Title |
Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2
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Published in |
BMC Genomics, November 2015
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DOI | 10.1186/s12864-015-2137-5 |
Pubmed ID | |
Authors |
Cinthya J. Zepeda-Mendoza, Swagatam Mukhopadhyay, Emily S. Wong, Nathalie Harder, Erik Splinter, Elzo de Wit, Melanie A. Eckersley-Maslin, Thomas Ried, Roland Eils, Karl Rohr, Alea Mills, Wouter de Laat, Paul Flicek, Anirvan M. Sengupta, David L. Spector |
Abstract |
Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq) data. We applied this strategy to the study of chromatin interaction changes upon a 4.3 Mb DNA deletion in mouse region 4E2. A significant number of differentially interacting regions (DIRs) and chromatin compaction changes were detected in the deletion chromosome compared to a wild-type (WT) control. Selected DIRs were validated by 3D DNA FISH experiments, demonstrating the robustness of our pipeline. Interestingly, significant overlaps of DIRs with CTCF/Smc1 binding sites and differentially expressed genes were observed. Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function. |
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