Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

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 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 transcriptome analysis (RNA-seq) and chromatin immunoprecipitation (ChIP-seq) of histone modifications. The method does not require specialized transgenic strains or growth conditions and can be readily applied 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. This series includes four ChIP-seq samples (IGN-H3K27ac and SOM-H3K27ac and IGN-H3K4me3 and SOM-H3K4me3) and two RNA-seq samples (IGN and SOM) performed in C. elegans. The ChIP-seq experiments were performed in duplicate with matching input for normalization, thus there are 16 ChIP-seq sequencing fastq files (8 ChIP and 8 input). The RNA-seq samples were done in duplicate, yielding two sequence files per sample, thus there are 4 RNA-seq sequencing fastq files. We are also submitting 4 combined normalized wig files for ChIP-seq samples (IGN-H3K27ac and SOM-H3K27ac and IGN-H3K4me3 and SOM-H3K4me3) and 4 bigwig files for RNA-seq (2 replicates of IGN RNA-seq and 2 replicates of SOM RNA-seq). Thus, we are submitting 20 fastq files (consisting of 16 fastq files for ChIP-seq and 4 fastq files for RNA-seq) and 8 wig/bigwig files for the series (consisting of 4 wig files for ChIP-seq and 4 bigwig files for RNA-seq).