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Am J Hum Genet DOI:10.1016/j.ajhg.2019.03.012

IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors.

Publication TypeJournal Article
Year of Publication2019
AuthorsAmariuta, T, Luo, Y, Gazal, S, Davenport, EE, van de Geijn, B, Ishigaki, K, Westra, H-J, Teslovich, N, Okada, Y, Yamamoto, K, Price, AL, Raychaudhuri, S
Corporate AuthorsRACI Consortium, GARNET Consortium
JournalAm J Hum Genet
Date Published2019 Apr 06

Despite significant progress in annotating the genome with experimental methods, much of the regulatory noncoding genome remains poorly defined. Here we assert that regulatory elements may be characterized by leveraging local epigenomic signatures where specific transcription factors (TFs) are bound. To link these two features, we introduce IMPACT, a genome annotation strategy that identifies regulatory elements defined by cell-state-specific TF binding profiles, learned from 515 chromatin and sequence annotations. We validate IMPACT using multiple compelling applications. First, IMPACT distinguishes between bound and unbound TF motif sites with high accuracy (average AUPRC 0.81, SE 0.07; across 8 tested TFs) and outperforms state-of-the-art TF binding prediction methods, MocapG, MocapS, and Virtual ChIP-seq. Second, in eight tested cell types, RNA polymerase II IMPACT annotations capture more cis-eQTL variation than sequence-based annotations, such as promoters and TSS windows (25% average increase in enrichment). Third, integration with rheumatoid arthritis (RA) summary statistics from European (N = 38,242) and East Asian (N = 22,515) populations revealed that the top 5% of CD4 Treg IMPACT regulatory elements capture 85.7% of RA h2, the most comprehensive explanation for RA h2 to date. In comparison, the average RA h2 captured by compared CD4 T histone marks is 42.3% and by CD4 T specifically expressed gene sets is 36.4%. Lastly, we find that IMPACT may be used in many different cell types to identify complex trait associated regulatory elements.


Alternate JournalAm. J. Hum. Genet.
PubMed ID31006511