title: Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture.
abstract: BACKGROUND
  Expression profiling of embryonic stem (ES) cell differentiation in the presence of serum has been performed previously. It remains unclear if transcriptional activation is dependent on complex growth factor mixtures in serum or whether this process is intrinsic to ES cells once the stem cell program has been inactivated. The aims of this study were to determine the transcriptional programs associated with the stem cell state and to characterize mesoderm differentiation between serum and serum-free culture.
  
  
  RESULTS
  ES cells were differentiated as embryoid bodies in 10% FBS or serum-free media containing BMP4 (2 ng/ml), and expression profiled using 47 K Illumina(R) Sentrix arrays. Statistical methods were employed to define gene sets characteristic of stem cell, epiblast and primitive streak programs. Although the initial differentiation profile was similar between the two culture conditions, cardiac gene expression was inhibited in serum whereas blood gene expression was enhanced. Also, expression of many members of the Kruppel-like factor (KLF) family of transcription factors changed dramatically during the first few days of differentiation. KLF2 and KLF4 co-localized with OCT4 in a sub-nuclear compartment of ES cells, dynamic changes in KLF-DNA binding activities occurred upon differentiation, and strong bio-informatic evidence for direct regulation of many stem cell genes by KLFs was found.
  
  
  CONCLUSIONS
  Down regulation of stem cell genes and activation of epiblast/primitive streak genes is similar in serum and defined media, but subsequent mesoderm differentiation is strongly influenced by the composition of the media. In addition, KLF family members are likely to be important regulators of many stem cell genes.
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia. s.bruce@imb.uq.edu.au
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Bruce
authors.forename: Brooke B
authors.initials: BB
authors.lastname: Gardiner
authors.forename: Les J
authors.initials: LJ
authors.lastname: Burke
authors.forename: M Milena
authors.initials: MM
authors.lastname: Gongora
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Perkins
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D055415:Bone Morphogenetic Protein 4; D019485:Bone Morphogenetic Proteins / Q000494:pharmacology*; D018929:Cell Culture Techniques / Q000379:methods*; D002454:Cell Differentiation / Q000187:drug effects* / Q000235:genetics*; D016000:Cluster Analysis; D016895:Culture Media, Serum-Free / Q000494:pharmacology*; D053595:Embryonic Stem Cells / Q000187:drug effects / Q000378:metabolism* / Q000502:physiology*; D004920:Erythropoiesis / Q000187:drug effects / Q000235:genetics; D020869:Gene Expression Profiling; D000090062:Kruppel-Like Factor 4; D008648:Mesoderm / Q000378:metabolism / Q000502:physiology*; D051379:Mice; D008969:Molecular Sequence Data; D032383:Myocytes, Cardiac / Q000378:metabolism / Q000502:physiology; D020411:Oligonucleotide Array Sequence Analysis; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: C525810:Bmp4 protein, mouse; D055415:Bone Morphogenetic Protein 4; D019485:Bone Morphogenetic Proteins; D016895:Culture Media, Serum-Free; C000715468:Klf4 protein, mouse; D000090062:Kruppel-Like Factor 4