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. 2018 Feb 28;9:859. doi: 10.1038/s41467-017-02809-1

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — Prediction and validation of sheep gene regulatory elements. a Human Epigenome Roadmap chromatin states and ENCODE features used in a reciprocal liftOver protocol to predict regulatory regions in sheep. b Overlap between chromosomal locations identified by experimental sheep tissue ChIP-Seq (H3K4me3 and H3K27ac) and regions predicted by liftOver. H3K4me3 peaks are compared against predicted Roadmap chromatin state TssA identifying active promoters (left) and unique H3K27ac peaks are compared to the Roadmap Enh state, excluding those regions overlapping with predicted TssAs, identifying distal enhancers (right). c The proportion of predicted promoters (left) and enhancers (right) recovered by ChIP-Seq using either H3K4me3 peaks (blue bar) or unique H3K27ac peaks (orange bar). This demonstrates the predicted annotations retain a level of specificity between components of the gene regulatory apparatus. d An example annotated region containing LCORL highlights the correspondence between ChIP-Seq data (Sheep H3K27ac) and liftOver predictions (TSSA, TSSAFlnk, ENCODE proximal, Enh, ENCODE distal)