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

Zepeda-Mendoza, Cinthya J., Mukhopadhyay, Swagatam, Wong, Emily S., Harder, Nathalie, Splinter, Erik, de Wit, Erik, Eckersley-Maslin, Melanie A., Ried, Thomas, Eils, Roland, Rohr, Karl, Mills, Alea, de Laat, Wouter, Flicek, Paul, Sengupta, Anirvan M. and Spector, David L. (2015) Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics, 16 982: 1-17. doi:10.1186/s12864-015-2137-5


Author Zepeda-Mendoza, Cinthya J.
Mukhopadhyay, Swagatam
Wong, Emily S.
Harder, Nathalie
Splinter, Erik
de Wit, Erik
Eckersley-Maslin, Melanie A.
Ried, Thomas
Eils, Roland
Rohr, Karl
Mills, Alea
de Laat, Wouter
Flicek, Paul
Sengupta, Anirvan M.
Spector, David L.
Title Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2015-11-21
Year available 2015
Sub-type Article (original research)
DOI 10.1186/s12864-015-2137-5
Open Access Status DOI
Volume 16
Issue 982
Start page 1
End page 17
Total pages 17
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2016
Language eng
Formatted 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Biological Sciences Publications
 
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Created: Wed, 13 Apr 2016, 15:46:36 EST by Anthony Yeates on behalf of School of Biological Sciences