Journal article
Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2
CJ Zepeda-Mendoza, S Mukhopadhyay, ES Wong, N Harder, E Splinter, E de Wit, MA Eckersley-Maslin, T Ried, R Eils, K Rohr, A Mills, W de Laat, P Flicek, AM Sengupta, DL Spector
BMC Genomics | BMC | Published : 2015
Open access
Abstract
Background: 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. Results: 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, demonstr..
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Awarded by European Molecular Biology Laboratory
Funding Acknowledgements
C.Z-M. is supported by the Gonzalo Rio Arronte Fellowship. Research in the Spector lab is supported by NIGMS 42694 and NCI 2P30CA45508. ESW is supported by the EMBO Long-term Fellowship program (ALTF 1518-2012). PF is supported by the Wellcome Trust (WT095908) and the European Molecular Biology Laboratory. The authors have no competing interests to declare.