GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis
GPSeq (Genomic loci Positioning by Sequencing) is a genome-wide method for mapping the radial organization of the genome in the nucleus of eukaryotic cells. GPSeq relies on in situ digestion of chromatin with a restriction enzyme that gradually diffuses inwards from the nuclear periphery, followed by ligation of sequencing adapters to the digested restriction sites and library preparation for high-throughput sequencing. By comparing samples in which chromatin has been digested for increasing time intervals, a GPSeq score is calculated for every genomic bin into which the genome is arbitrarily divided, and genome-wide radial maps are generated with a resolution as high as 25 kilobases. These maps allow for exploration of the radial distribution of (epi)genomic features, gene expression levels, mutational landscapes, and genomic profiles of DNA damage. Here, we present a detailed step-by-step protocol for performing GPSeq and pre-processing GPSeq data. The entire protocol requires ~2 weeks and intermediate levels of expertise in molecular biology, genomics, and microscopy.