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Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

View ORCID ProfileJiang Xu, Sanjeev Kumar, Nan Hua, Yi Kou, Xiao Lei, View ORCID ProfileMichael P. Rout, John D. Aitchison, Frank Alber, Lin Chen
doi: https://doi.org/10.1101/2022.02.03.478915
Jiang Xu
1Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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  • ORCID record for Jiang Xu
Sanjeev Kumar
3Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, USA
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Nan Hua
2Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
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Yi Kou
1Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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Xiao Lei
1Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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Michael P. Rout
5Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
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John D. Aitchison
3Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, USA
4Departments of Pediatrics and Biochemistry, University of Washington, Seattle, Washington 98195, USA
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Frank Alber
2Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
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Lin Chen
1Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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  • For correspondence: linchen@usc.edu
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Abstract

Traditional methods used to map the three-dimensional organization of chromatin in-situ generally involve chromatin conformation capture by formaldehyde crosslinking, followed by detergent solubilization and enzymatic digestion of DNA. Ligation of proximal DNA fragments followed by next generation sequencing (NGS) generates contact information that enables a global view of the chromatin conformation. Here, we explore the use of cryomilling to physically fragmentize the cells under cryogenic conditions to probe chromatin interactions in the cryomilled cell fragments by the tethered chromatin conformation capture (TCC). Our results show that cryomilling TCC (CTCC) can generate a global contact map similar to that obtained with in-situ Hi-C. This result suggests that summation of chromatin interactions mapped in individual subcellular fragments can reconstitute the global contact map of intact cells in an ensemble manner, paving the way for chromatin conformation analyses of solid tissue by CTCC. Compared with the conventional in-situ methods such as Hi-C, CTCC shows more uniform access to different subcompartments of the folded genome. On the other hand, most inter-chromosomal (trans) contacts are diminished or lost in CTCC except for a group of unique trans contacts that remain intact throughout the cryomilling and in- vitro crosslinking steps. These apparently ultra-stable trans interactions have much enhanced signal in CTCC due to the elimination of signals of most, presumably weak and transient trans interactions. Systematic and comparative analyses between CTCC and in-situ Hi-C provide further insights into the chromatin structure organization and reveal a generally unentangled chromosome interface and the existence of stable inter-chromosomal contacts that may represent intermingled inter-chromosomal interfaces.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • This version of the manuscript added data availability information, updated funding information, changed the author order as agreed by all authors, and revised some minor text errors.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted February 12, 2022.
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Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions
Jiang Xu, Sanjeev Kumar, Nan Hua, Yi Kou, Xiao Lei, Michael P. Rout, John D. Aitchison, Frank Alber, Lin Chen
bioRxiv 2022.02.03.478915; doi: https://doi.org/10.1101/2022.02.03.478915
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Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions
Jiang Xu, Sanjeev Kumar, Nan Hua, Yi Kou, Xiao Lei, Michael P. Rout, John D. Aitchison, Frank Alber, Lin Chen
bioRxiv 2022.02.03.478915; doi: https://doi.org/10.1101/2022.02.03.478915

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