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Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods
BACKGROUND: Circular chromosome conformation capture, when coupled with next-generation sequencing (4C-Seq), can be used to identify genome-wide interaction of a given locus (a “bait” sequence) with all of its interacting partners. Conventional 4C approaches used restriction enzyme digestion to frag...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679908/ https://www.ncbi.nlm.nih.gov/pubmed/23705979 http://dx.doi.org/10.1186/1471-2164-14-345 |
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author | Gao, Fan Wei, Zong Lu, Wange Wang, Kai |
author_facet | Gao, Fan Wei, Zong Lu, Wange Wang, Kai |
author_sort | Gao, Fan |
collection | PubMed |
description | BACKGROUND: Circular chromosome conformation capture, when coupled with next-generation sequencing (4C-Seq), can be used to identify genome-wide interaction of a given locus (a “bait” sequence) with all of its interacting partners. Conventional 4C approaches used restriction enzyme digestion to fragment chromatin, and recently sonication approach was also applied for this purpose. However, bioinformatics pipelines for analyzing sonication-based 4C-Seq data are not well developed. In addition, data consistency as well as similarity between the two methods has not been explored previously. Here we present a comparative analysis of 4C-Seq data generated by both methods, using an enhancer element of Pou5f1 gene in mouse embryonic stem (ES) cells. RESULTS: From biological replicates, we found good correlation (r>0.6) for inter-chromosomal interactions identified in either enzyme or sonication method. Compared to enzyme approach, sonication method generated less distal intra-chromosomal interactions, possibly due to the difference in chromatin fragmentation. From all mapped interactions, we further applied statistical models to identify enriched interacting regions. Interestingly, data generated from the two methods showed 30% overlap of the reproducible interacting regions. The interacting sites in the reproducible regions from both methods are similarly enriched with active histone marks. In addition, the interacting sites identified from sonication-based data are enriched with ChIP-Seq signals of transcription factors Oct4, Klf4, Esrrb, Tcfcp2i1, and Zfx that are critical for reprogramming and pluripotency. CONCLUSIONS: Both enzyme-based and sonication-based 4C-Seq methods are valuable tools to explore long-range chromosomal interactions. Due to the nature of sonication-based method, correlation analysis of the 4C interactions with transcription factor binding should be more straightforward. |
format | Online Article Text |
id | pubmed-3679908 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36799082013-06-25 Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods Gao, Fan Wei, Zong Lu, Wange Wang, Kai BMC Genomics Research Article BACKGROUND: Circular chromosome conformation capture, when coupled with next-generation sequencing (4C-Seq), can be used to identify genome-wide interaction of a given locus (a “bait” sequence) with all of its interacting partners. Conventional 4C approaches used restriction enzyme digestion to fragment chromatin, and recently sonication approach was also applied for this purpose. However, bioinformatics pipelines for analyzing sonication-based 4C-Seq data are not well developed. In addition, data consistency as well as similarity between the two methods has not been explored previously. Here we present a comparative analysis of 4C-Seq data generated by both methods, using an enhancer element of Pou5f1 gene in mouse embryonic stem (ES) cells. RESULTS: From biological replicates, we found good correlation (r>0.6) for inter-chromosomal interactions identified in either enzyme or sonication method. Compared to enzyme approach, sonication method generated less distal intra-chromosomal interactions, possibly due to the difference in chromatin fragmentation. From all mapped interactions, we further applied statistical models to identify enriched interacting regions. Interestingly, data generated from the two methods showed 30% overlap of the reproducible interacting regions. The interacting sites in the reproducible regions from both methods are similarly enriched with active histone marks. In addition, the interacting sites identified from sonication-based data are enriched with ChIP-Seq signals of transcription factors Oct4, Klf4, Esrrb, Tcfcp2i1, and Zfx that are critical for reprogramming and pluripotency. CONCLUSIONS: Both enzyme-based and sonication-based 4C-Seq methods are valuable tools to explore long-range chromosomal interactions. Due to the nature of sonication-based method, correlation analysis of the 4C interactions with transcription factor binding should be more straightforward. BioMed Central 2013-05-24 /pmc/articles/PMC3679908/ /pubmed/23705979 http://dx.doi.org/10.1186/1471-2164-14-345 Text en Copyright © 2013 Gao et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Gao, Fan Wei, Zong Lu, Wange Wang, Kai Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods |
title | Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods |
title_full | Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods |
title_fullStr | Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods |
title_full_unstemmed | Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods |
title_short | Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods |
title_sort | comparative analysis of 4c-seq data generated from enzyme-based and sonication-based methods |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679908/ https://www.ncbi.nlm.nih.gov/pubmed/23705979 http://dx.doi.org/10.1186/1471-2164-14-345 |
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