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

doi:10.1186/s12864-015-2137-5

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

Cancer

Research output: Contribution to journal › Article › Academic › peer-review

3 Downloads (Pure)

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.

Original language	English
Article number	982
Number of pages	17
Journal	BMC Genomics
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s12864-015-2137-5
Publication status	Published - 2015

Access to Document

10.1186/s12864-015-2137-5

art%3A10.1186%2Fs12864-015-2137-5Final published version, 2.35 MB

Cite this

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), Article 982. https://doi.org/10.1186/s12864-015-2137-5

@article{75405bd2f6564744949528b83cf6b75a,

title = "Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2",

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.",

author = "Zepeda-Mendoza, \{Cinthya J\} and Swagatam Mukhopadhyay and Wong, \{Emily S\} and Nathalie Harder and Erik Splinter and \{de Wit\}, Elzo and Eckersley-Maslin, \{Melanie A\} and Thomas Ried and Roland Eils and Karl Rohr and Alea Mills and \{de Laat\}, Wouter and Paul Flicek and Sengupta, \{Anirvan M\} and Spector, \{David L\}",

year = "2015",

doi = "10.1186/s12864-015-2137-5",

language = "English",

volume = "16",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central Ltd.",

number = "1",

}

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

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 982

ER -

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

Abstract

Access to Document

Fingerprint

Cite this