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

Instituto Politécnico Nacional

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

1 Citation (SciVal)

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

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).

Funding

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).

Keywords

Arabidopsis
Bioinformatics
Chromosome conformation
Differential interactions
Hi-C
Sequencing

ASJC Scopus subject areas

Molecular Biology
Genetics

Access to Document

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

Cite this

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. Advance online publication. 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 › Book chapter

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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AU - Nützmann, Hans Wilhelm

AU - Fernandez-Valverde, Selene L.

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KW - Chromosome conformation

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ER -

Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis

Abstract

Publication series

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

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