Essential and Redundant Functions of Caudal Family Proteins in Activating Adult Intestinal Genes

ABSTRACT Transcription factors that potently induce cell fate often remain expressed in the induced organ throughout life, but their requirements in adults are uncertain and varied. Mechanistically, it is unclear if they activate only tissue-specific genes or also directly repress heterologous genes. We conditionally inactivated mouse Cdx2, a dominant regulator of intestinal development, and mapped its genome occupancy in adult intestinal villi. Although homeotic transformation, observed in Cdx2-null embryos, was absent in mutant adults, gene expression and cell morphology were vitally compromised. Lethality was significantly accelerated in mice lacking both Cdx2 and its homolog Cdx1, with particular exaggeration of defects in villus enterocyte differentiation. Importantly, Cdx2 occupancy correlated with hundreds of transcripts that fell but not with equal numbers that rose with Cdx loss, indicating a predominantly activating role at intestinal cis-regulatory regions. Integrated consideration of a transcription factor's mutant phenotype and cistrome hence reveals the continued and distinct requirement in adults of a critical developmental regulator that activates tissue-specific genes.

[1]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[2]  K. Kaestner,et al.  Cdx2 regulates endo-lysosomal function and epithelial cell polarity. , 2010, Genes & development.

[3]  D. Silberg,et al.  The homeodomain transcription factor Cdx1 does not behave as an oncogene in normal mouse intestine. , 2008, Neoplasia.

[4]  P. Traber,et al.  Phosphorylation of the serine 60 residue within the Cdx2 activation domain mediates its transactivation capacity. , 2001, Gastroenterology.

[5]  Cdx1 induced intestinal metaplasia in the transgenic mouse stomach: comparative study with Cdx2 transgenic mice , 2004, Gut.

[6]  Daniel E. Newburger,et al.  Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences , 2008, Cell.

[7]  L. Zon,et al.  The caudal-related homeobox genes cdx1a and cdx4 act redundantly to regulate hox gene expression and the formation of putative hematopoietic stem cells during zebrafish embryogenesis. , 2006, Developmental biology.

[8]  Daniel Metzger,et al.  Tissue‐specific and inducible Cre‐mediated recombination in the gut epithelium , 2004, Genesis.

[9]  Susan E. Schonhoff,et al.  Minireview: Development and differentiation of gut endocrine cells. , 2004, Endocrinology.

[10]  J. Lynch,et al.  Cdx2 levels modulate intestinal epithelium maturity and Paneth cell development. , 2011, Gastroenterology.

[11]  M. Gerhard,et al.  The Cdx4 mutation affects axial development and reveals an essential role of Cdx genes in the ontogenesis of the placental labyrinth in mice , 2006, Development.

[12]  S. Forlani,et al.  Cdx1 and Cdx2 have overlapping functions in anteroposterior patterning and posterior axis elongation. , 2002, Development.

[13]  Stephanie Grainger,et al.  Cdx2 regulates patterning of the intestinal epithelium. , 2009, Developmental biology.

[14]  Janet Rossant,et al.  Cdx2 is essential for axial elongation in mouse development. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  C. Bonhomme,et al.  Cdx1, a dispensable homeobox gene for gut development with limited effect in intestinal cancer , 2008, Oncogene.

[16]  Clifford A. Meyer,et al.  Differentiation-specific histone modifications reveal dynamic chromatin interactions and alternative partners for the intestinal transcription factor CDX 2 , 2011 .

[17]  Jun Song,et al.  CEAS: cis-regulatory element annotation system , 2006, Nucleic Acids Res..

[18]  M. Rosenfeld,et al.  Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification. , 2000, Science.

[19]  Peng Wang,et al.  Regulation of Cdx2 expression by promoter methylation, and effects of Cdx2 transfection on morphology and gene expression of human esophageal epithelial cells. , 2006, Carcinogenesis.

[20]  R. James,et al.  Structure of the murine homeobox gene cdx-2. Expression in embryonic and adult intestinal epithelium. , 1994, The Journal of biological chemistry.

[21]  S. Philipsen,et al.  Ablation of Gata1 in adult mice results in aplastic crisis, revealing its essential role in steady-state and stress erythropoiesis. , 2008, Blood.

[22]  E. Suh,et al.  The role of Cdx proteins in intestinal development and cancer , 2004, Cancer biology & therapy.

[23]  K. Chawengsaksophak,et al.  Homeosis and intestinal tumours in Cdx2 mutant mice , 1997, Nature.

[24]  Ernest Fraenkel,et al.  Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. , 2009, Molecular cell.

[25]  Clifford A. Meyer,et al.  Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. , 2010, Developmental cell.

[26]  N. Pilon,et al.  Cdx1 and Cdx2 are functionally equivalent in vertebral patterning. , 2009, Developmental biology.

[27]  P. Rigby,et al.  The Myogenic Factor Myf5 Supports Efficient Skeletal Muscle Regeneration by Enabling Transient Myoblast Amplification , 2007, Stem cells.

[28]  K. Sugano,et al.  Conversion of gastric mucosa to intestinal metaplasia in Cdx2-expressing transgenic mice. , 2002, Biochemical and biophysical research communications.

[29]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[30]  C. Glass,et al.  Coregulator Codes of Transcriptional Regulation by Nuclear Receptors* , 2001, The Journal of Biological Chemistry.

[31]  E. Furth,et al.  CDX1 protein expression in normal, metaplastic, and neoplastic human alimentary tract epithelium. , 1997, Gastroenterology.

[32]  Kathleen R. Cho,et al.  CDX2 regulates liver intestine-cadherin expression in normal and malignant colon epithelium and intestinal metaplasia. , 2002, Gastroenterology.

[33]  Janet Rossant,et al.  Interaction between Oct3/4 and Cdx2 Determines Trophectoderm Differentiation , 2005, Cell.

[34]  T. Mizutani,et al.  Cdx2 and the Brm-type SWI/SNF complex cooperatively regulate villin expression in gastrointestinal cells. , 2009, Experimental cell research.

[35]  K. Kaestner,et al.  Establishment of intestinal identity and epithelial-mesenchymal signaling by Cdx2. , 2009, Developmental cell.

[36]  H. Zoghbi,et al.  Gfi1 functions downstream of Math1 to control intestinal secretory cell subtype allocation and differentiation. , 2005, Genes & development.

[37]  P. Traber,et al.  Cdx1 and cdx2 expression during intestinal development. , 2000, Gastroenterology.

[38]  G. Daley,et al.  Cdx gene deficiency compromises embryonic hematopoiesis in the mouse , 2008, Proceedings of the National Academy of Sciences.

[39]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[40]  D. Gumucio,et al.  cis Elements of the Villin Gene Control Expression in Restricted Domains of the Vertical (Crypt) and Horizontal (Duodenum, Cecum) Axes of the Intestine* , 2002, The Journal of Biological Chemistry.

[41]  Clifford A. Meyer,et al.  Nucleosome Dynamics Define Transcriptional Enhancers , 2010, Nature Genetics.

[42]  K. Kaestner,et al.  Cdx2 ectopic expression induces gastric intestinal metaplasia in transgenic mice. , 2002, Gastroenterology.

[43]  Hans Clevers,et al.  The intestinal stem cell. , 2008, Genes & development.

[44]  D S Latchman,et al.  Transcription factors: bound to activate or repress. , 2001, Trends in biochemical sciences.

[45]  Jacqueline Deschamps,et al.  Cdx and Hox genes differentially regulate posterior axial growth in mammalian embryos. , 2009, Developmental cell.