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Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

Although important for gene regulation, most studies of genome organization use either fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) methods. FISH directly visualizes the spatial relationship of sequences but is usually applied to a few loci at a time. The frequen...

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Autores principales: Williamson, Iain, Berlivet, Soizik, Eskeland, Ragnhild, Boyle, Shelagh, Illingworth, Robert S., Paquette, Denis, Dostie, Josée, Bickmore, Wendy A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265680/
https://www.ncbi.nlm.nih.gov/pubmed/25512564
http://dx.doi.org/10.1101/gad.251694.114
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author Williamson, Iain
Berlivet, Soizik
Eskeland, Ragnhild
Boyle, Shelagh
Illingworth, Robert S.
Paquette, Denis
Dostie, Josée
Bickmore, Wendy A.
author_facet Williamson, Iain
Berlivet, Soizik
Eskeland, Ragnhild
Boyle, Shelagh
Illingworth, Robert S.
Paquette, Denis
Dostie, Josée
Bickmore, Wendy A.
author_sort Williamson, Iain
collection PubMed
description Although important for gene regulation, most studies of genome organization use either fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) methods. FISH directly visualizes the spatial relationship of sequences but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde cross-linking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organization, but this has not been tested extensively. We investigated the murine HoxD locus with 3C carbon copy (5C) and FISH in different developmental and activity states and in the presence or absence of epigenetic regulators. We identified situations in which the two data sets are concordant but found other conditions under which chromatin topographies extrapolated from 5C or FISH data are not compatible. We suggest that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart, influenced by nuclear environment and chromatin composition. We conclude that results obtained at high resolution with either 3C methods or FISH alone must be interpreted with caution and that views about genome organization should be validated by independent methods.
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spelling pubmed-42656802014-12-16 Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization Williamson, Iain Berlivet, Soizik Eskeland, Ragnhild Boyle, Shelagh Illingworth, Robert S. Paquette, Denis Dostie, Josée Bickmore, Wendy A. Genes Dev Resource/Methodology Although important for gene regulation, most studies of genome organization use either fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) methods. FISH directly visualizes the spatial relationship of sequences but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde cross-linking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organization, but this has not been tested extensively. We investigated the murine HoxD locus with 3C carbon copy (5C) and FISH in different developmental and activity states and in the presence or absence of epigenetic regulators. We identified situations in which the two data sets are concordant but found other conditions under which chromatin topographies extrapolated from 5C or FISH data are not compatible. We suggest that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart, influenced by nuclear environment and chromatin composition. We conclude that results obtained at high resolution with either 3C methods or FISH alone must be interpreted with caution and that views about genome organization should be validated by independent methods. Cold Spring Harbor Laboratory Press 2014-12-15 /pmc/articles/PMC4265680/ /pubmed/25512564 http://dx.doi.org/10.1101/gad.251694.114 Text en © 2014 Williamson et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genes & Development, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0.
spellingShingle Resource/Methodology
Williamson, Iain
Berlivet, Soizik
Eskeland, Ragnhild
Boyle, Shelagh
Illingworth, Robert S.
Paquette, Denis
Dostie, Josée
Bickmore, Wendy A.
Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
title Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
title_full Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
title_fullStr Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
title_full_unstemmed Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
title_short Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
title_sort spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
topic Resource/Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265680/
https://www.ncbi.nlm.nih.gov/pubmed/25512564
http://dx.doi.org/10.1101/gad.251694.114
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