Architecture of a polycomb nucleoprotein complex.
Polycomb group (PcG) epigenetic silencing proteins act through cis-acting DNA sequences, named Polycomb response elements (PREs). Within PREs, Pleiohomeotic (PHO) binding sites and juxtaposed Pc binding elements (PBEs) function as an integrated DNA platform for the synergistic binding of PHO and the multisubunit Polycomb core complex (PCC). Here, we analyzed the architecture of the PHO/PCC/PRE nucleoprotein complex. DNase I footprinting revealed extensive contacts between PHO/PCC and the PRE. Scanning force microscopy (SFM) in combination with DNA topological assays suggested that PHO/PCC wraps the PRE DNA around its surface in a constrained negative supercoil. These features are difficult to reconcile with the simultaneous presence of nucleosomes at the PRE. Indeed, chromatin immunoprecipitations (ChIPs) and nuclease mapping demonstrated that PREs are nucleosome depleted in vivo. We discuss the implications of these findings for models explaining PRE function.
Mohd-Sarip
Adone
A
Department of Biochemistry, Centre for Biomedical Genetics, Erasmus University Medical Center, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands.
van der Knaap
Jan A
JA
Wyman
Claire
C
Kanaar
Roland
R
Schedl
Paul
P
Verrijzer
C Peter
CP
D000818:Animals; D001665:Binding Sites / Q000502:physiology; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D004330:Drosophila / Q000235:genetics / Q000378:metabolism; D029721:Drosophila Proteins / Q000737:chemistry / Q000378:metabolism; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation / Q000502:physiology; D018625:Microscopy, Atomic Force; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism; D063146:Polycomb-Group Proteins; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism* / Q000648:ultrastructure; D020218:Response Elements; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism
D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D009707:Nucleosomes; D063146:Polycomb-Group Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; C113295:pho protein, Drosophila; D004247:DNA