Whether stem cells have unique cell cycle machineries and how they integrate with niche interactions remains largely unknown. We identified a hypomorphic cyclin E allele WX that strongly impairs the maintenance of follicle stem cells (FSCs) in the Drosophila ovary but does not reduce follicle cell proliferation or germline stem cell maintenance. CycE WX protein can still bind to the cyclin-dependent kinase catalytic subunit Cdk2, but forms complexes with reduced protein kinase activity measured in vitro. By creating additional CycE variants with different degrees of kinase dysfunction and expressing these and CycE WX at different levels, we found that higher CycE-Cdk2 kinase activity is required for FSC maintenance than to support follicle cell proliferation. Surprisingly, cycE WX FSCs were lost from their niches rather than arresting proliferation. Furthermore, FSC function was substantially restored by expressing either excess DE-cadherin or excess E2F1/DP, the transcription factor normally activated by CycE-Cdk2 phosphorylation of retinoblastoma proteins. These results suggest that FSC maintenance through niche adhesion is regulated by inputs that normally control S phase entry, possibly as a quality control mechanism to ensure adequate stem cell proliferation. We speculate that a positive connection between central regulators of the cell cycle and niche retention may be a common feature of highly proliferative stem cells.cell cycle Ķ niche adhesion Ķ stem cell longevity T he ovary of Drosophila melanogaster provides an attractive model for studying stem cells because germline and somatic stem cells have well-defined locations and their behavior can be studied after directed genetic manipulations of single cell lineages (1, 2). Drosophila females have a pair of ovaries that are composed of 15-18 tube-like structures called ovarioles. Each ovariole produces eggs through an assembly line process. At the anterior tip of each ovariole is the germarium (Fig. 1A). Nonproliferating somatic cells, known as terminal filament and cap cells, reside at the anterior end of the germarium in contact with two to three germline stem cells (GSCs). A GSC divides asymmetrically to produce a new stem cell and a cystoblast, which divides four more times with incomplete cytokenesis to generate a cyst of 16 germline cells (1). Starting in region 2b (Fig. 1 A), each cyst is enveloped by a monolayer of follicle cells and is then separated from the next cyst by a short stalk as it buds from region 3 to form an egg chamber, which then progresses down the ovariole, increasing in size and maturity, and becomes an egg.The follicle cells and stalk cells are derived from the follicle stem cells (FSCs) (Fig. 1 A). Two FSC niches exist within each ovariole at the 2a/2b border region of the germarium (3). FSCs self-renew and produce ''prefollicle cell'' daughters, most of which proliferate for about eight cycles until reaching stage 6, before three cycles of endoreplication and overt differentiation (4-6). A wild-type, genetically marked FSC g...