Technical Report

RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites

  • Nature Structural & Molecular Biology 25109114 (2018)
  • doi:10.1038/s41594-017-0006-4
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Abstract

Thousands of long noncoding RNAs (lncRNAs) have been identified in eukaryotic genomes, many of which are expressed in spatially and temporally restricted patterns. Nonetheless, the roles of the majority of these transcripts are still unknown. One of the mechanisms by which lncRNAs function is through the modulation of chromatin states. To assess the functions of lncRNAs, we developed RNA-DamID, a novel approach that detects lncRNA–genome interactions in a cell-type-specific manner in vivo with high sensitivity and accuracy. Identifying the cell-type-specific genome occupancy of lncRNAs is vital to understanding their mechanisms of action in development and disease. We used RNA-DamID to investigate targeting of the lncRNAs in the Drosophila dosage-compensation complex (DCC) and show that initial targeting is cell-type specific.

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Acknowledgements

We thank M. Kuroda (Harvard University), V. Meller (Wayne State University), T. Megraw (Florida State University) and P. Amaral (Gurdon Institute) for reagents, T. Leonardi for advice on data visualization and P. Amaral, T. Southall, O. Marshall and members of the Brand Lab for advice and discussion. This work was funded by the Royal Society Darwin Trust Research Professorship, a Wellcome Trust Senior Investigator Award 103792 and Wellcome Trust Programme Grant 092545 to A.H.B. S.W.C. was funded by a Herchel Smith Research Studentship. A.H.B acknowledges core funding to the Gurdon Institute from the Wellcome Trust (092096) and CRUK (C6946/A14492).

Author information

Author notes

    • Seth W. Cheetham

    Present address: Mater Research Institute, University of Queensland, Wooloongabba, Queensland, Australia

Affiliations

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

    • Seth W. Cheetham
    •  & Andrea H. Brand

Authors

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Contributions

S.W.C. and A.H.B. designed the experiments. S.W.C. performed the experiments. S.W.C. and A.H.B. analyzed the data. S.W.C. and A.H.B. wrote the manuscript. Both authors reviewed the manuscript before submission.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Andrea H. Brand.

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Supplementary information