Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells

Abstract

Stem cells have the unique ability to self-renew and differentiate into specialized cell types. Epigenetic mechanisms, including histones and their post-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst stem cells (CySCs), the Drosophila testis provides an excellent in vivo model for studying adult stem cells. However, the small number of stem cells and the cellular heterogeneity of this tissue have limited comprehensive genomic studies. In this study, we develop cell-type-specific genomic techniques to analyze the transcriptome, histone modification patterns, and replication timing of germline stem cell (GSC)–like and somatic cyst stem cell (CySC)–like cells. Single-cell RNA sequencing validates previous findings on GSC–CySC intercellular communication and reveals a high expression of chromatin regulators in GSC-like cells. To characterize chromatin landscapes, we develop a cell-type-specific chromatin profiling assay to map H3K4me3-, H3K27me3-, and H3K9me3-enriched regions, corresponding to the euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively. Finally, we determine cell-type-specific replication timing profiles, integrating our in vivo data sets with published data using cultured cell lines. Our results reveal that GSC-like cells display a distinct replication program, compared with somatic lineages, that aligns with chromatin state differences. Collectively, our integrated transcriptomic, chromatin, and replication data sets provide a comprehensive framework for understanding genome regulation differences between these in vivo stem-cell populations, demonstrating the power of multiomics in uncovering cell-type-specific regulatory features.