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 All data generated were held to stringent data quality standards that closely mirrored the ENCODE consortium’s criteria31 (Supplementary Table 1, Supplementary Data 1 and 2). Hierarchical clustering based on the Pearson correlation of read depth in bins across the genome for the five ChIP-seq marks and the chromatin accessibility assays demonstrated data reproducibility between two biological replicates and specificity across tissues (Supplementary Figs. 2–4). The reproducibility of the RNA-seq data was similarly verified by principal component analysis (PCA) of gene expression values both within each species (Supplementary Fig. 5a) and across all three species (Supplementary Fig. 5b).

Identification and annotation of REs Simply Blessed Sunflower Dishwasher Cover

The data generated allowed the discovery of co-occurring histone modifications, CTCF binding, chromatin accessibility, and gene expression, which was used to identify regions with regulatory function and to link them with candidate target genes. We therefore first predicted genome-wide chromatin states in each tissue within each species using ChromHMM32 to categorize genomic regions into 14 distinct chromatin states defined by their combination of ChIP-seq marks (Fig. 1b). Labels assigned to each state were determined based on previously characterized chromatin states33 and include active promoter and transcription start site (TSS) states, primarily defined by the presence of H3K4me3, active enhancer states with H3K27ac and H3K4me1, polycomb repressed elements marked by H3K27me3, and insulators bound by CTCF. 53%, 40%, and 31% of the chicken, pig, and cattle genomes, respectively, was annotated with a ChromHMM state corresponding to any epigenetic signal in at least one tissue, i.E., any ChromHMM state except for “Low Signal” which indicated an absence of any of the five ChIP-seq marks profiled. The percentage of the genome annotated with some regulatory function varied from tissue to tissue (Fig. 1c), reflecting the different regulatory programs responsible for tissue-specific phenotypes, as exemplified by the tissue-specific activity of the albumin (ALB) gene, which is highly expressed in the liver (Supplementary Fig. 1b).

These predicted chromatin states were then used to identify REs in each of the domestic animal genomes and annotate them with the tissues in which they were active. Next, these REs were classified as TSS proximal, genic, or intergenic based on their genomic location relative to annotated coding genes. Enrichment for each of the histone modifications assayed indicated that TSS proximal REs are characterized primarily by a strong H3K4me3 enrichment, consistent with promoter activity34,35,36. A bimodal pattern of H3K4me1 enrichment in TSS proximal REs was present, with stronger enrichment flanking the central point where the peaks of H3K4me3, H3K27ac, and chromatin accessibility enrichment lie.

 

 

 

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