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

Zepeda-Mendoza, C. J., Mukhopadhyay, S., Wong, E. S., Harder, N., Splinter, E., de Wit, E., Eckersley-Maslin, M. A., Ried, T., Eils, R., Rohr, K., Mills, A., de Laat, W., Flicek, P., Sengupta, A. M., Spector, D. L. (2015) Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics, 16 (1). p. 982. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/26589460
DOI: 10.1186/s12864-015-2137-5

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, demonstrating the robustness of our pipeline. Interestingly, significant overlaps of DIRs with CTCF/Smc1 binding sites and differentially expressed genes were observed. CONCLUSIONS: Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function
CSHL Authors:
Communities: CSHL labs > Mills lab
CSHL labs > Spector lab
Depositing User: Matt Covey
Date Deposited: 25 Nov 2015 20:59
Last Modified: 25 Nov 2015 20:59
PMCID: PMC4654810
Related URLs:
URI: http://repository.cshl.edu/id/eprint/32004

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