The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development

Abstract

Lineage-restricted transcription factors, such as the intestine-specifying factor CDX2, often have dual requirements across developmental time. Embryonic loss of CDX2 triggers homeotic transformation of intestinal fate, whereas adult-onset loss compromises crucial physiological functions but preserves intestinal identity. It is unclear how such diverse requirements are executed across the developmental continuum. Using primary and engineered human tissues, mouse genetics, and a multi-omics approach, we demonstrate that divergent CDX2 loss-offunction phenotypes in embryonic versus adult intestines correspond to divergent CDX2 chromatin-binding profiles in embryonic versus adult stages. CDX2 binds and activates distinct target genes in developing versus adult mouse and human intestinal cells. We find that temporal shifts in chromatin accessibility correspond to these context-specific CDX2 activities. Thus, CDX2 is not sufficient to activate a mature intestinal program; rather, CDX2 responds to its environment, targeting stage-specific genes to contribute to either intestinal patterning or mature intestinal function. This study provides insights into the mechanisms through which lineage-specific regulatory factors achieve divergent functions over developmental time.

HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine

“…S1E,F). As reported by this group and others (Banerjee et al, 2018;Gao et al, 2009;Grainger et al, 2010;Kumar et al, 2019), Cdx2 KO in the early embryonic gut epithelium leads to an intestine exhibiting hindstomach characteristics (ATPase-and foveolar PAS-positive cells) in the jejunum and stratified squamous esophageal characteristics ( p63-positive cells) in the ileum. However, similar characteristics were not observed in the Hnf4αγ DKO embryos ( Fig.…”

“…The human ESC cell line H9 (WA09, NIH stem registry #0062) was obtained from the WiCell Research Institute. CDX2 CrisprKO human ESCs were generated as described previously (Kumar et al, 2019). Human ESCs were maintained and differentiated into endoderm, hind/ midgut and human intestinal organoids as previously described (Kumar et al, 2019;Tsai et al, 2017).…”

“…The accession numbers for the transcriptome and chromatin accessibility of time-course wild type and Cdx2 KO from our previous studies are GSE115314 (Kumar et al, 2019) and GSE115541 (Banerjee et al, 2018). The accession numbers for the CDX2 ChIP-seq and HNF4 ChIP-seq from our previous studies are GSE34568 (Verzi et al, 2013), GSE115314 (Kumar et al, 2019) and GSE112946 (Chen et al, 2019). GSE89684 (Kazakevych et al, 2017) was used to mark active chromatin with the time-course H3K27ac ChIP-seq.…”

“…In the early embryonic intestine (prior to E13.5), CDX2 is required for intestinal specification and loss of CDX2 leads to ectopic features of stomach and esophageal tissues in the intestine (Banerjee et al, 2018;Gao et al, 2009;Grainger et al, 2010;Kumar et al, 2019). Acute inactivation of CDX2 at later developmental timepoints (post E13.5) compromises mature tissue functions, but intestinal identity is maintained (Banerjee et al, 2018;Kumar et al, 2019;Verzi et al, 2011). Although CDX2 is a clear driver of intestinal specification and plays an additional role in driving fetal maturation, it remains unclear how this developmental transition occurs.…”

Insights Into Human Development and Disease From Human Pluripotent Stem Cell Derived Intestinal Organoids

“…By introducing a mutation in PHOX2B, researchers were able to demonstrate that PHOX2B deficient NCCs were impaired in their development into cells of the ENS and this resulted in impaired smooth muscle differentiation and in vivo growth of HIOs. CDX2 deficient hPSCs have also been generated and these cells were used to demonstrate the role of this transcription factor in the specification of mid/hindgut vs. foregut fate (39).…”