title: Approaches to studying subnuclear organization and gene-nuclear pore interactions.
abstract: Many genes in budding yeast Saccharomyces cerevisiae associate with the nuclear pore complex (NPC), which impacts their location within the nucleus and their transcriptional regulation. To understand how eukaryotic genomes are spatially organized, we have used multiple approaches for analyzing the localization and transcription of genes. We have used these approaches to study the role of DNA elements in targeting genomic loci to the NPC and how these interactions regulate transcription, chromatin structure and the spatial organization of the yeast genome. These studies combine yeast molecular genetics with live-cell microscopy and biochemistry. Here, we present detailed protocols for these cytological and molecular approaches.
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
authors.forename: Defne Emel
authors.initials: DE
authors.lastname: Egecioglu
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
authors.forename: Agustina
authors.initials: A
authors.lastname: D'Urso
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
authors.forename: Donna Garvey
authors.initials: DG
authors.lastname: Brickner
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
authors.forename: William H
authors.initials: WH
authors.lastname: Light
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
authors.forename: Jason H
authors.initials: JH
authors.lastname: Brickner
mesh_terms: D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods; D004271:DNA, Fungal / Q000235:genetics*; D014644:Genetic Variation; D005822:Genetic Vectors / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D049452:Green Fluorescent Proteins / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D007763:Lac Operon / Q000235:genetics*; D018613:Microscopy, Confocal / Q000379:methods; D022022:Nuclear Pore / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; C554167:URA3 protein, S cerevisiae; D049452:Green Fluorescent Proteins
keywords: Chromatin; Chromosome; Confocal microscopy; Nuclear architecture; Nuclear pore complex