nih roadmap epigenomics mapping consortium  (Epigenomics ag)

Journal: Nature Communications

Article Title: Integrating leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, genes, and cell types

doi: 10.1038/s41467-024-45382-0

Figure Lengend Snippet: a The dot plot shows the significance of SNPs in the rs78378222 lead SNP risk locus. ChIP-Seq track shows the signal intensity of H3K27ac and arc plots show the intensity of Hi-C measured chromatin contact frequency in the same genomic region for UF tissue and MyoF patient samples. Track heights are normalized to read depth. b The bar plot shows qPCR measured enrichment of H3K27ac chromatin immunoprecipitation levels at the target locus after recruitment of dCas9-fused P300 histone acetyltransferase with control sgRNA (sgRNA-targeting another chromosome) and lead SNP targeting sgRNA. c RNA-Seq bigwig tracks show relative expression at TP53 locus after recruitment of dCas9-P300 epigenetic activator with control and TP53 locus targeting sgRNA-1. Tracks heights are normalized to read depth. d Bar plots show RT-qPCR measured mRNA levels of indicated genes with and without recruitment of dCas9-P300 to the lead SNP target region. Two-tailed student t-tests were used for statistical comparisons. Error bars indicate the standard error of the mean. Error bars in Fig. 6b, d indicate the standard error of the mean of three independent biological replicates ( n = 3).

Article Snippet: To identify target genes that may be directly affected by UF-associated variants, we performed an integrative analysis of this GWAS data with several multi-omics data sets, including epigenomic maps from ENCODE and Roadmap Epigenomics Project , 3D chromatin organization map from Hi-C experiments , and GTEx gene expression data .

Techniques: ChIP-sequencing, Hi-C, Chromatin Immunoprecipitation, Control, RNA Sequencing, Expressing, Quantitative RT-PCR, Two Tailed Test