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In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions

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Plant Long Non-Coding RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1933))

Abstract

Recently, long noncoding RNAs (lncRNAs) are shown to be implicating nuclear domain organization and gene regulation by mediating long-range chromatin interactions. Chromosome conformation capture (3C) is a method used to study such long-range interaction between two different loci in the 3D nuclear space. Through successive improvement in resolution and throughput, 3C, chromosome conformation capture on chip (4C), and chromosome conformation capture carbon copy (5C) to Hi-C methods were developed to study interactions between loci from one versus one scale to an unprecedented genome-wide resolution. In situ Hi-C is a variant of Hi-C in which proximity ligation is performed at the intact nuclei to improve the signal-to-noise ratio and throughput of the experiment to provide useful genome-wide contact frequency matrix/maps. The contact frequency maps obtained could be used for physical ordering of scaffolds in complex genome assembly projects, in deducing the nuclear domain organization in high resolution and in identifying specific long-range interactions between genomic regions of interest. In this chapter, we describe in detail a protocol for in situ Hi-C used on crops like barley, wheat, rye, oat, and evening primrose.

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Acknowledgments

This work was financially supported by core funding of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, and project funding (“SHAPE”) from the German Federal Ministry of Education and Research (BMBF, Grant no. 031B0190A) to Dr. Nils Stein and Dr. Martin Mascher. We thank Dr. Erez Lieberman-Aiden and Dr. Olga Dudchenko for helpful discussions on the in situ Hi-C method. We thank Ines Walde and Manuela Knauft for excellent technical assistance during protocol development and TCC/Hi-C library construction.

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Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany

    Sudharsan Padmarasu, Axel Himmelbach, Martin Mascher & Nils Stein

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  1. Sudharsan Padmarasu
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  2. Axel Himmelbach
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Correspondence to Nils Stein .

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Editors and Affiliations

  1. Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China

    Julia A. Chekanova  & Hsiao-Lin V. Wang  & 

  2. Department of Biology, Emory University, Atlanta, Georgia, USA

    Hsiao-Lin V. Wang

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Padmarasu, S., Himmelbach, A., Mascher, M., Stein, N. (2019). In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions. In: Chekanova, J.A., Wang, HL.V. (eds) Plant Long Non-Coding RNAs. Methods in Molecular Biology, vol 1933. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9045-0_28

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  • DOI: https://doi.org/10.1007/978-1-4939-9045-0_28

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9044-3

  • Online ISBN: 978-1-4939-9045-0

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