AUTHOR CONTRIBUTIONS R.C.W. designed and performed all scRNAseq experiments, analyzed the scRNAseq data, performed the RNAscope in-situ hybridization assays, performed and analyzed the CITE-seq and FACS experiments, analyzed the immunofluorescence data, performed the eQTL analyses, assisted with mouse colony breeding, drafted the manuscript, and led the study. D.W. assisted with the design of the scRNAseq experiments and performed scRNAseq capture and library preparation for all samples. D.T.P. performed scRNAseq capture and helped obtain human coronary samples. J.C. assisted with the scRNAseq capture, library preparation and sequencing. T.N. performed qPCR experiments, analyzed the qPCR data and performed TCF21 ChIPseq. M.P., C.L.M., B.L. and S.B.M. performed the eQTL analyses. R.K. performed the immunohistochemistry experiments and bred the mouse colonies. M.N. performed and analyzed immunohistochemistry experiments. K.Z., M.A. and R.C. assisted with network analysis. T.K.K., R.F. and Y.J.W. prepared the human tissue samples. M.D.T. and J.C.W. provided critical expert guidance on the manuscript. J.B.K. helped plan the mouse in situ histology studies, managed the mouse colonies, performed the TCF21 over-expression experiment and performed the quantitative immunohistochemistry analysis of lesion characteristics. T.Q. conceived and supervised the study. All authors discussed the results and contributed critical review to the manuscript.
The challenge of linking intergenic mutations to target genes has limited
molecular understanding of human diseases. Here we show that H3K27ac HiChIP
generates high-resolution contact maps of active enhancers and target genes in
rare primary human T cell subtypes and coronary artery smooth muscle cells.
Differentiation of naive T cells into T helper 17 cells or regulatory T cells
creates subtype-specific enhancer–promoter interactions, specifically at
regions of shared DNA accessibility. These data provide a principled means of
assigning molecular functions to autoimmune and cardiovascular disease risk
variants, linking hundreds of noncoding variants to putative gene targets.
Target genes identified with HiChIP are further supported by CRISPR interference
and activation at linked enhancers, by the presence of expression quantitative
trait loci, and by allele-specific enhancer loops in patient-derived primary
cells. The majority of disease-associated enhancers contact genes beyond the
nearest gene in the linear genome, leading to a fourfold increase in the number
of potential target genes for autoimmune and cardiovascular diseases.
Precise editing of human genomes in pluripotent stem cells by
homology-driven repair of targeted nuclease-induced cleavage has been hindered
by the difficulty of isolating rare clones. We developed an efficient method to
capture rare mutational events, enabling isolation of mutant lines with
single-base substitutions without antibiotic selection. This method facilitates
efficient induction or reversion of mutations associated with human disease in
isogenic human induced pluripotent stem cells.
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