Abstract

Tissue-specific transcriptional regulation is central to human disease1. To identify regulatory DNA active in human pancreatic islets, we profiled chromatin by formaldehyde-assisted isolation of regulatory elements2,3,4 coupled with high-throughput sequencing (FAIRE-seq). We identified 80,000 open chromatin sites. Comparison of FAIRE-seq data from islets to that from five non-islet cell lines revealed 3,300 physically linked clusters of islet-selective open chromatin sites, which typically encompassed single genes that have islet-specific expression. We mapped sequence variants to open chromatin sites and found that rs7903146, a TCF7L2 intronic variant strongly associated with type 2 diabetes5, is located in islet-selective open chromatin. We found that human islet samples heterozygous for rs7903146 showed allelic imbalance in islet FAIRE signals and that the variant alters enhancer activity, indicating that genetic variation at this locus acts in cis with local chromatin and regulatory changes. These findings illuminate the tissue-specific organization of cis-regulatory elements and show that FAIRE-seq can guide the identification of regulatory variants underlying disease susceptibility.

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Acknowledgements

We thank X. Garcia for experimental support in rs7903146 functional studies, I. Moran for insights and help in the analysis of COREs, P. Maechler (Univ. Geneva Medical Center) for generously providing insulin release data, L. Piemonti and R. Nano (San Raffaele Scientific Institute), and M. Nacher (IDIBELL) for human islets. This work was supported by the European Union VI Framework Programme project Eurodia to J.F., Ministerio de Ciencia e Innovación (SAF2008-03116) to J.F., Juvenile Diabetes Research Foundation (26-2008-633 to J.F., 31-2008-416 to T.B., 6-2005-1178 and 31-2008-416 to A.S.), the US National Human Genome Research Institute Encyclopedia Of DNA Elements (NHGRI ENCODE) project (U54 HG004563 subcontract to J.D.L.) and R01 DK072193 (US National Institutes of Health) to K.L.M. K.L.M. is a Pew Scholar in the Biomedical Sciences.

Author information

Author notes

    • Kyle J Gaulton
    • , Takao Nammo
    •  & Lorenzo Pasquali

    Authors contributed equally to this work.

Affiliations

  1. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

    • Kyle J Gaulton
    • , Jeremy M Simon
    • , Marie P Fogarty
    • , Tami M Panhuis
    • , Piotr Mieczkowski
    •  & Karen L Mohlke
  2. Genomic Programming of Beta Cells, Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain.

    • Takao Nammo
    • , Lorenzo Pasquali
    •  & Jorge Ferrer
  3. Centro de Investigación Biomédica en Red (CIBER) de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain.

    • Takao Nammo
    • , Lorenzo Pasquali
    • , Eduard Montanya
    •  & Jorge Ferrer
  4. Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

    • Jeremy M Simon
    • , Paul G Giresi
    •  & Jason D Lieb
  5. Clinical Transplant Unit, San Raffaele Scientific Institute, Milano, Italy.

    • Antonio Secchi
  6. Cell Isolation and Transplantation Center, Geneva, Switzerland.

    • Domenico Bosco
    •  & Thierry Berney
  7. Laboratory of Diabetes and Experimental Endocrinology, Endocrine Unit, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)-Hospital Universitari Bellvitge, University of Barcelona, Spain.

    • Eduard Montanya
  8. Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

    • Karen L Mohlke
    •  & Jason D Lieb
  9. Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

    • Karen L Mohlke
    •  & Jason D Lieb
  10. Department of Endocrinology, Hospital Clínic de Barcelona, Barcelona, Spain.

    • Jorge Ferrer

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Contributions

J.F. and J.D.L. conceived the study. K.J.G., T.N., L.P., J.M.S., K.L.M., J.D.L. and J.F. designed the experiments, interpreted results and wrote the manuscript. T.N. conducted FAIRE experiments, and developed and performed allelic imbalance assays. P.G.G. optimized the FAIRE protocol and performed microarray studies. K.J.G., J.M.S., and P.G.G. performed sequence analysis and K.J.G., L.P., T.N. and J.M.S. performed data analysis. L.P. conducted the analysis of COREs. M.P.F. and T.M.P. conducted reporter assays. P.M. conducted high-throughput sequencing. A.S., D.B., T.B. and E.M. provided purified human islet samples.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Karen L Mohlke or Jason D Lieb or Jorge Ferrer.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–4 and Supplementary Tables 1–9.

Excel files

  1. 1.

    Supplementary Table 2

    RefSeq transcripts with preferential islet FAIRE enrichment

  2. 2.

    Supplementary Table 4

    Over- and under-represented transcription factor binding motifs in intergenic islet FAIRE sites

  3. 3.

    Supplementary Table 5

    Islet-selective Clusters of Open Regulatory Elements (COREs)

  4. 4.

    Supplementary Table 7

    Islet-selective CORES that extend > 2 kb from the transcription start or termination site of overlapping genes

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DOI

https://doi.org/10.1038/ng.530

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