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

TY - JOUR

T1 - Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

AU - Zepeda-Mendoza, Cinthya J

AU - Mukhopadhyay, Swagatam

AU - Wong, Emily S

AU - Harder, Nathalie

AU - Splinter, Erik

AU - de Wit, Elzo

AU - Eckersley-Maslin, Melanie A

AU - Ried, Thomas

AU - Eils, Roland

AU - Rohr, Karl

AU - Mills, Alea

AU - de Laat, Wouter

AU - Flicek, Paul

AU - Sengupta, Anirvan M

AU - Spector, David L

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

U2 - 10.1186/s12864-015-2137-5

DO - 10.1186/s12864-015-2137-5

M3 - Article

C2 - 26589460

SN - 1471-2164

VL - 16

SP - 982

JO - BMC Genomics

JF - BMC Genomics

IS - 1

ER -