Fig. 1. Tissue and molecular anatomy of mouse intestine development. (A) Histology of the mid-gestation small intestine revealed in Hematoxylin- and Eosin-stained transverse sections. Gut endoderm (arrows) transforms into a simple villous epithelium between E13 and E15. Also shown are temporal clusters of a subset of SAGE tags representing 703 genes that vary significantly (P<0.015) over the E12-E15 interval. Each colored line corresponds to one SAGE tag and denotes its relative frequency among the three SAGE libraries. (B) Validation and extension of SAGE results for representative transcripts from three classes of temporally regulated genes [increasing: apolipoprotein 1A (Apoa1) and apoptosis-specific protein with CARD domain (Asc; Pycard – Mouse Genome Informatics); decreasing: parathyroid hormone receptor (Pthr1) and Gli1; and dynamically regulated: zinc-finger regulator of apoptosis and cell-cycle arrest (Zac1; Plagl1 – Mouse Genome Informatics)]. RT-PCR analysis of gut tissue isolated at four fetal stages is compared with E13 and E15 SAGE data (tag numbers). Glyceraldehyde 3-phosphate dehydrogenase (Gapd) serves as a loading control and the lack of PCR products in samples not treated with reverse transcriptase (RT–) indicates absence of DNA in the RNA preparations. (C) RNA in situ hybridization analysis to distinguish predominantly epithelial (e.g. CD151) from stromal (e.g. growth receptor-binding protein 10, Grb10) transcripts. Sense probes (not shown) gave negligible staining. (D) Characterization of one gene product (proline-rich acidic protein 1, Prap1) suggested in SAGE to represent a marker of intestine differentiation. RT-PCR and in situ hybridization analysis confirm onset of epithelial expression after E13. In adults, Prap1 expression is concentrated in rostral segments, duodenum (D) and jejunum (J), compared with the ileum (I) or colon (C). (E) Northern analysis confirms SAGE data that a group of genes traditionally associated with the cellular stress response peaks in expression around E13, coincident with the villous epithelial transition. Sample results are shown for peptidylprolyl isomerase C (Ppic), calreticulin (Calr), FK506-binding protein 9 (Fkbp9) and stress-induced phosphoprotein 1 (Stip1). N.T., not tested. In situ hybridization localized expression of these transcripts to the epithelial compartment, as shown for Calr.