title: Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization.
abstract: The association of genes with the nuclear pore complex (NPC) and nuclear transport factors has been implicated in transcriptional regulation. We therefore examined the association of components of the nuclear transport machinery including karyopherins, nucleoporins, and the Ran guanine-nucleotide exchange factor (RanGEF) with the Saccharomyces cerevisiae genome. We find that most nucleoporins and karyopherins preferentially associate with a subset of highly transcribed genes and with genes that possess Rap1 binding sites whereas the RanGEF preferentially associates with transcriptionally inactive genes. Consistent with coupling of transcription to the nuclear pore, we show that transcriptional activation of the GAL genes results in their association with nuclear pore proteins, relocation to the nuclear periphery, and loss of RanGEF association. Taken together, these results indicate that the organization of the genome is coupled via transcriptional state to the nuclear transport machinery.
authors.affiliation: Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, MA 02115, USA.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Casolari
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Brown
authors.forename: Suzanne
authors.initials: S
authors.lastname: Komili
authors.forename: Jason
authors.initials: J
authors.lastname: West
authors.forename: Haley
authors.initials: H
authors.lastname: Hieronymus
authors.forename: Pamela A
authors.initials: PA
authors.lastname: Silver
mesh_terms: D021581:Active Transport, Cell Nucleus / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D002467:Cell Nucleus / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal / Q000235:genetics; D005809:Genes, Regulator / Q000235:genetics*; D016681:Genome, Fungal; D028884:Karyopherins / Q000235:genetics; D022022:Nuclear Pore / Q000235:genetics; D028861:Nuclear Pore Complex Proteins / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins; D015533:Transcriptional Activation / Q000235:genetics; D020931:ran GTP-Binding Protein / Q000378:metabolism; D020827:rap1 GTP-Binding Proteins / Q000235:genetics
chemical_list: D002352:Carrier Proteins; D028884:Karyopherins; D028861:Nuclear Pore Complex Proteins; D009687:Nuclear Proteins; D029701:Saccharomyces cerevisiae Proteins; C410219:MOG1 protein, S cerevisiase; D020931:ran GTP-Binding Protein; D020827:rap1 GTP-Binding Proteins