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Abstract

Gene regulation in eukaryotes involves complex interactions between promoters and regulatory elements that can be located thousands of base pairs away from each other. By the three-dimensional folding of chromatin these distal elements can be brought into spatial proximity to modulate gene expression. However, the specific contacting genomic elements, which are often cell- and stage specific, are widely unknown. The advent of chromosome conformation capture (3C) methodologies in combination with high-throughput sequencing started to shed light on the three-dimensional structure of chromatin in the nucleus. Additionally, an increasing amount of information about chromatin states, the location of enhancer and boundary elements, as well as transcription factor binding sites becomes available by chromatin immunoprecipitation sequencing (ChIP-seq) experiments. Here, we use three-dimensional chromatin contact frequencies from 3C experiments in combination with ChIP-seq data to identify functional chromatin interactions between promoters and their cis-regulatory elements.