Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [ATAC-seq]

Intestinal villus enterocytes exist in spatially restricted cell states, called zones, and continuously transdifferentiate as they migrate toward the villus tip. Bone morphogenetic protein (BMP) signaling through the BMPR1A receptor is required for zonation of enterocytes; however, the molecular mechanisms and transcriptional regulators downstream of BMP ligands/receptors are unclear. Using compound genetic mouse models and epigenomic techniques, we find that SMAD1 and SMAD5 are necessary for activation of middle villus zone genes via direct binding and control of a transcription factor hierarchy. Spatial transcriptomics reveal a homeotic-like shift in the villus pattern of SMAD1/SMAD5 double mutants, with the villus bottom and tip domains expanding at the expense of the middle. Surprisingly, SMAD1 and SMAD5 are not required for regulation of villus tip identity, which is dependent on SMAD4. Epigenomics approaches identify a mechanism for villus patterning in which SMAD1/5 directly activate some mid-villus genes and control others via a transcription factor hierarchy, including a SMAD-regulated transcription factor, TBX3, as a downstream effector of villus zonation.