Single-cell staging of meiotic entry identifies a sequential order in meiotic sex chromosome activation

The switch from mitosis to meiosis is a major transition that takes place during germ cell development. The precise sequence and the different gene expression programs activated during this process are only partly known. Here, we applied single-cell mRNA sequencing to interrogate the transcriptional changes that occur during the early steps of male germ cell differentiation. We isolated single cells from testes using a Dazl-GFP reporter mouse, which allowed us to focus on germ cells undergoing the mitotic to meiotic transition. We identified 4 distinct meiotic stages with unique transcriptome profiles and reconstructed the timeline of the meiotic entry in silico, from spermatogonia up to the pachytene stage, identifying transcriptional changes with an unprecedented resolution. This allowed us to characterize 3 major transitions in the meiotic prophase 1 of the male germline: meiotic entry, the meiotic sex chromosome inactivation (MSCI), and concomitant pachytene transcriptional activation. Meiotic entry is initiated following the downregulation of a tightly connected set of pluripotency factors and accompanied by a global transcriptional silencing. In contrast, during subsequent sex chromosome inactivation at the zygotene stage, gene silencing proceeds in a defined order, related to gene function. Overall design: Single-cell mRNA sequencing on isolated cells from testes from three Dazl-GFP reporter mice.Testes were isolated from Dazl-GFP mice (Chen 2014, PMID: 25418731), and extracted cells were prepared into a single-cell suspension. Live, Dazl-GFP+ cells were sorted intro 384 well plates with either 96 CEL-seq1 or 384 CEL-seq2 barcodes (see "CEL-seq.demultiplexing.barcodes.pdf"). CEL-seq1 plates have 4 libraries, CEL-seq2 plates have 1 library per plate. Sequencing lanes concatenated in fastq-files uploaded here. See Supplementary Methods for details.