Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters.
Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analysis to show substantial differences in chromatin structure of pol II and pol III promoters, and between subtypes of pol III genes. Notably, the nucleosome depleted region at the transcription start site of pol III genes extends past the termination sequences, resulting in nucleosome free gene bodies. The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1 nucleosome may be involved in the transcriptional regulation of pol III genes. We find that expression and DNA methylation patterns correlate with distinct accessibility patterns, where DNA methylation associates with the silencing and inaccessibility at promoters. Taken together, this study provides the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide.
Department of Hematology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2100, Denmark.
Alexandra Søgaard
AS
Helbo
Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA.
Fides D
FD
Lay
Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA.|Van Andel Research Institute, Grand Rapids, 49503, USA.
Peter A
PA
Jones
Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA.
Gangning
G
Liang
Department of Hematology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2100, Denmark.
Kirsten
K
Grønbæk
D042002:Chromatin Assembly and Disassembly; D019175:DNA Methylation; D006801:Humans; D020014:K562 Cells; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics; D012320:RNA Polymerase III / Q000235:genetics*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
D009707:Nucleosomes; D012319:RNA Polymerase II; D012320:RNA Polymerase III