title: Nucleosome-positioning sequence repeats impact chromatin silencing in yeast minichromosomes.
abstract: Eukaryotic gene expression occurs in the context of structurally distinct chromosomal domains such as the relatively open, gene-rich, and transcriptionally active euchromatin and the condensed and gene-poor heterochromatin where its specific chromatin environment inhibits transcription. To study gene silencing by heterochromatin, we created a minichromosome reporter system where the gene silencer elements were used to repress the URA3 reporter gene. The minichromosome reporters were propagated in yeast Saccharomyces cerevisiae at a stable copy number. Conduction of gene silencing through nucleosome arrays was studied by placing various repeats of clone-601 DNA with high affinity for histones between the silencer and reporter in the yeast minichromosomes. High-resolution chromatin mapping with micrococcal nuclease showed that the clone-601 nucleosome positioning downstream of the HML-E gene silencing element was not significantly altered by chromatin silencing. Using URA3 reporter assays, we observed that gene silencing was conducted through arrays of up to eight nucleosomes. We showed that the shorter nucleosome repeat lengths, typical of yeast (167 and 172 bp), were more efficient in conducting silencing in vivo compared to the longer repeats (207 bp) typical of higher eukaryotes. Both the longer and the shorter repeat lengths were able to conduct silencing in minichromosomes independently of clone-601 nucleosome positioning orientations vs. the silencer element. We suggest that the shorter nucleosome linkers are more suitable for conducting gene silencing than the long repeats in yeast due to their higher propensity to support native-like chromatin higher-order folding.
authors.affiliation: Department of Biochemistry and Molecular Biology and Hershey Medical Center, Hershey, Pennsylvania 17033-0850 szc104@psu.edu sag17@psu.edu.
authors.forename: Sangita A
authors.initials: SA
authors.lastname: Chakraborty
authors.affiliation: Hershey Medical Center, Hershey, Pennsylvania 17033-0850.
authors.forename: Abid A
authors.initials: AA
authors.lastname: Kazi
authors.affiliation: Department of Biochemistry and Molecular Biology and Hershey Medical Center, Hershey, Pennsylvania 17033-0850.
authors.forename: Tamreen M
authors.initials: TM
authors.lastname: Khan
authors.affiliation: Department of Biochemistry and Molecular Biology and Hershey Medical Center, Hershey, Pennsylvania 17033-0850 szc104@psu.edu sag17@psu.edu.
authors.forename: Sergei A
authors.initials: SA
authors.lastname: Grigoryev
mesh_terms: D001483:Base Sequence; D002843:Chromatin / Q000378:metabolism*; D015825:Chromosomes, Fungal / Q000235:genetics; D020868:Gene Silencing; D017930:Genes, Reporter; D016681:Genome, Fungal / Q000235:genetics; D038101:Insulator Elements / Q000235:genetics; D008836:Micrococcal Nuclease / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D008836:Micrococcal Nuclease
keywords: Saccharomyces cerevisiae; antisilencing; clone-601 nucleosomes; heterochromatin boundary; transcriptional silencing