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Mapping RNA–Chromatin Interactions In Vivo with RNA-DamID

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RNA-Chromatin Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2161))

Abstract

Long-noncoding RNAs (lncRNAs) are emerging as regulators of development and disease. lncRNAs are expressed in exquisitely precise expression patterns in vivo and many interact with chromatin to regulate gene expression. However, the limited sensitivity of RNA-purification techniques has precluded the identification of genomic targets of cell-type specific lncRNAs. RNA-DamID is a powerful new approach to understand the mechanisms by which lncRNAs act in vivo. RNA-DamID is highly sensitive and accurate, and can resolve cell-type-specific chromatin binding patterns without cell isolation. The determinants of RNA-chromatin interactions can be identified with RNA-DamID by analyzing RNA and protein cofactor mutants. Here we describe how to implement RNA-DamID and the design considerations to take into account to accurately identify lncRNA-chromatin interactions in vivo.

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Acknowledgments

A.H.B is funded by a Royal Society Darwin Trust Research Professorship and Wellcome Trust Senior Investigator Award 103792. A.H.B acknowledges core funding to The Gurdon Institute from the Wellcome Trust (092096) and CRUK (C6946/A14492). S.W.C. acknowledges support from a National Health and Medical Research Council (NHMRC) Early Career Fellowship (GNT1161832) and Mater Foundation.

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Authors and Affiliations

  1. Mater Research Institute-University of Queensland, Woolloongabba, QLD, Australia

    Seth W. Cheetham

  2. The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK

    Andrea H. Brand

Authors
  1. Seth W. Cheetham
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  2. Andrea H. Brand
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Corresponding author

Correspondence to Andrea H. Brand .

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Editors and Affiliations

  1. Department for Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark

    Ulf Andersson Vang Ørom

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Cheetham, S.W., Brand, A.H. (2020). Mapping RNA–Chromatin Interactions In Vivo with RNA-DamID. In: Ørom, U. (eds) RNA-Chromatin Interactions. Methods in Molecular Biology, vol 2161. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0680-3_18

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  • DOI: https://doi.org/10.1007/978-1-0716-0680-3_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0679-7

  • Online ISBN: 978-1-0716-0680-3

  • eBook Packages: Springer Protocols

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