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Nat Commun. 2018 Nov 29;9(1):4938. doi: 10.1038/s41467-018-06961-0.

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method.

Author information

1
Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149, Muenster, Germany.
2
Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Muenster, Germany.
3
Department of Clinical Pathology, Robert-Bosch-Hospital, Auerbachstrasse 110, 70376, Stuttgart, Germany.
4
Dr. Margarete Fischer Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, 70376, Stuttgart, Germany.
5
Eberhard Karls Universität Tübingen, Geschwister-Scholl-Platz, 72074, Tübingen, Germany.
6
Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149, Muenster, Germany. jmv@mpi-muenster.mpg.de.

Abstract

Chromatin conformation constitutes a fundamental level of eukaryotic genome regulation. However, our ability to examine its biological function and role in disease is limited by the large amounts of starting material required to perform current experimental approaches. Here, we present Low-C, a Hi-C method for low amounts of input material. By systematically comparing Hi-C libraries made with decreasing amounts of starting material we show that Low-C is highly reproducible and robust to experimental noise. To demonstrate the suitability of Low-C to analyse rare cell populations, we produce Low-C maps from primary B-cells of a diffuse large B-cell lymphoma patient. We detect a common reciprocal translocation t(3;14)(q27;q32) affecting the BCL6 and IGH loci and abundant local structural variation between the patient and healthy B-cells. The ability to study chromatin conformation in primary tissue will be fundamental to fully understand the molecular pathogenesis of diseases and to eventually guide personalised therapeutic strategies.

PMID:
30498195
PMCID:
PMC6265268
DOI:
10.1038/s41467-018-06961-0
[Indexed for MEDLINE]
Free PMC Article

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