The Open Chromatin Landscape of the Chicken Genome

By performing DNase-seq assays from two biological replicates and eight tissues, we have constructed the first comprehensive view of the open chromatin regions in the chicken genome, including identifying tissue-specific regions. A total of 259,149 DNase I hypersensitivity sites (DHSs) from adipose, cerebellum, cortex, hypothalamus, liver, lung, muscle, and spleen covers 4.1% of the genome, compared with 6.3% in mouse using comparable ENCODE data. However less than 2% of the genome is covered by DHSs in any single tissue, indicating that the open chromatin landscape is highly variable between tissues. Additionally, 33.1% of all DHSs are expressed in only a single tissue, with the highest rate of tissue-specific DHSs in liver, lung, spleen, and hypothalamus. 36.8% of the identified DHSs are found in promoter regions and 21.9% in intergenic regions. We examined the conservation of our chicken DHSs with mouse DHSs from the ENCODE project. While only 4.0% of DHSs could be mapped to syntenic locations on the mouse genome, 63.3% of those matched DHS locations in mouse, with the majority of conserved DHSs in promoter regions. Still, overall only 2.5% of chicken DHSs are preserved in mouse, demonstrating the importance of profiling the open chromatin regions on a per-species basis rather than using a small set of model organisms. We have made the full set of chicken DHSs, sequencing data, and analysis pipeline code publicly available, which works not only with DNase-seq data, but also with ATAC-seq data.