A cautionary note on the use of chromosome conformation capture in plants

Abstract

Background The chromosome conformation capture (3C) technique is a method to study chromatin interactions at specific genomic loci. Initially established for yeast the 3C technique has been adapted to plants in recent years in order to study chromatin interactions and their role in transcriptional gene regulation. As the plant scientific community continues to implement this technology, a discussion on critical controls, validations steps and interpretation of 3C data is essential to fully benefit from 3C in plants.ResultsHere we assess the reliability and robustness of the 3C technique for the detection of chromatin interactions in Arabidopsis. As a case study, we applied this methodology to the genomic locus of a floral integrator gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), and demonstrate the need of several controls and standard validation steps to allow a meaningful interpretation of 3C data. The intricacies of this promising but challenging technique are discussed in depth.ConclusionsThe 3C technique offers an interesting opportunity to study chromatin interactions at a resolution infeasible by microscopy. However, for interpretation of 3C interaction data and identification of true interactions, 3C technology demands a stringent experimental setup and extreme caution.Electronic supplementary materialThe online version of this article (10.1186/s13007-017-0251-x) contains supplementary material, which is available to authorized users.

A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics

“…12a ). We then confirmed the PPIs detected in our CAP-C in the wild-type plants using 3C and reciprocal 3C experiments 14 , 34 (Supplementary Fig. 12b, c ).…”

An upgraded method of high-throughput chromosome conformation capture (Hi-C 3.0) in cotton (Gossypium spp.)

“…In the nuclei of multicellular eukaryotes, chromatin forms hierarchical three-dimensional (3D) structures on top of its linear conformation ( Ouyang et al., 2020b ). With the development of chromosome conformation capture (3C) methods ( Louwers et al., 2009 ; Hakim and Misteli, 2012 ; Jamge et al., 2017 ; Hua et al., 2021 ), functional structures have been revealed at various genomic scales, including chromatin territories, A/B compartments, topologically associating domains (TADs), and chromatin loops ( Meaburn and Misteli, 2007 ; Lieberman-Aiden et al., 2009 ; Dixon et al., 2012 ; Grob and Grossniklaus, 2017 ; Zheng et al., 2019 ). From territory to loop, the detection resolution required increases in order ( Rodriguez-Granados et al., 2016 ).…”