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Myc-binding-site recognition in the human genome is determined by chromatin context

Nature Cell Biology volume 8, pages 764–770 (2006)Cite this article

Abstract

Large-scale chromatin immunoprecipitation (ChIP) studies have been effective in unravelling the distribution of DNA-binding transcription factors along eukaryotic genomes1, but specificity determinants remain elusive. Gene-regulatory regions display distinct histone variants and modifications (or marks)2,3,4,5,6,7,8,9,10,11,12,13,14,15. An attractive hypothesis is that these marks modulate protein recognition16,17,18, but whether or not this applies to transcription factors remains unknown. Based on large-scale datasets2,19,20,21 and quantitative ChIP, we dissect the correlations between 35 histone marks and genomic binding by the transcription factor Myc. Our data reveal a relatively simple combinatorial organization of histone marks in human cells, with a few main groups of marks clustering on distinct promoter populations. A stretch of chromatin bearing high H3 K4/K79 methylation and H3 acetylation (or 'euchromatic island'), which is generally associated with a pre-engaged basal transcription machinery12,13, is a strict pre-requisite for recognition of any target site by Myc (whether the consensus CACGTG or an alternative sequence)22. These data imply that tethering of a transcription factor to restricted chromatin domains is rate-limiting for sequence-specific DNA binding in vivo.

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Figure 1: Clustering analysis of histone marks on human promoters.
Figure 2: Myc binding is correlated with pre-existing H3K4me3.
Figure 3: Analysis of CpG methylation at Myc-binding sites.
Figure 4: qChIP analysis of genomic sites identified in ChIP-chip datasets.
Figure 5: Pre-loaded RNA polII and menin correlate with H3K4me3 and Myc-binding affinity.

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Acknowledgements

We thank G. Natoli, A. Musacchio and M. Eilers for critical reading of the manuscript; I. Dellino, S. Segalla and M. Cirò for stimulating discussions throughout this work; A. Verrecchia and F. Contegno for laboratory set-up and management; P.-G. Pelicci for his support; B. Ren for sharing sequence information; B. Bernstein for communicating results prior to publication; and T. Jenuwein for providing the antibodies as a gift. This work was supported by the Italian Association for Cancer Research (AIRC).

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Authors and Affiliations

  1. Department of Experimental Oncology, European Institute of Oncology (IEO), IFOM-IEO Campus, Milan, 20139, Italy

    Ernesto Guccione, Francesca Martinato, Giacomo Finocchiaro, Lucilla Luzi, Loris Bernard & Bruno Amati

  2. FIRC Institute of Molecular Oncology (IFOM), IFOM-IEO Campus, Milan, 20139, Italy

    Giacomo Finocchiaro & Lucilla Luzi

  3. Real-Time PCR Facility, IFOM-IEO Campus, Milan, 20139, Italy

    Laura Tizzoni, Valentina Dall' Olio & Loris Bernard

  4. Department of Cellular Biotechnologies and Hematology, University of Rome 'La Sapienza', Italy

    Giuseppe Zardo

  5. San Raffaele Bio-Medical Park Foundation, Rome, 00128, Italy

    Giuseppe Zardo & Clara Nervi

  6. Department of Histology and Medical Embryology, University of Rome 'La Sapienza', Italy

    Clara Nervi

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  1. Ernesto Guccione
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Contributions

E.G. and B.A. designed the study and interpreted the data. E.G. and F.M. performed cell culture, ChIP and RNA extractions. G.F. and L.L. performed bioinformatics and statistical analysis. E.G., F.M., L.T., V.D. and L.B. performed quantitative PCR. G.Z. and C.N. performed the bisulphite sequencing.

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Correspondence to Bruno Amati.

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Guccione, E., Martinato, F., Finocchiaro, G. et al. Myc-binding-site recognition in the human genome is determined by chromatin context. Nat Cell Biol 8, 764–770 (2006). https://doi.org/10.1038/ncb1434

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