Article | Published:

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Nature Structural & Molecular Biology volume 24, pages 515524 (2017) | Download Citation

Abstract

Gene expression states influence the 3D conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation states in mouse embryonic stem (ES) cells. To predict possible folding scenarios, we performed computer simulations of polymer models informed with different chromatin occupancy features that define promoter activation states or binding sites for the transcription factor CTCF. Single-cell imaging of the locus folding was performed to test model predictions. While CTCF occupancy alone fails to predict the in vivo folding at genomic length scale of 10 kb, we found that homotypic interactions between active and Polycomb-repressed promoters co-occurring in the same DNA fiber fully explain the HoxB folding patterns imaged in single cells. We identify state-dependent promoter interactions as major drivers of chromatin folding in gene-dense regions.

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Acknowledgements

We thank K.J. Morris for help growing the mouse ES cells, E. Brookes, R.A. Beagrie and C. Ribeiro de Almeida for help and advice, and W. Bickmore for providing the ESC-OS25 cell line (MRC Human Genetic Unit, Edinburgh, UK). The work was supported by the Medical Research Council, UK (A.P., S.Q.X., I.d.S., M.R.B., D.R.), the Helmholtz Foundation (A.P., M.B., E.T.T.), and the Berlin Institute of Health (A.P., M.B., M.N.). This work was supported by grants to M.N. from CINECA ISCRA ID HP10CYFPS5. M.N. also acknowledges computer resources from INFN, CINECA, and Scope at the University of Naples.

Author information

Author notes

    • Mariano Barbieri
    •  & Sheila Q Xie

    These author contributed equally to this work.

Affiliations

  1. Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max Delbrück Centre for Molecular Medicine, Berlin, Germany.

    • Mariano Barbieri
    • , Elena Torlai Triglia
    •  & Ana Pombo
  2. Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy.

    • Mariano Barbieri
    • , Andrea M Chiariello
    • , Simona Bianco
    •  & Mario Nicodemi
  3. Berlin Institute of Health (BIH), Berlin, Germany.

    • Mariano Barbieri
    • , Mario Nicodemi
    •  & Ana Pombo
  4. Genome Function Group, MRC London Institute of Medical Sciences (LMS) (previously MRC Clinical Sciences Centre), Imperial College London, Hammersmith Hospital Campus, London, UK.

    • Sheila Q Xie
    • , Inês de Santiago
    • , Miguel R Branco
    •  & Ana Pombo
  5. Single Molecule Imaging Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Hammersmith Hospital Campus, London, UK.

    • Sheila Q Xie
    •  & David Rueda
  6. Section of Virology, Department of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.

    • Sheila Q Xie
    •  & David Rueda
  7. Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.

    • Ana Pombo

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Contributions

A.P. and M.N. designed the project. M.B., A.M.C., and S.B. performed the polymer modeling analysis. S.Q.X. performed the wet-lab experiments and image analysis. I.d.S. and E.T.T. performed the bioinformatics analyses. D.R. provided conceptual advice and co-mentored the work of S.Q.X. with A.P. M.R.B. developed the image analysis pipeline. A.P., M.N., M.B., S.Q.X., A.M.C. and S.B. wrote the paper, and all authors revised the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Mario Nicodemi or Ana Pombo.

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DOI

https://doi.org/10.1038/nsmb.3402