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 |
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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 | |
Publication status | E-pub ahead of print - 12 Jul 2022 |
Publication series
Name | Methods in Molecular Biology |
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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