Gene transcription is controlled by interplay of transcription factors and non-coding cis-regulatory elements (CREs) - promoters, enhancers and silencers. Since association mapping in maize indicated connection of putative CREs with expression QTLs for important traits, localization of these elements and linking them to their target genes become a vital background for crop breeding and bioengineering. In the project, we aim to precisely delimit and characterize promoter and putative enhancer regions in barley embryo by combining available RNA-seq data for two stages of embryo development with Cap Analysis of Gene Expression and transposase-accessible-chromatin, histone-modification and DNA-methylation profiles. Interactions of putative enhancers with their targets will be identified using a 3C-based technique Hi-ChIP. Thus predicted CREs and generated chromatin-state and interactome maps of barley embryo will improve functional annotation of the barley genome. Comparison of epigenomes in two embryo stages sheds light on processes controlling grain development in cereals