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Analysis of vertebrate SCL loci identifies conserved enhancers

Nature Biotechnology volume 18, pages 181–186 (2000)Cite this article

Abstract

The SCL gene encodes a highly conserved bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis. We have sequenced and analyzed 320 kb of genomic DNA composing the SCL loci from human, mouse, and chicken. Long-range sequence comparisons demonstrated multiple peaks of human/mouse homology, a subset of which corresponded precisely with known SCL enhancers. Comparisons between mammalian and chicken sequences identified some, but not all, SCL enhancers. Moreover, one peak of human/mouse homology (+23 region), which did not correspond to a known enhancer, showed significant homology to an analogous region of the chicken SCL locus. A transgenic Xenopus reporter assay was established and demonstrated that the +23 region contained a new neural enhancer. This combination of long-range comparative sequence analysis with a high-throughput transgenic bioassay provides a powerful strategy for identifying and characterizing developmentally important enhancers.

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Figure 1: Characterization of vertebrate SCL loci.
Figure 2: Large-scale alignment of the human and mouse SCL loci.
Figure 3: Conserved noncoding regions identified by comparative sequence analysis.
Figure 4: Murine SCL enhancers direct tissue-specific expression in transgenic frogs.

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Acknowledgements

Work in the authors' laboratories is supported by the Wellcome Trust, the Medical Research Council, the Leukaemia Research Fund, and the Kay Kendall Leukaemia Fund. We are grateful to Christine Holt for expert help in characterizing neural expression patterns, Kathy Hartley for the polyGFP3 plasmid, Rima Zoorob for a filter set of the chicken PAC library, and Jonathan Frampton for the HD57 RNA. We have enjoyed stimulating discussions with Doug Higgs, Sam Aparicio, Rob Krumlauf, and Victor Solovyev, and would also like to acknowledge the unstinting support of Jane Rogers and sequencing team 32 at the Sanger Centre.

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Authors and Affiliations

  1. Department of Haematology, University of Cambridge, MRC Centre, Hills Road, Cambridge, CB2 2QH, UK

    Berthold Göttgens, Linda M. Barton, James G.R. Gilbert, Anthony J. Bench, Maria-José Sanchez & Anthony R. Green

  2. Department of Psychiatry, Addenbrooke's Hospital, Cambridge, CB2 2QQ, UK

    Sabine Bahn

  3. The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 ISA, UK

    Shailesh Mistry, Darren Grafham, Amanda McMurray, Mark Vaudin & David R. Bentley

  4. Wellcome/CRC Institute for Developmental Biology and Cancer Research, Cambridge, CB2 1QR, UK

    Enrique Amaya

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Correspondence to Anthony R. Green.

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Göttgens, B., Barton, L., Gilbert, J. et al. Analysis of vertebrate SCL loci identifies conserved enhancers . Nat Biotechnol 18, 181–186 (2000). https://doi.org/10.1038/72635

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