Abstract
BackgroundSpatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare.ResultsWe generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps.ConclusionsOur findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.
Highlights
Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease
The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international consortia mostly focussing on model organisms, such as the Encyclopedia of DNA Elements (ENCODE) in humans [4, 5], the mouseENCODE for mouse [6] and the modENCODE for fruitfly and C. elegans [7, 8]
Samples resulted in an average of 82,988,361 uniquely mapped reads (Additional file 1), in agreement with the quality standards determined by ENCODE ATAC-seq pipeline [24]
Summary
Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Nucleosomes are known to be depleted at regulatory loci, including enhancers, insulators, and transcribed gene bodies, making binding sites available to transcription factors (TFs) and the transcription machinery [3] These epigenetic changes are instrumental to cell differentiation, environmental signaling, and disease development. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international consortia mostly focussing on model organisms, such as the Encyclopedia of DNA Elements (ENCODE) in humans [4, 5], the mouseENCODE for mouse [6] and the modENCODE for fruitfly and C. elegans [7, 8]
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