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.
Highlights
Chromatin conformation constitutes a fundamental level of eukaryotic genome regulation
We validate this method by comparing chromatin conformation maps for a controlled cell titration, demonstrating that the obtained maps are robust down to 1,000 cells of starting material and are able to detect all conformational features— compartments, topologically associating domains (TADs) and loops— as maps produced with a higher number of cells
The development of high-throughput genome-wide techniques to measure chromatin conformation has been instrumental to further our understanding of the biological importance of the threedimensional organisation of chromatin in the nucleus
Summary
Chromatin conformation constitutes a fundamental level of eukaryotic genome regulation. The most widely used current experimental approaches rely on the availability of a substantial amount of starting material—on the order of millions of cells—below which experimental noise and low sequencing library complexity become limiting factors[7] Far, this restricts high-resolution analyses of population Hi-C to biological questions for which large numbers of cells are available and limits the implementation of chromatin conformation analyses for rare cell populations such as those commonly obtained in clinical settings. We present Low-C, an improved in situ Hi-C method that allows the generation of high-quality genome-wide chromatin conformation maps using very low amounts of starting material We validate this method by comparing chromatin conformation maps for a controlled cell titration, demonstrating that the obtained maps are robust down to 1,000 cells of starting material and are able to detect all conformational features— compartments, topologically associating domains (TADs) and loops— as maps produced with a higher number of cells. Computational analysis of the data allows us to detect patientspecific translocations and substantial amounts of variation in topological features
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