“Digital chromosome banding”: A scRNA-seq-based chromosome banding method distinguishes real and pseudo sex body

To investigate the hypothesis that silencing of meiotic silencing of unsynapsed chromatin (MSUC)-affected regions in defective germline cells could suppress essential genes and lead to cell apoptosis, we developed a new method "digital chromosome banding" to measure transcriptional levels within each 1 MB chromosomal region via single-cell RNA sequencing (scRNA-seq) datasets from wild type and spo11-/- spermatocytes. We successfully detected meiotic sex chromosome inactivation (MSCI) but no obvious MSUC at the pachytene stage.

Furthermore, we revealed that pseudo sex bodies are unable efficiently silence chromosomes while gel-like structure of mature sex bodies potentially plays a key role in MSCI by blocking access to transcription factors and small molecules, indicating the crucial role of phase separation in meiotic silencing. This research has thus deepened the understanding of MSUC and MSCI mechanisms and introduced a novel approach for investigating chromosome-wise transcriptional regulation.