Xiaoming Lu, Xiaoting Chen, Carmy Forney, Omer Donmez, Daniel Miller et al.
Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we construct a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 reveals 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Comparison of MPRA results in GM12878 and Jurkat T cell lines highlights shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around allelic variants identifies one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second class of TFs that bind allelically without direct alteration of their motif by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE.
Xiaoming Lu, Xiaoting Chen, Carmy Forney, Omer Donmez, Daniel Miller, Sreeja Parameswaran, Ted Hong, Yongbo Huang, Mario Pujato, Tareian Cazares, Emily R. Miraldi, John P. Ray, Carl G. de Boer, John B. Harley, Matthew T. Weirauch, Leah C. Kottyan. Global discovery of lupus genetic risk variant allelic enhancer activity. 2021-03-12. https://doi.org/10.1038/s41467-021-21854-5
The study's allele-focused MPRA library was transiently electroporated into the human Jurkat T-cell line in five independent biological replicates, followed by TNFα stimulation. Matched DNA and reporter RNA barcode counts were used to quantify enhancer activity and published allelic Student's t-test results were retained for enVars.
The study's allele-focused MPRA library was transiently electroporated into the Epstein–Barr virus-transformed human B-cell line GM12878 in three independent biological replicates. Reporter RNA barcode counts were compared with plasmid-control barcode counts to quantify enhancer activity for each reference and non-reference allele.
The study's allele-focused MPRA library was transiently electroporated into the human Jurkat T-cell line in five independent biological replicates under basal conditions. Reporter DNA and RNA barcode counts were used to quantify allele-linked enhancer activity, with published Student's t-test comparisons for enVars.
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