Preliminary functional annotation of the sheep genome

Full description

In the absence of detailed functional annotation for any livestock genome, we used comparative genomics to predict ovine regulatory elements using human data. Reciprocal liftOver was used to predict the ovine genome location of ENCODE promoters and enhancers, along with 12 chromatin states built using 127 diverse epigenome.
Here we make available the following files:
a) Sheep_epigenome_predicted_features.tar.gz: contains the final reciprocal best alignment from ENCODE proximal as well as chromHMM ROADMAP features. The result of reciprocal liftOver.
b) liftOver_sheep_temporary_files.tar.gz: We have
added a new tar file with liftOver temporary files
containing
i) LiftOver temporary files mapping human to sheep,
ii) LiftOver temporary files mapping sheep back to human and
iii) Dictionary files containing the link between human to sheep coordinates for exact best-reciprocal files.

Lineage: Building a comparative sheep functional annotation.
Our approach exploited the wealth of functional annotation data generated by the Epigenome Roadmap and ENCODE studies. We performed reciprocal liftOver (minMatch=0.1), meaning elements that mapped to sheep also needed to map in the reverse direction back to human with high quality. This bi-directional comparative mapping approach was applied to 12 chromatin states defined using 5 core histone modification marks, H3K4me3, H3K4me1, H3K36me3, H3K9me3, H3K27me3. Mapping success is given in Supplementary Table 9. The same approach was applied to ENCODE marks derived from 94 cell types (https://www.encodeproject.org/data/annotations/v2/) with DNase-seq and TF ChIP-seq.