Robust 4C-seq data analysis to screen for regulatory DNA interactions. Mus musculus

Regulatory DNA elements can control expression of distant genes via physical interactions. Here, we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using Chromosome Conformation Capture combined with high-throughput sequencing (4C-seq) data. Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation. Overall design: A high resolution 4C-seq protocol involving two restriction digests and a revised analysis pipeline was applied to several viewpoints in four genomic loci (the well-characterized alpha-globin and beta-globin loci, and the novel Oct4 and Satb1 loci), allowing robust detection of physical interactions between regulatory DNA elements.