Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation

Abstract

DNA-binding transcription factors bind to promoters that carry their binding sites. Transcription factors therefore function as nodes in gene regulatory networks. In the present work we used a bioinformatic approach to search for transcription factors that might function as nodes in gene regulatory networks during the differentiation of the small intestinal epithelial cell. In addition we have searched for connections between transcription factors and the villus metabolome. Transcriptome data were generated from mouse small intestinal villus, crypt, and fetal intestinal epithelial cells. Metabolome data were generated from crypt and villus cells. Our results show that genes that are upregulated during fetal to adult and crypt to villus differentiation have an overrepresentation of potential hepatocyte nuclear factor (HNF)-4 binding sites in their promoters. Moreover, metabolome analyses by magic angle spinning (1)H nuclear magnetic resonance spectroscopy showed that the villus epithelial cells contain higher concentrations of lipid carbon chains than the crypt cells. These findings suggest a model where the HNF-4 transcription factor influences the villus metabolome by regulating genes that are involved in lipid metabolism. Our approach also identifies transcription factors of importance for crypt functions such as DNA replication (E2F) and stem cell maintenance (c-Myc).

Hepatocyte nuclear factor-4α promotes differentiation of intestinal epithelial cells in a coculture system

“…Conditional knockout of HNF-4␣ demonstrated its crucial role into the embryonic development of the mouse colonic epithelium, but its role in the small intestinal context still remains to be investigated (14). Metabolome, transcriptome, and bioinformatic analyses indicated that HNF-4␣ could be implicated in intestinal lipid metabolism with the regulation of apolipoprotein synthesis (53). Our findings demonstrate that HNF-4␣ is a potent activator of several intestinal genes normally associated with mature enterocyte functions.…”

“…HNF-4␣ is considered to be the master regulator of the human hepatocyte where it controls the expression of molecules implicated in lipid uptake and transport (20,28,36,61). HNF-4␣ is expressed along both the vertical and horizontal axis of the gut epithelium and regulates intestinal epithelial expression of alkaline phosphatase, ApoA-IV, and meprin-1␣ genes (37,49,53). Conditional knockout of HNF-4␣ demonstrated its crucial role into the embryonic development of the mouse colonic epithelium, but its role in the small intestinal context still remains to be investigated (14).…”

“…HNF-1␣ was shown to participate in the transcriptional regulation of several intestinal specific genes (6,11,31,46,57,60). HNF-4␣ was recently suggested to act as a regulator of villus specific epithelial genes (53). However, the specific functional role of these regulators on IEC differentiation has never been directly assessed.…”

“…Restriction of apolipoprotein A-IV (ApoA-IV) expression to villus-differentiated enterocytes has been functionally linked to hepatocyte nuclear factor-4␣ (HNF-4␣) (49). Computer-based analyses recently suggested that HNF-4␣ could act as a regulator of villus genes involved in lipid metabolism (53). However, no functional data have clearly demonstrated the role of HNF-4␣ in small intestinal epithelial functions.…”

Genome-wide Analysis of CDX2 Binding in Intestinal Epithelial Cells (Caco-2)

“…Some of the pathways identified to date include the Wnt pathway (2), the Notch pathway (3), the Hedgehog system (4), members of the transforming growth factor-␤ family including the bone morphogenetic proteins (5), and the phosphatidylinositol 3-kinase pathway (6). The intestine specific gene expression requires the tightly regulated activity of transcription factors, including the well characterized key factors HNF1␣/␤, 2 HNF4␣, GATA factors, ETS, CDX1, and CDX2 (7)(8)(9)(10)(11)(12)(13). These transcription factors often cooperate to control the expression of the intestinal specific genes; until now, in particular HNF1␣, GATA4 -6, and CDX2 have been found to interact in order to regulate the activity of several promoters in the intestine (7, 14 -20).…”