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Cut-C: cleavage under tethered nuclease for conformational capture
BACKGROUND: Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enabled the identification of novel aspects of chromatin structure. Further identif...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664727/ https://www.ncbi.nlm.nih.gov/pubmed/31357933 http://dx.doi.org/10.1186/s12864-019-5989-2 |
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author | Shimbo, Takashi Kawamura, Machika Wijaya, Edward Takaki, Eiichi Kaneda, Yasufumi Tamai, Katsuto |
author_facet | Shimbo, Takashi Kawamura, Machika Wijaya, Edward Takaki, Eiichi Kaneda, Yasufumi Tamai, Katsuto |
author_sort | Shimbo, Takashi |
collection | PubMed |
description | BACKGROUND: Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enabled the identification of novel aspects of chromatin structure. Further identification of protein-centric chromatin conformation is enabled by coupling the Hi-C procedure with a conventional chromatin immunoprecipitation assay. However, these methods are time-consuming and require independent methods for validation. RESULTS: To simultaneously identify protein-centric chromatin conformation and target protein localization, we have developed Cut-C, a method that combines antibody-mediated cleavage by tethered nuclease with chromosome conformation capture to identify chromatin interactions mediated by a protein of interest. Applying Cut-C to H3K4me3, a histone modification enriched at active gene promoters, we have successfully identified chromatin loops mediated by H3K4me3 along with the genome-wide distribution of H3K4me3. Cut-C also identified chromatin loops mediated by CTCF, validating the general applicability of the method. CONCLUSIONS: Cut-C identifies protein-centric chromatin conformations along with the genome-wide distribution of target proteins using simple procedures. The simplified protocol will improve the efficiency of analysing chromatin conformation using precious materials, such as clinical samples. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5989-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6664727 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-66647272019-08-05 Cut-C: cleavage under tethered nuclease for conformational capture Shimbo, Takashi Kawamura, Machika Wijaya, Edward Takaki, Eiichi Kaneda, Yasufumi Tamai, Katsuto BMC Genomics Methodology Article BACKGROUND: Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enabled the identification of novel aspects of chromatin structure. Further identification of protein-centric chromatin conformation is enabled by coupling the Hi-C procedure with a conventional chromatin immunoprecipitation assay. However, these methods are time-consuming and require independent methods for validation. RESULTS: To simultaneously identify protein-centric chromatin conformation and target protein localization, we have developed Cut-C, a method that combines antibody-mediated cleavage by tethered nuclease with chromosome conformation capture to identify chromatin interactions mediated by a protein of interest. Applying Cut-C to H3K4me3, a histone modification enriched at active gene promoters, we have successfully identified chromatin loops mediated by H3K4me3 along with the genome-wide distribution of H3K4me3. Cut-C also identified chromatin loops mediated by CTCF, validating the general applicability of the method. CONCLUSIONS: Cut-C identifies protein-centric chromatin conformations along with the genome-wide distribution of target proteins using simple procedures. The simplified protocol will improve the efficiency of analysing chromatin conformation using precious materials, such as clinical samples. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5989-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-07-29 /pmc/articles/PMC6664727/ /pubmed/31357933 http://dx.doi.org/10.1186/s12864-019-5989-2 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Shimbo, Takashi Kawamura, Machika Wijaya, Edward Takaki, Eiichi Kaneda, Yasufumi Tamai, Katsuto Cut-C: cleavage under tethered nuclease for conformational capture |
title | Cut-C: cleavage under tethered nuclease for conformational capture |
title_full | Cut-C: cleavage under tethered nuclease for conformational capture |
title_fullStr | Cut-C: cleavage under tethered nuclease for conformational capture |
title_full_unstemmed | Cut-C: cleavage under tethered nuclease for conformational capture |
title_short | Cut-C: cleavage under tethered nuclease for conformational capture |
title_sort | cut-c: cleavage under tethered nuclease for conformational capture |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664727/ https://www.ncbi.nlm.nih.gov/pubmed/31357933 http://dx.doi.org/10.1186/s12864-019-5989-2 |
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