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Differential viral accessibility (DIVA) identifies alterations in chromatin architecture through large-scale mapping of lentiviral integration sites

Nature Protocols volume 14, pages 153–170 (2019)Cite this article

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Abstract

Alterations in chromatin structure play a major role in the epigenetic regulation of gene expression. Here, we describe a step-by-step protocol for differential viral accessibility (DIVA), a method for identifying changes in chromatin accessibility genome-wide. Commonly used methods for mapping accessible genomic loci have strong preferences toward detecting ‘open’ chromatin found at regulatory regions but are not well suited to studying chromatin accessibility in gene bodies and intergenic regions. DIVA overcomes this limitation, enabling a broader range of sites to be interrogated. Conceptually, DIVA is similar to ATAC-seq in that it relies on the integration of exogenous DNA into the genome to map accessible chromatin, except that chromatin architecture is probed through mapping integration sites of exogenous lentiviruses. An isogenic pair of cell lines are transduced with a lentiviral vector, followed by PCR amplification and Illumina sequencing of virus–genome junctions; the resulting sequences define a set of unique lentiviral integration sites, which are compared to determine whether genomic loci exhibit significantly altered accessibility between experimental and control cells. Experienced researchers will take 6 d to generate lentiviral stocks and transduce the target cells, a further 5 d to prepare the Illumina sequencing libraries and a few hours to perform the bioinformatic analysis.

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Fig. 1: Conceptual overview of DIVA.
Fig. 2: Workflow of a DIVA experiment.
Fig. 3: Genome coverage and sequencing depth required for DIVA.
Fig. 4: Anticipated results of a DIVA experiment.

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Acknowledgements

We thank S. Andrews for assistance with data analysis using SeqMonk. This work was supported by the Wellcome Trust, through a Principal Research Fellowship to P.J.L. (101835/Z/13/Z), a Sir Henry Wellcome Fellowship to R.T.T. (201387/Z/16/Z) and a PhD studentship to I.A.T. I.A.T. is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRG-2277-16).

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Author notes

  1. These authors contributed equally: Richard T. Timms, Iva A. Tchasovnikarova.

Authors and Affiliations

  1. Department of Medicine, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge, UK

    Richard T. Timms, Iva A. Tchasovnikarova & Paul J. Lehner

  2. Department of Genetics, Harvard Medical School, Boston, MA, USA

    Richard T. Timms & Iva A. Tchasovnikarova

  3. Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA

    Iva A. Tchasovnikarova

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  1. Richard T. Timms
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Contributions

R.T.T., I.A.T. and P.J.L. conceived the method. I.A.T. and R.T.T. performed all the experiments and, together with P.J.L., analyzed the data and wrote the manuscript.

Corresponding authors

Correspondence to Iva A. Tchasovnikarova or Paul J. Lehner.

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Key reference using this protocol

Tchasovnikarova, I. A. et al. Nat. Genet. 49, 1035–1044 (2017): https://doi.org/10.1038/ng.3878

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Timms, R.T., Tchasovnikarova, I.A. & Lehner, P.J. Differential viral accessibility (DIVA) identifies alterations in chromatin architecture through large-scale mapping of lentiviral integration sites. Nat Protoc 14, 153–170 (2019). https://doi.org/10.1038/s41596-018-0087-5

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