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UMI-4C for quantitative and targeted chromosomal contact profiling

Nature Methods volume 13, pages 685–691 (2016)Cite this article

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Abstract

We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMIs) to derive high-complexity quantitative chromosome contact profiles with controlled signal-to-noise ratios. UMI-4C detects chromosomal interactions with improved sensitivity and specificity, and it can easily be multiplexed to allow robust comparison of contact distributions between loci and conditions. This approach may open the way to the incorporation of contact distributions into quantitative models of gene regulation.

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Figure 1: Description of UMI-4C.
Figure 2: UMI-4C reproducibility.
Figure 3: UMI-4C analysis of GATA1.
Figure 4: Multiplexing UMI-4C in the HBB locus.

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Acknowledgements

Research in the Tanay Lab was supported by the European Research Council, the MODHEP project and the Israeli Science Foundation. Research in the Izraeli Lab was supported by the Israel Science Foundation, the Waxman Cancer Research Foundation and the Dotan Center for Hematological Malignancies at Tel Aviv University. This work was performed in partial fulfillment of the requirements for a PhD degree by O.S.

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Authors and Affiliations

  1. Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel

    Omer Schwartzman & Shai Izraeli

  2. Functional Genomics and Childhood Leukemia Research Section, Cancer Research Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel

    Omer Schwartzman & Shai Izraeli

  3. Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel

    Omer Schwartzman, Zohar Mukamel, Noa Oded-Elkayam, Pedro Olivares-Chauvet, Yaniv Lubling, Gilad Landan & Amos Tanay

  4. Department of Biological Regulation, Weizmann Institute, Rehovot, Israel

    Omer Schwartzman, Zohar Mukamel, Noa Oded-Elkayam, Pedro Olivares-Chauvet, Yaniv Lubling, Gilad Landan & Amos Tanay

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  1. Omer Schwartzman
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Contributions

O.S., S.I. and A.T. designed the study. O.S. and Z.M. developed the experimental protocol with help and reagents from N.O.-E., P.O.-C., Y.L. and G.L. O.S. performed experiments. O.S. and A.T. analyzed the data and developed the pipeline. O.S. and A.T. wrote the paper. S.I. and A.T. supervised research.

Corresponding author

Correspondence to Amos Tanay.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10 and Supplementary Tables 1–4 (PDF 17266 kb)

Supplementary Software

UMI-4C analysis software. (ZIP 1488 kb)

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Schwartzman, O., Mukamel, Z., Oded-Elkayam, N. et al. UMI-4C for quantitative and targeted chromosomal contact profiling. Nat Methods 13, 685–691 (2016). https://doi.org/10.1038/nmeth.3922

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