<p>Supplemental Information Table Legends</p><p>Supplemental Figure 1: Correlation between Genome Occupancy, Transcriptional </p><p>Activation, and Peripheral Localization</p><p>All genes in the genomic occupancy profiles of Xpo1, Nup116, and Mlp2 were assigned a percentile rank ranging from 0% (unbound) to 100% (highest binding). The distributions of the 49 genes induced ≥ 3-fold upon alpha factor treatment (Spellman et al., 1998) within the (A) Xpo1, (B) Nup116, and (C) Mlp2 datasets are shown for untreated cells (white bars) and cells treated with 30 nM alpha factor for 2 hours (black bars). A bin size of 10% was used. </p><p>Supplemental Table 1: Functional Gene Category Enrichment in Alpha Factor </p><p>Stimulated Genomic Occupancy Profiles</p><p>Target genes from the nuclear transport factor genomic occupancy profiles (IP/WCE ≥ </p><p>1.0, p value  0.02) were examined for gene category enrichment within the S. cerevisiae </p><p>Gene Ontology Consortium (Ashburner et al., 2000) using Funcassociate (Berriz et al., </p><p>2003). All experiments denoted with “alpha” represent genomic location analysis carried out in cells stimulated with 30 nm alpha factor for 2 hours before fixation. “5 min fix” denotes the 5 minute crosslinking time of the control and experimental samples in the </p><p>RNase treatment experiment. The significance of enrichment for the listed functional categories was determined by Fisher’s exact test, corrected for multiple hypothesis testing, and is displayed as a p value. The values in italics represent statistically signficiant under-enrichment for gene categories in each profile. Tiled data tables</p><p>Tiled data is organized in the following format: (Column 1) probe ID, (Column 2) probe midpoint coordinate moving left to right on chromosome III, (Column 3-N) normalized </p><p>IP/input ratios for independent biological replicates of Mlp1 binding under the given condition (untreated or with 30 nM alpha factor for 2 hours).</p><p>ORF data tables</p><p>ORF data output from the Rosetta Resolver microarray analysis platform is organized in the following format: (Column 1) sequence code, or systematic gene identifier from the </p><p>Saccharomyces Genome Database; (Column 2) sequence name(s), or common names of the genes; (Column 3) IP/input ratio for three or more arrays combined and weighted by the Rosetta Resolver, implemented as previously described (Casolari et al., 2004); </p><p>(Column 4) P-value for each gene, as calculated by Rosetta Resolver (Casolari et al., </p><p>2004); (Column 5) Sequence description of each gene.</p>