Investigating the Physiological Regulation of Transposable Elements In Vivo: Nuclei Preparation from Primary Mouse Tissues for Epigenomic Analyses and Computational Approaches to Interrogate the Repeat Genome.

Investigating the physiological regulation of the epigenome using genetically engineered mouse models, with a focus on heterochromatic regions of DNA, presents two major challenges: (i) the isolation and preparation of high-quality nuclei from tissue for analysis, (ii) the computational considerations for repetitive regions of the genome. Here we outline the experimental methods for tissue procurement and cryopreservation used in our laboratory, and the steps for nuclei isolation, which can be used for several downstream epigenomic and transcriptomic applications, including ATAC-seq, CUT&RUN, and single-nucleus RNA-sequencing. We then describe the computational considerations and bioinformatics pipelines for interrogating the repeat genome, with a particular focus on transposable elements.