title: Characterization of Z-DNA as a nucleosome-boundary element in yeast Saccharomyces cerevisiae.
abstract: In this article, the effect of a d(CG) DNA dinucleotide repeat sequence on RNA polymerase II transcription is examined in yeast Saccharomyces cerevisiae. Our previous report shows that a d(CG)n dinucleotide repeat sequence located proximally upstream of the TATA box enhances transcription from a minimal CYC1 promoter in a manner that depends on its surrounding negative supercoiling. Here, we demonstrate that the d(CG)9 repeat sequence stimulates gene activity by forming a Z-DNA secondary structure. Furthermore, the extent of transcriptional enhancement by Z-DNA is promoter-specific and determined by its separation distance relative to the TATA box. The stimulatory effect exerted by promoter proximal Z-DNA is not affected by helical phasing relative to the TATA box, suggesting that Z-DNA effects transcription without interacting with the general transcription machinery by looping-out the intervening DNA. A nucleosome-scanning assay reveals that the d(CG)9 repeat sequence in the Z conformation blocks nucleosome formation, and it is found in the linker DNA with two flanking nucleosomes. This result suggests that Z-DNA formation proximally upstream of a promoter is sufficient to demarcate the boundaries of its neighboring nucleosomes, which produces transcriptionally favorable locations for the TATA box near the nucleosomal DNA-entry site and at dyad positions on the nucleosome. These findings suggest that Z-DNA formation in chromatin is a part of the "genomic code" for nucleosome positioning in vivo.
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Wong
authors.forename: Shuai
authors.initials: S
authors.lastname: Chen
authors.forename: Jin-Ah
authors.initials: JA
authors.lastname: Kwon
authors.forename: Alexander
authors.initials: A
authors.lastname: Rich
mesh_terms: D002843:Chromatin; D043542:DNA, Z-Form / Q000502:physiology*; D038101:Insulator Elements / Q000235:genetics*; D009690:Nucleic Acid Conformation; D009707:Nucleosomes; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D016385:TATA Box; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D043542:DNA, Z-Form; D009707:Nucleosomes