Trithorax balances ISC fate decisions via Ptx1-mediated repression of EE specification [RNA-seq]
Adult stem cells must coordinate transcriptional programs with external cues to maintain tissue homeostasis. In the Drosophila midgut, intestinal stem cells (ISCs) generate enterocytes (ECs) or enteroendocrine (EE) cells through Notch-dependent fate decisions, but how chromatin regulators influence this balance remains unclear. In this study we identified the Trithorax gene (trx) as a key factor that safeguards ISC lineage fidelity. Trx depletion biases ISCs toward EE differentiation without affecting proliferation, a phenotype exacerbated during aging or DSS-induced damage. Transcriptomic and chromatin profiling revealed the homeobox transcription factor Ptx1 as a Trx-dependent target. Ptx1 knockdown phenocopies Trx loss, whereas Ptx1 overexpression reverts trx-RNAi-induced EE overproduction, establishing Ptx1 as a critical mediator of Trx function. These findings support a model in which Trx constrains the scute–prospero axis through Ptx1-mediated repression, thereby limiting inappropriate EE specification and maintaining ISC plasticity. Overall design: To identify genes regulated by Trx, we performed RNA-seq on FACS-sorted adult GFP? progenitor cells from control (esgtsGFP x w1118) and trx RNAi (esgtsGFP x UAS-trxRNAi BDSC#33703)  female midguts under homeostatic (sucrose-fed) and regenerative (DSS-treated) conditions. We then performed gene expression profiling analysis using RNA extracted with miRNeasy Micro Kit and libraries were prepared with the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen).