Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis

Francisco J. Pérez-de los Santos, Jesús Emiliano Sotelo-Fonseca, América Ramírez-Colmenero, Hans Wilhelm Nützmann, Selene L. Fernandez-Valverde, Katarzyna Oktaba

Research output: Chapter or section in a book/report/conference proceedingChapter or section

1 Citation (SciVal)


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.

Original languageEnglish
Title of host publicationPlant Comparative Genomics
EditorsA. Pereira-Santana, S. D. Gamboa-Tuz, L. C. Rodríguez-Zapata
Place of PublicationNew York, U. S. A.
PublisherHumana Press
Number of pages31
ISBN (Electronic)9781071624296
ISBN (Print)9781071624289
Publication statusE-pub ahead of print - 12 Jul 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Bibliographical note

Funding Information:
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).


  • Arabidopsis
  • Bioinformatics
  • Chromosome conformation
  • Differential interactions
  • Hi-C
  • Sequencing

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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