title: Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro.
abstract: BACKGROUND
  Hydroxymethylation of DNA at the C5 position of cytosine (5hmC) is recognized as an important epigenetic mark. The molecular role of 5hmC in gene regulation, however, is not well understood.
  
  
  METHODS
  We studied the effects of 5-hydroxymethylation (5hmC) on nucleosome properties in vitro using a combination of biochemical and fluorescence assays. Competitive reconstitution was used to evaluate the effect of 5hmC on nucleosome formation. The effects of 5hmC on nucleosome compactness and stability were characterized using FRET assays. These findings have also been compared with another important epigenetic mark, the cytosine methylation (5mC) of DNA.
  
  
  RESULTS
  We observed that hydroxymethylation increases the binding affinity of DNA for the histone octamer. The formed nucleosome exhibits slightly different conformations based on the sequence and epigenetic context of DNA. DNA hydroxymethylation decreases the stability of formed nucleosomes in salt-induced dissociation processes.
  
  
  CONCLUSIONS
  DNA containing 5hmC is more likely to be incorporated into nucleosomes. Once formed, the 5hmC nucleosomes might be in an open and transcriptionally active state due to the weakened interaction of hydroxymethylated DNA with the H2A-H2B dimers.
  
  
  CONCLUSIONS
  Our results reveal the effect of 5hmC on regulating nucleosome compactness and stability in vitro.
authors.affiliation: School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA.
authors.forename: Agnes
authors.initials: A
authors.lastname: Mendonca
authors.affiliation: School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA.
authors.forename: En Hyung
authors.initials: EH
authors.lastname: Chang
authors.affiliation: School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA.
authors.forename: Wenjie
authors.initials: W
authors.lastname: Liu
authors.affiliation: School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA. Electronic address: cyuan@purdue.edu.
authors.forename: Chongli
authors.initials: C
authors.lastname: Yuan
mesh_terms: D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D019175:DNA Methylation; D042003:DNA Packaging; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D066298:In Vitro Techniques; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D055503:Protein Multimerization; D055550:Protein Stability
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes; D004247:DNA
keywords: Chromatin; DNA hydroxymethylation; FRET; Nucleosome