A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation

Research output: Contribution to journal › Journal article › Research

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A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation. / Viturawong, Tar; Meissner, Felix; Butter, Falk; Mann, Matthias.

In: Plant Cell Reports, Vol. 5, No. 2, 31.10.2013, p. 531-45.

Research output: Contribution to journal › Journal article › Research

Harvard

Viturawong, T, Meissner, F, Butter, F & Mann, M 2013, 'A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation', Plant Cell Reports, vol. 5, no. 2, pp. 531-45. https://doi.org/10.1016/j.celrep.2013.09.022

APA

Viturawong, T., Meissner, F., Butter, F., & Mann, M. (2013). A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation. Plant Cell Reports, 5(2), 531-45. https://doi.org/10.1016/j.celrep.2013.09.022

Vancouver

Viturawong T, Meissner F, Butter F, Mann M. A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation. Plant Cell Reports. 2013 Oct 31;5(2):531-45. https://doi.org/10.1016/j.celrep.2013.09.022

Author

Viturawong, Tar ; Meissner, Felix ; Butter, Falk ; Mann, Matthias. / A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation. In: Plant Cell Reports. 2013 ; Vol. 5, No. 2. pp. 531-45.

Bibtex

@article{c6f8cdcac2a5447ba9ea237cf6ba93c2,
title = "A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation",
abstract = "Ultraconserved elements (UCEs) have been the subject of great interest because of their extreme sequence identity and their seemingly cryptic and largely uncharacterized functions. Although in vivo studies of UCE sequences have demonstrated regulatory activity, protein interactors at UCEs have not been systematically identified. Here, we combined high-throughput affinity purification, high-resolution mass spectrometry, and SILAC quantification to map intrinsic protein interactions for 193 UCE sequences. The interactome contains over 400 proteins, including transcription factors with known developmental roles. We demonstrate based on our data that UCEs consist of strongly conserved overlapping binding sites. We also generated a fine-resolution interactome of a UCE, confirming the hub-like nature of the element. The intrinsic interactions mapped here are reflected in open chromatin, as indicated by comparison with existing ChIP data. Our study argues for a strong contribution of protein-DNA interactions to UCE conservation and provides a basis for further functional characterization of UCEs.",
author = "Tar Viturawong and Felix Meissner and Falk Butter and Matthias Mann",
note = "Copyright {\textcopyright} 2013 The Authors. Published by Elsevier Inc. All rights reserved.",
year = "2013",
month = oct,
day = "31",
doi = "10.1016/j.celrep.2013.09.022",
language = "English",
volume = "5",
pages = "531--45",
journal = "Plant Cell Reports",
issn = "0721-7714",
publisher = "Springer",
number = "2",

}

RIS

TY - JOUR

T1 - A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation

AU - Viturawong, Tar

AU - Meissner, Felix

AU - Butter, Falk

AU - Mann, Matthias

N1 - Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

PY - 2013/10/31

Y1 - 2013/10/31

N2 - Ultraconserved elements (UCEs) have been the subject of great interest because of their extreme sequence identity and their seemingly cryptic and largely uncharacterized functions. Although in vivo studies of UCE sequences have demonstrated regulatory activity, protein interactors at UCEs have not been systematically identified. Here, we combined high-throughput affinity purification, high-resolution mass spectrometry, and SILAC quantification to map intrinsic protein interactions for 193 UCE sequences. The interactome contains over 400 proteins, including transcription factors with known developmental roles. We demonstrate based on our data that UCEs consist of strongly conserved overlapping binding sites. We also generated a fine-resolution interactome of a UCE, confirming the hub-like nature of the element. The intrinsic interactions mapped here are reflected in open chromatin, as indicated by comparison with existing ChIP data. Our study argues for a strong contribution of protein-DNA interactions to UCE conservation and provides a basis for further functional characterization of UCEs.

AB - Ultraconserved elements (UCEs) have been the subject of great interest because of their extreme sequence identity and their seemingly cryptic and largely uncharacterized functions. Although in vivo studies of UCE sequences have demonstrated regulatory activity, protein interactors at UCEs have not been systematically identified. Here, we combined high-throughput affinity purification, high-resolution mass spectrometry, and SILAC quantification to map intrinsic protein interactions for 193 UCE sequences. The interactome contains over 400 proteins, including transcription factors with known developmental roles. We demonstrate based on our data that UCEs consist of strongly conserved overlapping binding sites. We also generated a fine-resolution interactome of a UCE, confirming the hub-like nature of the element. The intrinsic interactions mapped here are reflected in open chromatin, as indicated by comparison with existing ChIP data. Our study argues for a strong contribution of protein-DNA interactions to UCE conservation and provides a basis for further functional characterization of UCEs.

U2 - 10.1016/j.celrep.2013.09.022

DO - 10.1016/j.celrep.2013.09.022

M3 - Journal article

C2 - 24139795

VL - 5

SP - 531

EP - 545

JO - Plant Cell Reports

JF - Plant Cell Reports

SN - 0721-7714

IS - 2

ER -

ID: 88182503