Effect of natural genetic variation on enhancer selection and function

S. Heinz, C. E. Romanoski, C. Benner, K. A. Allison, M. U. Kaikkonen, L. D. Orozco and C. K. Glass ()
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S. Heinz: University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA
C. E. Romanoski: University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA
C. Benner: University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA
K. A. Allison: University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA
M. U. Kaikkonen: University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA
L. D. Orozco: University of California, Los Angeles, 3000 Terasaki Life Sciences Building, Los Angeles, California 90095, USA
C. K. Glass: University of California, San Diego, 9500 Gilman Drive, Mail Code 0651, La Jolla, California 92093, USA

Nature, 2013, vol. 503, issue 7477, 487-492

Abstract: Abstract 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.

Date: 2013
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DOI: 10.1038/nature12615

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