Exploiting native forces to capture chromosome conformation in mammalian cell nuclei
Abstract Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure‐to‐function relationship. H...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2016-12-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.20167311 |
| _version_ | 1797279802395197440 |
|---|---|
| author | Lilija Brant Theodore Georgomanolis Milos Nikolic Chris A Brackley Petros Kolovos Wilfred vanIjcken Frank G Grosveld Davide Marenduzzo Argyris Papantonis |
| author_facet | Lilija Brant Theodore Georgomanolis Milos Nikolic Chris A Brackley Petros Kolovos Wilfred vanIjcken Frank G Grosveld Davide Marenduzzo Argyris Papantonis |
| author_sort | Lilija Brant |
| collection | DOAJ |
| description | Abstract Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure‐to‐function relationship. However, all 3C‐based methods rely on chemical cross‐linking to stabilize spatial interactions. This step remains a “black box” as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed “i3C”, a novel approach for capturing spatial interactions without a need for cross‐linking. We apply i3C to intact nuclei of living cells and exploit native forces that stabilize chromatin folding. Using different cell types and loci, computational modeling, and a methylation‐based orthogonal validation method, “TALE‐iD”, we show that native interactions resemble cross‐linked ones, but display improved signal‐to‐noise ratios and are more focal on regulatory elements and CTCF sites, while strictly abiding to topologically associating domain restrictions. |
| first_indexed | 2024-03-07T16:31:18Z |
| format | Article |
| id | doaj.art-2e4769f6383046958f190470f85f6feb |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2024-03-07T16:31:18Z |
| publishDate | 2016-12-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-2e4769f6383046958f190470f85f6feb2024-03-03T10:20:05ZengSpringer NatureMolecular Systems Biology1744-42922016-12-011212n/an/a10.15252/msb.20167311Exploiting native forces to capture chromosome conformation in mammalian cell nucleiLilija Brant0Theodore Georgomanolis1Milos Nikolic2Chris A Brackley3Petros Kolovos4Wilfred vanIjcken5Frank G Grosveld6Davide Marenduzzo7Argyris Papantonis8Center for Molecular Medicine University of Cologne Cologne GermanyCenter for Molecular Medicine University of Cologne Cologne GermanyCenter for Molecular Medicine University of Cologne Cologne GermanySchool of Physics and Astronomy University of Edinburgh Edinburgh UKDepartment of Cell Biology Erasmus Medical Center Rotterdam The NetherlandsBiomics Department Erasmus Medical Center Rotterdam The NetherlandsDepartment of Cell Biology Erasmus Medical Center Rotterdam The NetherlandsSchool of Physics and Astronomy University of Edinburgh Edinburgh UKCenter for Molecular Medicine University of Cologne Cologne GermanyAbstract Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure‐to‐function relationship. However, all 3C‐based methods rely on chemical cross‐linking to stabilize spatial interactions. This step remains a “black box” as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed “i3C”, a novel approach for capturing spatial interactions without a need for cross‐linking. We apply i3C to intact nuclei of living cells and exploit native forces that stabilize chromatin folding. Using different cell types and loci, computational modeling, and a methylation‐based orthogonal validation method, “TALE‐iD”, we show that native interactions resemble cross‐linked ones, but display improved signal‐to‐noise ratios and are more focal on regulatory elements and CTCF sites, while strictly abiding to topologically associating domain restrictions.https://doi.org/10.15252/msb.20167311chromatin loopingchromosome conformation capturecross‐linkingnuclear compartmentsnuclear organization |
| spellingShingle | Lilija Brant Theodore Georgomanolis Milos Nikolic Chris A Brackley Petros Kolovos Wilfred vanIjcken Frank G Grosveld Davide Marenduzzo Argyris Papantonis Exploiting native forces to capture chromosome conformation in mammalian cell nuclei Molecular Systems Biology chromatin looping chromosome conformation capture cross‐linking nuclear compartments nuclear organization |
| title | Exploiting native forces to capture chromosome conformation in mammalian cell nuclei |
| title_full | Exploiting native forces to capture chromosome conformation in mammalian cell nuclei |
| title_fullStr | Exploiting native forces to capture chromosome conformation in mammalian cell nuclei |
| title_full_unstemmed | Exploiting native forces to capture chromosome conformation in mammalian cell nuclei |
| title_short | Exploiting native forces to capture chromosome conformation in mammalian cell nuclei |
| title_sort | exploiting native forces to capture chromosome conformation in mammalian cell nuclei |
| topic | chromatin looping chromosome conformation capture cross‐linking nuclear compartments nuclear organization |
| url | https://doi.org/10.15252/msb.20167311 |
| work_keys_str_mv | AT lilijabrant exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei AT theodoregeorgomanolis exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei AT milosnikolic exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei AT chrisabrackley exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei AT petroskolovos exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei AT wilfredvanijcken exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei AT frankggrosveld exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei AT davidemarenduzzo exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei AT argyrispapantonis exploitingnativeforcestocapturechromosomeconformationinmammaliancellnuclei |