Z Gastroenterol 2011; 49 - P2_92
DOI: 10.1055/s-0030-1269609

Regulatory modules of miRNA and transcription factors affect gene expression in cultivated hepatocytes

S Zellmer 1, W Schmidt-Heck 2, JG Hengstler 3, R Guthke 2, R Gebhardt 1
  • 1Institut für Biochemie, Medizinische Fakultät der Universität Leipzig, Leipzig
  • 2Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie - Hans-Knöll-Institut, Jena
  • 3Leibniz Research Centre for Working Environment and Human Factors, Dortmund

Introduction: Gene expression pattern of isolated mouse hepatocytes differ from the in vivo situation. The following study was performed to identify transcription factors (TF) and miRNAs that modulate the gene expression in cultivated hepatocytes.

Material and Methods: Primary mouse hepatocytes were cultivated for 48h on collagen coated monolayers and gene expression changes were determined at 24, 27, 30, 36 and 48h after seeding using Affymetrix gene arrays. The promoter regions of the differentially expressed genes were analyzed for over-represented transcription factor binding sites (TFBS) using EXPANDER (EXPression ANalyzer and DisplayER) algorithm (1). EXPANDER was also used to analyze for miRNA binding motifs. The obtained motif information of the TFBS-gene or miRNA-gene interactions in combination with the time-dependent gene expression allowed to infer two annotated global temporal maps using an input-output hidden Markov model (2). These maps describe the main transcriptional regulatory events and the factors affecting gene expression during hepatocytes cultivation.

Results and conclusion: Genes were clustered into 7 different groups; 3 for upregulated genes, 3 for downregulated genes and one for genes with minor changes. These clusters were associated with 20 overrepresented TFs. The most prominent TFs were ETF, Elk1, ZF5 and E2F for the upregulated genes, NF-Y and Stat1 for the downregulated genes and MAZR for genes with minor changes. Analyzing the clusters for miRNA showed that at least 8 miRNAs regulate the gene expression pattern. To our surprise, each cluster could be characterized by a set of TFs as well as a set of miRNAs. It seems that TFs and miRNAs act in a coordinated manner on gene expression. This is supported by a recent publication (3) on miR-TF, regulatory modules composed of miRNAs and TFs. We conclude that regulation of gene expression should consider always the combined action of TFs and miRNAs.

Literatur:

(1) Ulitsky et al. Nat Protoc 5, 303-322. (2010)(2) Ernst et al. Nature-EMBO Molecular Systems Biology 3, 74 (2007)(3) Tran et al. Bioinformation 4, 371-377 (2010)