Journal article

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

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

BMC Genomics | BIOMED CENTRAL LTD | Published : 2015

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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Grants

Awarded by NIGMS


Awarded by NCI


Awarded by EMBO Long-term Fellowship program


Awarded by Wellcome Trust


Awarded by NATIONAL CANCER INSTITUTE


Awarded by NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES


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.