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

• Published in: Cell reports (Cambridge) Vol. 5; no. 2; pp. 531 - 545
• Main Authors: Viturawong, Tar, Meissner, Felix, Butter, Falk, Mann, Matthias
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.10.2013; Elsevier
• Subjects: Base Sequence; Chromatin - metabolism; Chromatin Immunoprecipitation; Conserved Sequence; DNA - metabolism; HeLa Cells; Humans; Isotope Labeling; Mass Spectrometry; Mutagenesis; Peptides - analysis; Protein Binding; Protein Interaction Maps; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2013.09.022

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. [Display omitted] •Proteomics generates a large-scale, unbiased, cell-type-specific UCE interactome•UCE interactors bind overlapped TFBSs possessing conservation bias•A fine-resolution scanning map illustrates multiple binding constraints of a UCE•Comparison with ChIP-seq data suggests epigenetic priming by UCE interactions Ultraconserved elements (UCEs) are genomic regions with extreme sequence identity, many of which possess tissue- or stage-specific developmental enhancer activity. In this paper, Butter, Mann, and colleagues use quantitative proteomics to generate a comprehensive DNA-centric map of intrinsic binders to almost 200 UCEs, revealing a rich interaction profile favoring developmental- and chromatin-accessibility factors. The authors show that the transcription factor “hubs” are closely related to in cellulo chromatin modification states,as well as the per-nucleotide conservation of UCEs.