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

Hubrecht Institute

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

1 Citaat (Scopus)

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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.

Originele taal-2	Engels
Pagina's (van-tot)	982
Tijdschrift	BMC Genomics
Volume	16
Nummer van het tijdschrift	1
DOI's	https://doi.org/10.1186/s12864-015-2137-5
Status	Gepubliceerd - 2015

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10.1186/s12864-015-2137-5

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

@article{46e958d9c4284d76b85a0c64479c0981,

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",

pages = "982",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central",

number = "1",

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Zepeda-Mendoza, CJ, Mukhopadhyay, S, Wong, ES, Harder, N, Splinter, E, de Wit, E, Eckersley-Maslin, MA, Ried, T, Eils, R, Rohr, K, Mills, A, de Laat, W, Flicek, P, Sengupta, AM & Spector, DL 2015, 'Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2', BMC Genomics, vol. 16, nr. 1, blz. 982. https://doi.org/10.1186/s12864-015-2137-5

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 -

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

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