TY - JOUR

T1 - Genome-wide analysis of CDX2 binding in intestinal epithelial cells (Caco-2)

AU - Boyd, Mette

AU - Hansen, Morten

AU - Jensen, Tine G K

AU - Perearnau, Anna

AU - Olsen, Anders K

AU - Bram, Lotte L

AU - Bak, Mads

AU - Tommerup, Niels

AU - Olsen, Jørgen

AU - Troelsen, Jesper T

N1 - Keywords: Caco-2 Cells; Cell Differentiation; Chromatin Immunoprecipitation; Computational Biology; Electrophoretic Mobility Shift Assay; Enhancer Elements, Genetic; Epithelial Cells; Genome, Human; Hepatocyte Nuclear Factor 4; High Mobility Group Proteins; Homeodomain Proteins; Humans; Intestines; Membrane Proteins; Metalloendopeptidases; Mutation; Promoter Regions, Genetic; Protein Binding; Repressor Proteins; Reverse Transcriptase Polymerase Chain Reaction; Trans-Activators

PY - 2010/8

Y1 - 2010/8

N2 - The CDX2 transcription factor is known to play a crucial role in inhibiting proliferation, promoting differentiation and the expression of intestinal specific genes in intestinal cells. The overall effect of CDX2 in intestinal cells has previously been investigated in conditional knock-out mice, revealing a critical role of CDX2 in the formation of the normal intestinal identity. The identification of direct targets of transcription factors is a key problem in the study of gene regulatory networks. The ChIP-seq technique combines chromatin immunoprecipitation (ChIP) with next generation sequencing resulting in a high throughput experimental method of identifying direct targets of specific transcription factors. The method was applied to CDX2, leading to the identification of the direct binding of CDX2 to several known and novel target genes in the intestinal cell. Examination of the transcript levels of selected genes verified the regulatory role of CDX2 binding. The results place CDX2 as a key node in a transcription factor network controlling the proliferation and differentiation of intestinal cells.

AB - The CDX2 transcription factor is known to play a crucial role in inhibiting proliferation, promoting differentiation and the expression of intestinal specific genes in intestinal cells. The overall effect of CDX2 in intestinal cells has previously been investigated in conditional knock-out mice, revealing a critical role of CDX2 in the formation of the normal intestinal identity. The identification of direct targets of transcription factors is a key problem in the study of gene regulatory networks. The ChIP-seq technique combines chromatin immunoprecipitation (ChIP) with next generation sequencing resulting in a high throughput experimental method of identifying direct targets of specific transcription factors. The method was applied to CDX2, leading to the identification of the direct binding of CDX2 to several known and novel target genes in the intestinal cell. Examination of the transcript levels of selected genes verified the regulatory role of CDX2 binding. The results place CDX2 as a key node in a transcription factor network controlling the proliferation and differentiation of intestinal cells.

U2 - 10.1074/jbc.M109.089516

DO - 10.1074/jbc.M109.089516

M3 - Journal article

C2 - 20551321

VL - 285

SP - 25115

EP - 25125

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

IS - 33

ER -