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Text and Figures, plus Web-only Figures and Tables
Important note: The links in this section are to documents in PDF format and to tab-delimited text files. If you click the link, the file will open in your web browser. To save the file to your computer, please use the "Save link as..." or "Save target as..." feature of your browser. Windows users right-click the link, and Mac users control-click or click-and-hold the link. Adobe Acrobat Reader 3.0 or later is required. If you need the Adobe Acrobat Reader, click here. See also the References and Disclaimer for the supplemental data.

Published Text and Figures

The paper in PDF format

Figure 1 The determination of Rap1p targets

Figure 2 A map of the interaction between Rap1p and the S. cerevisiae genome

Please use the "Zoom" function (magnifying-glass icon) of the Acrobat reader to get close-up views of chromosomal regions of interest.

Figure 3 Rap1p binds preferentially to potential promoters

Figure 4 Rap1p binds to the promoters of the most heavily transcribed yeast genes

Web Figures (Tables are here)

Web Figure A, A map of the distribution of Sir2p on the yeast genome.

Web Figure B, A map of the distribution of Sir3p on the yeast genome.

Web Figure C, A map of the distribution of Sir4p on the yeast genome.

Web Figure D, showing the extent of each protein's association with each chromosome end (keeping in mind the caveats discussed in the text).

Web Figure E, showing the extent of each protein's association with the silent mating loci HML and HMR.

Web Figure F, PDF (or higher-resolution GIF), an annotated glycolysis pathway showing Rap1p's role in regulating glycolysis.

Rap1p targets form a continuous enzymatic pathway in glycolysis from fructose-1,6-biphosphate to ethanol. Genes in red are Rap1p targets. Genes in green are not Rap1p targets. An asterisk (*) marks previously known targets, and (hc) marks spots that had a high rank in both IP and control experiments. This map was based on the glycolysis pathway provided by the Kyoto Encyclopedia of Genes and Genomes (KEGG).

Web Figure G, graphs showing the functional classifications of Rap1p targets compared to functional classification of all yeast ORFs.

Web Figure H, the .cdt and .gtr files corresponding to the cluster of gene expression profiles for the genes downstream of intergenic fragments selected by the Rap1p IP. Treeview is required to view the clusters.

    Please note the the clusters were created using more experiments than are shown. Only published experiments, or experiments for which researchers agreed to have thier data released in this form are shown.

Web Figure I, a graph of the relationship between an ORF's correlation to the average RPG expression profile and the position of any upstream occurrence(s) of the Rap1p consensus binding site.

Rap1p binding sites tend to occur from 225 to 400 base pairs upstream of genes that are regulated like RPGs. The graph was created by finding all occurrences of the degenerate sequence MAYCCRNNCA that occur within 1000 base pairs of the start codon of any ORF, and sorting based on the position of each hit. A moving average of each ORF's correlation to the ribosomal protein gene expression pattern was then calculated, with a window size of 40.

Web Figure J, a graph of the relationship between an ORF's correlation to the average RPG expression profile and the relative strandedness of upstream Rap1p binding sites.

Rap1p binding sites tend to occur on the (-) strand relative to genes that are regulated like RPGs. The graph was created by sorting according to each ORF's correlation to the ribosomal protein gene expression pattern, then taking a moving average of the strandedness of any MAYCCRNNCA hits that were recorded within 1000 base pairs of the start codon. A value of 1 was assigned to each hit recorded on the + strand (the same strand as the coding sequence) and a score of -1 was assigned to each hit recorded on the - strand (the strand opposite the coding sequence). Only ORFs with an upstream MAYCCRNNCA hit are included in this plot.

Web Figure K, A map of the interaction between Rap1p and the S. cerevisiae genome (retains chromosomal landmarks)

Please use the "Zoom" function (magnifying-glass icon) of the Acrobat reader to get close-up views of chromosomal regions of interest.

 

Web Tables

Web Table A, the tabular data for the spotted segments that made the cutoff for significance for Rap1p IPs.

Web Table B, the tabular data for non-RPG ORFs whose upstream regions are bound by Rap1p.

Web Table C, all RPGs and whether Rap1p is bound to their promoters, ORFs, or 3'UTRs.

Web Table D, a list of all ORFs and their corresponding "gene-ness"score. ORFs with a score below 0 were considered "questionable".

Each ORF has been given a single score that reflects the likelihood of it being a gene, based on the following criteria:

Codon Usage
MIPS Class
Overlap with another ORF
SAGE Tag
YPD description
Amino Acid Length
Gene Expression Data

Each criterion was subjectively weighted, and is listed above from heaviest to lightest weight. Among ORFs with a score <0, there are 10 named genes (1.1%). 1 is an RNA gene, 1 is known to be non-coding, 7 have no references or functions associated with them, and only 1 has strong similarity to a known gene. Using the 0 cutoff, 874 ORFs are classified as "questionable".

Web Table E, motif matrices for Rap1p binding sequence, as determined by BioProspector's analysis of Rap1p IP'd fragments.

Web Table F, strandedness of Rap1p hits at promoters

The table was created by finding all occurrences of the degenerate sequence MAYCCRNNCA that occur within 1 000 base pairs of the start codon of any ORF, and sorting based on the position of each hit. A moving average of each ORF's correlation to the ribosomal protein gene expression pattern was then calculated, with a window size of 40.

Web Table G, a list of the non-telomeric, non-mating type ORFs affected by the distribution of Sir2p.

Web Table H, a list of the non-telomeric, non-mating type loci ORFs affected by the distribution of Sir3p.

Web Table I, a list of the non-telomeric, non-mating type loci ORFs affected by the distribution of Sir4p.


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