title: Sequence specificity incompletely defines the  genome-wide occupancy of Myc.
abstract: BACKGROUND
  The Myc-Max heterodimer is a transcription factor that regulates expression of a large number of genes. Genome occupancy of Myc-Max is thought to be driven by Enhancer box (E-box) DNA elements, CACGTG or variants, to which the heterodimer binds in vitro.
  
  
  RESULTS
  By analyzing ChIP-Seq datasets, we demonstrate that the positions occupied by Myc-Max across the human genome correlate with the RNA polymerase II, Pol II, transcription machinery significantly better than with E-boxes. Metagene analyses show that in promoter regions, Myc is uniformly positioned about 100 bp upstream of essentially all promoter proximal paused polymerases with Max about 15 bp upstream of Myc. We re-evaluate the DNA binding properties of full length Myc-Max proteins. Electrophoretic mobility shift assay results demonstrate Myc-Max heterodimers display significant sequence preference, but have high affinity for any DNA. Quantification of the relative affinities of Myc-Max for all possible 8-mers using universal protein-binding microarray assays shows that sequences surrounding core 6-mers significantly affect binding. Compared to the in vitro sequence preferences,Myc-Max genomic occupancy measured by ChIP-Seq is largely, although not completely, independent of sequence specificity.
  
  
  CONCLUSIONS
  We quantified the affinity of Myc-Max to all possible 8-mers and compared this with the sites of Myc binding across the human genome. Our results indicate that the genomic occupancy of Myc cannot be explained by its intrinsic DNA specificity and suggest that the transcription machinery and associated promoter accessibility play a predominant role in Myc recruitment.
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Jiannan
authors.initials: J
authors.lastname: Guo
authors.forename: Tiandao
authors.initials: T
authors.lastname: Li
authors.forename: Joshua
authors.initials: J
authors.lastname: Schipper
authors.forename: Kyle A
authors.initials: KA
authors.lastname: Nilson
authors.forename: Francis K
authors.initials: FK
authors.lastname: Fordjour
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Cooper
authors.forename: Raluca
authors.initials: R
authors.lastname: Gordân
authors.forename: David H
authors.initials: DH
authors.lastname: Price
mesh_terms: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D047369:Chromatin Immunoprecipitation; D024721:E-Box Elements; D024202:Electrophoretic Mobility Shift Assay; D015894:Genome, Human; D006801:Humans; D011401:Promoter Regions, Genetic; D016271:Proto-Oncogene Proteins c-myc / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D012319:RNA Polymerase II / Q000378:metabolism / Q000502:physiology; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic / Q000502:physiology
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; C499330:MAX protein, human; D016271:Proto-Oncogene Proteins c-myc; D012319:RNA Polymerase II