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Nature Genetics
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Genetic dissection of the α-globin super-enhancerin vivo

Nature Geneticsvolume 48, pages895–903 (2016)Cite this article

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Abstract

Many genes determining cell identity are regulated by clusters of Mediator-bound enhancer elements collectively referred to as super-enhancers. These super-enhancers have been proposed to manifest higher-order properties important in development and disease. Here we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer individually and in informative combinations, we demonstrate that each constituent enhancer seems to act independently and in an additive fashion with respect to hematological phenotype, gene expression, chromatin structure and chromosome conformation, without clear evidence of synergistic or higher-order effects. Our study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.

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Figure 1: The α-globin regulatory region typifies a super-enhancer in erythroid cells.
Figure 2: Erythroid super-enhancer constituents vary in transcription factor binding and chromatin signature.
Figure 3: Enhancer assays of individual elements in the α-globin super-enhancer.
Figure 4: Hematological impact of single and double enhancer knockouts.
Figure 5: α-globin gene transcription in single- and double-enhancer knockouts.
Figure 6: Analysis of chromatin structure in the α-globin super-enhancer.

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Acknowledgements

This manuscript is dedicated to the memory of Professor Bill Wood who initiated the project and died in 2014 during the course of this work. The work was supported by the Wellcome Trust (D.H.), the UK Medical Research Council (MRC) and the National Institute for Health Research Biomedical Research Centre, Oxford. L.A.P. was supported by NIDCR FaceBase grant U01DE020060NIH and by NHGRI grants R01HG003988 and U54HG006997, and research was conducted at the E.O. Lawrence Berkeley National Laboratory and performed under US Department of Energy contract DE-AC02-05CH11231, University of California.

Author information

Author notes

  1. William G Wood: Deceased.

  2. Christian Babbs, James O J Davies, Bryony J Graham, Lars L P Hanssen, Mira T Kassouf, A Marieke Oudelaar, Jacqueline A Sharpe, Maria C Suciu, Jelena Telenius and Ruth Williams: These authors contributed equally to this work.

Authors and Affiliations

  1. MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK

    Deborah Hay, Jim R Hughes, Christian Babbs, James O J Davies, Bryony J Graham, Lars L P Hanssen, Mira T Kassouf, A Marieke Oudelaar, Jacqueline A Sharpe, Maria C Suciu, Jelena Telenius, Christina Rode, Pik-Shan Li, Len A Pennacchio, Jacqueline A Sloane-Stanley, Helena Ayyub, Sue Butler, Richard J Gibbons, Andrew J H Smith, William G Wood & Douglas R Higgs

  2. Weatherall Institute of Molecular Medicine, Oxford, UK

    Ruth Williams & Tatjana Sauka-Spengler

  3. Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Len A Pennacchio

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  1. Deborah Hay

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  9. Jacqueline A Sharpe

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Contributions

D.R.H. and W.G.W. conceived the project. D.R.H., J.R.H., D.H., J.O.J.D., L.L.P.H., M.C.S. and J.T. designed experiments. J.R.H., C.B., D.H., J.O.J.D., B.J.G., L.L.P.H., M.T.K., J.A.S., M.C.S., J.T., R.W., P.-S.L., J.A.S.-S., H.A., A.M.O., C.R. and S.B. performed experiments. D.R.H., J.R.H., C.B., D.H., J.O.J.D., B.J.G., L.L.P.H., M.T.K., M.C.S., J.T., R.W., J.A.S., A.M.O. and P.-S.L. analyzed data. D.R.H., J.R.H., C.B., D.H., J.O.J.D., B.J.G., L.L.P.H., M.T.K., M.C.S., J.T., R.W. and J.A.S. wrote the manuscript. L.A.P., A.J.H.S. and T.S.-S. provided reagents and expertise. D.R.H., J.R.H., R.J.G. and A.J.H.S. provided supervision.

Corresponding author

Correspondence toDouglas R Higgs.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Tables 1–6. (PDF 47502 kb)

Circulating blood cells show R1 enhancer activity.

R1 enhancer activity in circulating blood cells, captured using a Red Epic camera attached to an Olympus MVX10 microscope, recorded at 240 frames per second at 1,280 iso, 20× magnification. (MP4 1799 kb)

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Hay, D., Hughes, J., Babbs, C.et al. Genetic dissection of the α-globin super-enhancerin vivo.Nat Genet48, 895–903 (2016). https://doi.org/10.1038/ng.3605

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