Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation

Purpose: A systematic analysis of how lamina association of chromosome regions influences their gene regulation in response to stimuli. Here, Lamin associated domains (LADs) of prostate cancer cell lines LNCaP and VCaP were experimentally measured using Lamin B1 ChIP-Seq so that these could be compared to previously published expression data in these cell lines and published LAD data from other cell types. Overall design: LNCaP and VCAP cells growing in culture were crosslinked with formaldehyde, chromatin was sonicated, and then lamin associated regions were immunoprecipitated with Lamin B1 antibody. ChIP and INPUT (not treated with antibody) DNA samples were prepared and sequenced on an Illumina sequencing instrument.