3K4me1 (ENCFF542GAS) for hindbrain; H3K27ac (ENCFF954URD) and H3K4me1 (ENCFF737FNO) for heart. Data sets corresponding to the GRO–seq experiments were obtained from the GEO database under accession no. GSE64748.

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Acknowledgements

S.B. is a senior investigator of the Wellcome Trust (grant no. 099232/z/12/z). The Balasubramanian laboratory is also supported by core funding from Cancer Research UK (C14303/A17197). Z.L. is supported by a studentship from A*STAR (Singapore). M.A.D is supported by the Leukaemia Foundation Australia senior fellowship and Howard Hughes Medical Institute international research scholarship. The Reik laboratory is supported by BBSRC (BB/ K010867/1) and the Wellcome Trust (095645/Z/11/Z).

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E.A.R., S.B., W.R. and M.A.D. designed the study. E.A.R., R.H., Z.L., W.D., M.I., J.S. and Z.L. performed the experiments. G.P., S.M.C. and D.B. performed the computational analysis. All authors analysed and interpreted the data. E.A.R., G.P. and S.B. wrote the manuscript, with contributions from all authors.

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Correspondence to Shankar Balasubramanian.

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S.B. is a founder, shareholder and scientific advisor to Cambridge Epigenetix Ltd. W.F. and M.A.D. are scientific advisors to Cambridge Epigenetix Ltd.

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Raiber, EA., Portella, G., Martínez Cuesta, S. et al. 5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells. Nature Chem 10, 1258–1266 (2018). https://doi.org/10.1038/s41557-018-0149-x

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