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Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis

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Plant Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2512))

Abstract

Hi-C enables the characterization of the 0conformation of the genome in the three-dimensional nuclear space. This technique has revolutionized our ability to detect interactions between linearly distant genomic sites on a genome-wide scale. Here, we detail a protocol to carry out in situ Hi-C in plants and describe a straightforward bioinformatics pipeline for the analysis of such data, in particular for comparing samples from different organs or conditions.

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Acknowledgments

FJP-d, JES-F, and AR-C were funded by fellowships from the Consejo Nacional de Ciencia y Tecnología (CONACYT). N-HW, SF-V, and KO are funded by the Newton Advanced Fellowship (No. NAF\R1\180303) awarded to SF-V. KO is supported by the Consejo Nacional de Ciencia y Tecnología (CONACYT, CB-2016-01/285847).

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Authors and Affiliations

  1. Unidad de Genómica Avanzada, Langebio, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico

    Francisco J. Pérez-de los Santos, Jesús Emiliano Sotelo-Fonseca, América Ramírez-Colmenero & Selene L. Fernandez-Valverde

  2. Unidad Irapuato, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico

    Jesús Emiliano Sotelo-Fonseca, América Ramírez-Colmenero & Katarzyna Oktaba

  3. Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK

    Hans-Wilhelm Nützmann

Authors
  1. Francisco J. Pérez-de los Santos
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  2. Jesús Emiliano Sotelo-Fonseca
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  3. América Ramírez-Colmenero
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  4. Hans-Wilhelm Nützmann
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  5. Selene L. Fernandez-Valverde
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  6. Katarzyna Oktaba
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Corresponding authors

Correspondence to Hans-Wilhelm Nützmann , Selene L. Fernandez-Valverde or Katarzyna Oktaba .

Editor information

Editors and Affiliations

  1. Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Jalisco, Mexico

    Alejandro Pereira-Santana

  2. Unidad de Biotecnología, Centro de Investigación CientÚfica de Yucatán, Mérida, Yucatán, Mexico

    Samuel David Gamboa-Tuz

  3. Unidad de Biotecnología., Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico

    Luis Carlos Rodríguez-Zapata

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Pérez-de los Santos, F.J., Sotelo-Fonseca, J.E., Ramírez-Colmenero, A., Nützmann, HW., Fernandez-Valverde, S.L., Oktaba, K. (2022). Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis. In: Pereira-Santana, A., Gamboa-Tuz, S.D., Rodríguez-Zapata, L.C. (eds) Plant Comparative Genomics. Methods in Molecular Biology, vol 2512. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2429-6_13

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  • DOI: https://doi.org/10.1007/978-1-0716-2429-6_13

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2428-9

  • Online ISBN: 978-1-0716-2429-6

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