Journal:

Article Title: Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes

doi: 10.1016/j.cell.2009.12.054

Figure Lengend Snippet: (A) A representative example of Nup98 target sites obtained from ChIP-on-chip analysis, plotted relative to Lamin binding sites and annotated genes. (B) Distribution of Nup98 target and non-target genes relative to expression levels. (C) ChIP analysis of candidate target genes of Sec13 and Nup98 (CG6014/78D, Hph/82EF, CG13800/62E) and of control neighboring genes in Drosophila S2 cells, showing enrichment of target genes in fractions immunoprecipitated by Nup antisera (blue and red bars, respectively) as percentage of input DNA, with levels immunoprecipitated by the normal rabbit IgG subtracted. (D) Fold decrease in mRNA levels of Nup target genes in S2 cells treated with dsRNA against Sec13 or Nup98, relative to S2 cells treated with control dsRNA, as detected by microarray analysis. See also Figures S6 and S7.

Article Snippet: For ChIP-on-chip analysis, the Nup98 antibody- or normal rabbit IgG- immunoprecipitated DNA in duplicates was labeled and co-hybridized with input DNA to 2.1M Drosophila whole genome arrays by NimbleGen Systems, Inc. ChIP peak data were generated by NimbleGen, and genes with peaks of scaled log 2 -ratio ≥1 and FDR score ≤ 0.05 were selected as Nup98 targets.

Techniques: Binding Assay, Expressing, Control, Immunoprecipitation, Microarray