A simple and effective method to isolate germ nuclei from C. elegans for genomic assays.

Abstract

The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity and purity from living animals is necessary to address these open questions, but no straightforward methods are currently available. Here we present an experimental paradigm that permits the isolation of the nuclei from C. elegans germ cells at quantities sufficient for genomic analyses. We demonstrate that these nuclei represent a very pure population and are suitable for both chromatin immunoprecipitation (ChIP-seq) and transcriptome (RNA-seq) analyses. The method does not require specialized transgenic strains or growth conditions and can be readily adopted by other researchers with minimal troubleshooting. This new capacity removes a major barrier in the field to dissect gene expression mechanisms in the germ line of C. elegans. Consequent discoveries using this technology will be relevant to conserved regulatory mechanisms across species.