title: Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2.
abstract: BACKGROUND
  HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors. The protein harbours three basically charged DNA binding domains and an acidic protein binding C-terminal domain. DNA binding induces changes of DNA conformation and hence results in global overall change of gene expression patterns. Recently, using a PCR-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure two consensus sequences for HMGA2 binding have been identified.
  
  
  RESULTS
  In this investigation chromatin immunoprecipitation (ChIP) experiments and bioinformatic methods were used to analyze if these binding sequences can be verified on chromatin of living cells as well.
  
  
  CONCLUSIONS
  After quantification of HMGA2 protein in different cell lines the colon cancer derived cell line HCT116 was chosen for further ChIP experiments because of its 3.4-fold higher HMGA2 protein level. 49 DNA fragments were obtained by ChIP. These fragments containing HMGA2 binding sites have been analyzed for their AT-content, location in the human genome and similarities to sequences generated by a SELEX study. The sequences show a significantly higher AT-content than the average of the human genome. The artificially generated SELEX sequences and short BLAST alignments (11 and 12 bp) of the ChIP fragments from living cells show similarities in their organization. The flanking regions are AT-rich, whereas a lower conservation is present in the center of the sequences.
authors.affiliation: Centre for Human Genetics, University of Bremen, Bremen, Germany.
authors.forename: Nina
authors.initials: N
authors.lastname: Winter
authors.forename: Rolf
authors.initials: R
authors.lastname: Nimzyk
authors.forename: Carolin
authors.initials: C
authors.lastname: Bösche
authors.forename: Anke
authors.initials: A
authors.lastname: Meyer
authors.forename: Jörn
authors.initials: J
authors.lastname: Bullerdiek
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D015153:Blotting, Western; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000378:metabolism*; D017931:DNA Primers; D025743:HMGA2 Protein / Q000378:metabolism*; D006801:Humans
chemical_list: D017931:DNA Primers; D025743:HMGA2 Protein; D004247:DNA