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Effect of natural genetic variation on enhancer selection and function

Nature volume 503, pages 487492 (28 November 2013) | Download Citation


The mechanisms by which genetic variation affects transcription regulation and phenotypes at the nucleotide level are incompletely understood. Here we use natural genetic variation as an in vivo mutagenesis screen to assess the genome-wide effects of sequence variation on lineage-determining and signal-specific transcription factor binding, epigenomics and transcriptional outcomes in primary macrophages from different mouse strains. We find substantial genetic evidence to support the concept that lineage-determining transcription factors define epigenetic and transcriptomic states by selecting enhancer-like regions in the genome in a collaborative fashion and facilitating binding of signal-dependent factors. This hierarchical model of transcription factor function suggests that limited sets of genomic data for lineage-determining transcription factors and informative histone modifications can be used for the prioritization of disease-associated regulatory variants.

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Gene Expression Omnibus

Data deposits

Data are available in the Gene Expression Omnibus (GEO) under accession GSE46494.


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We thank A. J. Lusis for providing access to eQTL data ( and for productive conversations. We thank D. Pollard for discussions and suggestions, and L. Bautista for assistance with figure preparation. These studies were supported by National Institutes of Health (NIH) grants DK091183, CA17390 and DK063491 (C.K.G.). M.U.K. was supported by the Foundation Leducq Career Development award and grants from Academy of Finland, Finnish Foundation for Cardiovascular Research and Finnish Cultural Foundation, North Savo Regional fund. C.E.R. was supported by the American Heart Association Western States Affiliates (12POST11760017) and the NIH (5T32DK007494).

Author information

Author notes

    • S. Heinz
    •  & C. E. Romanoski

    These authors contributed equally to this work.


  1. Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA

    • S. Heinz
    • , C. E. Romanoski
    • , C. Benner
    • , K. A. Allison
    • , M. U. Kaikkonen
    •  & C. K. Glass
  2. Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA

    • C. Benner
  3. San Diego Center for Systems Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA

    • C. Benner
    •  & C. K. Glass
  4. Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland

    • M. U. Kaikkonen
  5. Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, 3000 Terasaki Life Sciences Building, Los Angeles, California 90095, USA

    • L. D. Orozco
  6. Department of Medicine, University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA

    • C. K. Glass


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S.H., C.K.G. and C.E.R. designed the study; S.H., C.E.R., K.A.A., M.U.K. and L.D.O. performed experiments; C.E.R. performed all genetic-variation-related analysis; C.B. wrote custom code for HOMER2 and analysed data; K.A.A. and S.H. analysed data; C.E.R., S.H. and C.K.G. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to C. K. Glass.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1 - HOMER-formatted motif files for the motifs used for strain-specific motif finding listed in Extended Data Figure 3a,b

    The header rows, which begin with ">", list the consensus motif, the motif name, and the log-odds threshold above which a given sequence is considered to be positive for the motif. Below each header is the position weight matrix that lists the frequency of each nucleotide (A, C, G, T in the columns from left to right, respectively) at each position (rows) of the motif from top to bottom.

  2. 2.

    Supplementary Table 2 - Strain-specific PU.1-bound loci where NOD broke the C57BL6/BALBc haplotypes

    Loci are shown in rows. The number of variants at each region is shown between C57BL/6J and BALB/cJ in column 4. The number of variants with alleles matching the binding pattern observed across NOD, C57BL/6J, and BALB/cJ are shown in column 5.

  3. 3.

    Supplementary Table 3 - Strain-similar loci cloned for luciferase reporter assays

    The genomic location, variant information, strain-specific motif information, and primer sequences used to clone strain-similar loci are shown in columns for the 9 loci tested (data in Extended Data Figure 10a).

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