title: Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing.
abstract: Nucleosomes often undergo extensive rearrangement when genes are activated for transcription. We have shown previously, using paired-end sequencing of yeast nucleosomes, that major changes in chromatin structure occur when genes are activated by 3-aminotriazole (3AT), an inducer of the transcriptional activator Gcn4. Here, we provide a global analysis of these data. At the genomic level, nucleosomes are regularly phased relative to the transcription start site. However, for a subset of 234 strongly induced genes, this phasing is much more irregular after induction, consistent with the loss of some nucleosomes and the re-positioning of the remaining nucleosomes. To address the nature of this rearrangement, we developed the inter-nucleosome distance auto-correlation (DAC) function. At long range, DAC analysis indicates that nucleosomes have an average spacing of 162 bp, consistent with the reported repeat length. At short range, DAC reveals a 10.25-bp periodicity, implying that nucleosomes in overlapping positions are rotationally related. DAC analysis of the 3AT-induced genes suggests that transcription activation coincides with rearrangement of nucleosomes into irregular arrays with longer spacing. Sequence analysis of the +1 nucleosomes belonging to the 45 most strongly activated genes reveals a distinctive periodic oscillation in the A/T-dinucleotide occurrence that is present throughout the nucleosome and extends into the linker. This unusual pattern suggests that the +1 nucleosomes might be prone to sliding, thereby facilitating transcription.
authors.affiliation: Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Building 37, Room 3035A, Convent Dr., Bethesda, MD 20892, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Cui
authors.forename: Hope A
authors.initials: HA
authors.lastname: Cole
authors.forename: David J
authors.initials: DJ
authors.lastname: Clark
authors.forename: Victor B
authors.initials: VB
authors.lastname: Zhurkin
mesh_terms: D000639:Amitriptyline / Q000494:pharmacology; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D003851:Deoxyribonucleases; D015966:Gene Expression Regulation, Fungal; D008780:Methyltransferases / Q000235:genetics; D009707:Nucleosomes / Q000737:chemistry* / Q000187:drug effects; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D015533:Transcriptional Activation
chemical_list: D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D000639:Amitriptyline; D004247:DNA; C084864:MRM1 protein, S cerevisiae; D008780:Methyltransferases; D003851:Deoxyribonucleases