Regional Cell-Specific Transcriptome Mapping Reveals Regulatory Complexity in the Adult Drosophila Midgut

Abstract

Deciphering contributions of specific cell types to organ function is experimentally challenging. The Drosophila midgut is a dynamic organ with five morphologically and functionally distinct regions (R1-R5), each composed of multipotent intestinal stem cells (ISCs), progenitor enteroblasts (EBs), enteroendocrine cells (EEs), enterocytes (ECs), and visceral muscle (VM). To characterize cellular specialization and regional function in this organ, we generated RNA-sequencing transcriptomes of all five cell types isolated by FACS from each of the five regions, R1-R5. In doing so, we identify transcriptional diversities among cell types and document regional differences within each cell type that define further specialization. We validate cell-specific and regional Gal4 drivers; demonstrate roles for transporter Smvt and transcription factors GATAe, Sna, and Ptx1 in global and regional ISC regulation, and study the transcriptional response of midgut cells upon infection. The resulting transcriptome database (http://flygutseq.buchonlab.com) will foster studies of regionalization, homeostasis, immunity, and cell-cell interactions.

Diversity of fate outcomes in cell pairs under lateral inhibition

“…S6E-F), indicating that adhesion properties are not fundamentally different between cell pair types (at least as far as adherens junctions are concerned). This fits well with the observation that the transcriptional profiles of ISCs and EBs are not particularly enriched with genes involved in cell adhesion (Dutta et al, 2015).…”

Intestinal stem cell response to injury: lessons from Drosophila

“…Recent gene expression profiling studies indicate that the Drosophila midgut can be functionally divided into several different regions [1, 37, 38]. In particular, the middle region of Drosophila midgut, commonly known as the copper cell region, actually functions as the equivalent of mammalian stomach with its special cell types and physiological features, such as extremely low pH, and cells in this region are maintained by relatively quiescent ISCs known as gastric stem cells [39, 40].…”

“…Using various dpp reporters including enhancer trap line and promoter fusion constructs, it was found that dpp is expressed in trachea cells [60], VMs [41, 56], and ECs [11, 42]. A transcriptome study using sorted midgut cells revealed that dpp is expressed in VMs [37]. On the other hand, RNA in situ hybridization detected dpp expression in ECs [11, 42].…”

Apoptosis restores cellular density by eliminating a physiologically or genetically induced excess of enterocytes in the Drosophila midgut

“…To complete our study, we assessed the functional impacts that the ingestion of low amounts of Btk may have knowing that bacterial intoxication, cell death or the presence of too many immature cells in the gut can affect its digestive functions (Biteau et al, 2008;Buchon et al, 2009b;Chakrabarti et al, 2012;Dutta et al, 2015;Erkosar et al, 2015). Therefore, we monitored several metabolic and enzymatic parameters in the midgut.…”