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G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD

Nature Chemical Biology volume 10, pages 313–318 (2014)Cite this article

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Abstract

G4 motifs are greatly enriched near promoters, suggesting that quadruplex structures may be targets of transcriptional regulation. Here we show, by ChIP-Seq analysis of human cells, that 40% of the binding sites of the transcription-associated helicases, XPB and XPD, overlap with G4 motifs. The highly significant overlap of XPB and XPD binding sites with G4 motifs cannot be explained by GC richness or parameters of the genomewide analysis, but instead suggests that these proteins are recruited to quadruplex structures that form in genomic DNA (G4 DNA). Biochemical analysis demonstrates that XPD is a robust G4 DNA helicase and that XPB binds G4 DNA. XPB and XPD are enriched near the transcription start site at 20% of genes, especially highly transcribed genes. XPB and XPD enrichment at G4 motifs characterizes specific signaling pathways and regulatory pathways associated with specific cancers. These results identify new candidate pathways for therapies targeted to quadruplexes.

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Figure 1: XPD is a robust G4 DNA helicase.
Figure 2: XPB binds but does not unwind G4 DNA and binding is ATP sensitive.
Figure 3: Enrichment of XPB and XPD at TSS is correlated with transcription.

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Acknowledgements

Research reported in this manuscript was supported by US National Institutes of Health–National Cancer Institute grant P01 CA077852. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. We thank our Program Project colleagues for active discussions, M. White (St. Andrews University, Scotland) for the XPD expression construct; J. Tainer (Scripps Research Institute) for the XPB expression construct; A. Bailey for help with sequencing library preparation and C. Lee and J. Shendure for sequencing of ChIP-Seq libraries on an Illumina Hi-Seq 2000 (University of Washington).

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Author notes

  1. Aarthy C Vallur

    Present address: Present address: Infectious Disease Research Institute, Seattle, Washington, USA.,

  2. Johanna Eddy: Deceased.

Authors and Affiliations

  1. Department of Immunology, University of Washington, Seattle, Washington, USA

    Lucas T Gray, Aarthy C Vallur & Nancy Maizels

  2. Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA

    Johanna Eddy & Nancy Maizels

  3. Department of Biochemistry, University of Washington, Seattle, Washington, USA

    Nancy Maizels

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  1. Lucas T Gray
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  2. Aarthy C Vallur
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Contributions

L.T.G. performed ChIP-Seq and expression array experiments and analyzed those results. A.C.V. and J.E. performed biochemical studies of XPB and XPD. L.T.G., A.C.V., J.E. and N.M. conceived the study and designed experiments. L.T.G., A.C.V., J.E. and N.M. interpreted the data and wrote the manuscript.

Corresponding author

Correspondence to Nancy Maizels.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–4 and Supplementary Tables 1–3. (PDF 5952 kb)

Supplementary Data Set 1

Gene expression data for HT1080 cell lines. (XLSX 766 kb)

Supplementary Data Set 2

Genes with enrichment of XPB or XPD within 1 kb of TSS. (XLSX 264 kb)

Supplementary Data Set 3

Selected online GREAT results for XPB and XPD peaks containing motifs (XLSX 56 kb)

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Gray, L., Vallur, A., Eddy, J. et al. G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD. Nat Chem Biol 10, 313–318 (2014). https://doi.org/10.1038/nchembio.1475

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