Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome.
A canonical nucleosome architecture around promoters establishes the context in which proteins regulate gene expression. Whether gene regulatory proteins that interact with nucleosomes are selective for individual nucleosome positions across the genome is not known. Here, we examine on a genomic scale several protein-nucleosome interactions, including those that (1) bind histones (Bdf1/SWR1 and Srm1), (2) bind specific DNA sequences (Rap1 and Reb1), and (3) potentially collide with nucleosomes during transcription (RNA polymerase II). We find that the Bdf1/SWR1 complex forms a dinucleosome complex that is selective for the +1 and +2 nucleosomes of active genes. Rap1 selectively binds to its cognate site on the rotationally exposed first and second helical turn of nucleosomal DNA. We find that a transcribing RNA polymerase creates a delocalized state of resident nucleosomes. These findings suggest that nucleosomes around promoter regions have position-specific functions and that some gene regulators have position-specific nucleosomal interactions.
Koerber
R Thomas
RT
Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Rhee
Ho Sung
HS
Jiang
Cizhong
C
Pugh
B Franklin
BF
D000251:Adenosine Triphosphatases / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D042002:Chromatin Assembly and Disassembly; D004257:DNA Polymerase II / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D020662:Guanine Nucleotide Exchange Factors / Q000235:genetics / Q000378:metabolism; D051548:Histone Acetyltransferases / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D046912:Multiprotein Complexes; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D000092468:Bromodomain Containing Proteins
D000251:Adenosine Triphosphatases; D004257:DNA Polymerase II; D004268:DNA-Binding Proteins; D020662:Guanine Nucleotide Exchange Factors; D051548:Histone Acetyltransferases; D006657:Histones; D046912:Multiprotein Complexes; D009687:Nuclear Proteins; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins; D014157:Transcription Factors; C091342:BDF1 protein, S cerevisiae; D000092468:Bromodomain Containing Proteins; C440829:RAP1 protein, S cerevisiae; C065681:REB1 protein, S cerevisiae; C067050:SRM1 protein, S cerevisiae; C504740:NuA4 protein, S cerevisiae; C481261:Swr1 protein, S cerevisiae