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Systematic evaluation of chromosome conformation capture assays

Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, Sergey V. Venev, Nils Krietenstein, Krishna Mohan Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan MJ Genga, Rene Maehr, Oliver J. Rando, Leonid A. Mirny, Johan Harmen Gibcus, View ORCID ProfileJob Dekker
doi: https://doi.org/10.1101/2020.12.26.424448
Betul Akgol Oksuz
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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Liyan Yang
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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Sameer Abraham
8Department of Physics, Massachusetts Institute of Technology, Cambridge, MA
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Sergey V. Venev
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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Nils Krietenstein
6Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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Krishna Mohan Parsi
5Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
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Hakan Ozadam
7Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA. Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
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Marlies E. Oomen
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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Ankita Nand
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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Hui Mao
5Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
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Ryan MJ Genga
5Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
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Rene Maehr
5Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
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Oliver J. Rando
6Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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Leonid A. Mirny
3Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA
4Graduate Program in Biophysics, Harvard University, Cambridge, MA
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Johan Harmen Gibcus
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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  • For correspondence: Johan.Gibcus@umassmed.edu Job.Dekker@umassmed.edu
Job Dekker
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
2Howard Hughes Medical Institute, Chevy Chase, MD, USA
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  • ORCID record for Job Dekker
  • For correspondence: Johan.Gibcus@umassmed.edu Job.Dekker@umassmed.edu
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Abstract

Chromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of cross-linkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthens the compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results for multiple cell types and cell cycle stages. We find that cell type-specific quantitative differences in chromosome folding are not detected or underestimated by some protocols. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using conventional Hi-C, Micro-C and Hi-C 3.0 for commonly used cell lines in the 4D Nucleome Project.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Supplemental Table 1 added

  • https://data.4dnucleome.org/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 27, 2020.
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Systematic evaluation of chromosome conformation capture assays
Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, Sergey V. Venev, Nils Krietenstein, Krishna Mohan Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan MJ Genga, Rene Maehr, Oliver J. Rando, Leonid A. Mirny, Johan Harmen Gibcus, Job Dekker
bioRxiv 2020.12.26.424448; doi: https://doi.org/10.1101/2020.12.26.424448
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Systematic evaluation of chromosome conformation capture assays
Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, Sergey V. Venev, Nils Krietenstein, Krishna Mohan Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan MJ Genga, Rene Maehr, Oliver J. Rando, Leonid A. Mirny, Johan Harmen Gibcus, Job Dekker
bioRxiv 2020.12.26.424448; doi: https://doi.org/10.1101/2020.12.26.424448

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