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

Suraj Jamge, Maike Stam, Gerco C. Angenent, Richard G.H. Immink*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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. Results: Here 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. Conclusions: The 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.
Original languageEnglish
Article number101
JournalPlant Methods
Volume13
Issue number1
DOIs
Publication statusPublished - 16 Nov 2017

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Chromatin
Chromosomes
chromosomes
chromatin
Suppressor Genes
Technology
methodology
Arabidopsis
Microscopy
suppressor genes
Yeasts
genomics
loci
microscopy
Genes
yeasts
case studies
genes

Keywords

  • 3C
  • Arabidopsis
  • Chromatin interactions
  • Plants

Cite this

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title = "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. Results: Here 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. Conclusions: The 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.",
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A cautionary note on the use of chromosome conformation capture in plants. / Jamge, Suraj; Stam, Maike; Angenent, Gerco C.; Immink, Richard G.H.

In: Plant Methods, Vol. 13, No. 1, 101, 16.11.2017.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Stam, Maike

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AU - Immink, Richard G.H.

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