A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface
Name
Ferreira-2016-A distant trophoblas.pdf
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1.07 MB
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Author(s)
Ferreira, Leonardo M. R.
Meissner, Torsten B.
Mikkelsen, Tarjei S.
Mallard, William
O’Donnell, Charles W.
Tilburgs, Tamara
Gomes, Hannah A. B.
Camahort, Raymond
Sherwood, Richard I.
Rinn, John L.
Date Issued
April 2016
Journal
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences (U.S.)
Citation
Ferreira, Leonardo M. R. et al. “A Distant Trophoblast-Specific Enhancer Controls HLA-G Expression at the Maternal–fetal Interface.” Proceedings of the National Academy of Sciences 113.19 (2016): 5364–5369. © 2017 National Academy of Sciences
Version
Final published version
Abstract
HLA-G, a nonclassical HLA molecule uniquely expressed in the placenta, is a central component of fetus-induced immune tolerance during pregnancy. The tissue-specific expression of HLA-G, however, remains poorly understood. Here, systematic interrogation of the HLA-G locus using massively parallel reporter assay (MPRA) uncovered a previously unidentified cis-regulatory element 12 kb upstream of HLA-G with enhancer activity, Enhancer L. Strikingly, clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9-mediated deletion of this enhancer resulted in ablation of HLA-G expression in JEG3 cells and in primary human trophoblasts isolated from placenta. RNA-seq analysis demonstrated that Enhancer L specifically controls HLA-G expression. Moreover, DNase-seq and chromatin conformation capture (3C) defined Enhancer L as a cell type-specific enhancer that loops into the HLA-G promoter. Interestingly, MPRA-based saturation mutagenesis of Enhancer L identified motifs for transcription factors of the CEBP and GATA families essential for placentation. These factors associate with Enhancer L and regulate HLA-G expression. Our findings identify long-range chromatin looping mediated by core trophoblast transcription factors as the mechanism controlling tissue-specific HLA-G expression at the maternal–fetal interface. More broadly, these results establish the combination of MPRA and CRISPR/Cas9 deletion as a powerful strategy to investigate human immune gene regulation.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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DOI of Published Version
https://doi.org/10.1073/pnas.1602886113
