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

doi:10.1007/978-1-0716-2429-6_13

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 proceeding › Chapter or section

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.

Original language	English
Title of host publication	Plant Comparative Genomics
Editors	A. Pereira-Santana, S. D. Gamboa-Tuz, L. C. Rodríguez-Zapata
Place of Publication	New York, U. S. A.
Publisher	Humana Press
Pages	217-247
Number of pages	31
ISBN (Electronic)	9781071624296
ISBN (Print)	9781071624289
DOIs	https://doi.org/10.1007/978-1-0716-2429-6_13
Publication status	E-pub ahead of print - 12 Jul 2022

Publication series

Name	Methods in Molecular Biology
Volume	2512
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

Arabidopsis
Bioinformatics
Chromosome conformation
Differential interactions
Hi-C
Sequencing

ASJC Scopus subject areas

Molecular Biology
Genetics

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10.1007/978-1-0716-2429-6_13

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Pérez-de los Santos, F. J., Sotelo-Fonseca, J. E., Ramírez-Colmenero, A., Nützmann, H. W., Fernandez-Valverde, S. L., & Oktaba, K. (2022). Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis. In A. Pereira-Santana, S. D. Gamboa-Tuz, & L. C. Rodríguez-Zapata (Eds.), Plant Comparative Genomics (pp. 217-247). (Methods in Molecular Biology; Vol. 2512). Humana Press. https://doi.org/10.1007/978-1-0716-2429-6_13

Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis. / Pérez-de los Santos, Francisco J.; Sotelo-Fonseca, Jesús Emiliano; Ramírez-Colmenero, América et al.
Plant Comparative Genomics. ed. / A. Pereira-Santana; S. D. Gamboa-Tuz; L. C. Rodríguez-Zapata. New York, U. S. A.: Humana Press, 2022. p. 217-247 (Methods in Molecular Biology; Vol. 2512).

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

Pérez-de los Santos, FJ, Sotelo-Fonseca, JE, Ramírez-Colmenero, A, Nützmann, HW, Fernandez-Valverde, SL & Oktaba, K 2022, Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis. in A Pereira-Santana, SD Gamboa-Tuz & LC Rodríguez-Zapata (eds), Plant Comparative Genomics. Methods in Molecular Biology, vol. 2512, Humana Press, New York, U. S. A., pp. 217-247. https://doi.org/10.1007/978-1-0716-2429-6_13

Pérez-de los Santos FJ, Sotelo-Fonseca JE, Ramírez-Colmenero A, Nützmann HW, Fernandez-Valverde SL, Oktaba K. Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis. In Pereira-Santana A, Gamboa-Tuz SD, Rodríguez-Zapata LC, editors, Plant Comparative Genomics. New York, U. S. A.: Humana Press. 2022. p. 217-247. (Methods in Molecular Biology). Epub 2022 Jul 12. doi: 10.1007/978-1-0716-2429-6_13

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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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AU - Nützmann, Hans Wilhelm

AU - Fernandez-Valverde, Selene L.

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Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis

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