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High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Marina V Granovskaia1, Lars J Jensen12, Matthew E Ritchie34, Joern Toedling5, Ye Ning6, Peer Bork1, Wolfgang Huber15 and Lars M Steinmetz1*

  • * Corresponding author: Lars M Steinmetz larsms@embl.de

  • † Equal contributors

Author Affiliations

1 EMBL - European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr. 1, D-69117 Heidelberg, Germany

2 Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark

3 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

4 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia

5 EMBL - European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

6 Plant Biochemistry Lab, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark

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Genome Biology 2010, 11:R24  doi:10.1186/gb-2010-11-3-r24

Published: 1 March 2010

Additional files

Additional file 1:

A table providing control data on the synchronous division of the yeast cells. Excel sheet 1 contains a table of the number and percentage of budded cells and dividing nuclei over time with the progression of the cell cycle; sheet 2 contains a chart of these data.

Format: XLS Size: 30KB Download file

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Additional file 2:

A figure showing categories of expressed segments. The pie chart shows the categories and the numbers of all identified transcribed segments. The unassigned categories encompass the segments that did not meet filter criteria and were excluded from further analyses [11]; correspondingly, the filtered categories are those that did pass the filtering criteria.

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Additional file 3:

A table listing antisense and novel intergenic transcripts identified in our study. Excel sheet 1 is a table of all 523 antisense transcripts, characterized by their genomic position, length and overlapping sense feature; sheet 2 is a table of all 135 unannotated intergenic transcripts, categorized by genomic position and length. Cycling intergenic transcripts are highlighted in sheet 2.

Format: XLS Size: 80KB Download file

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Additional file 4:

A figure showing a comparison of our dataset with the published datasets on the cell cycle in yeast. Three ROC-like plots compare: (a) our combined dataset with that of Gauthier et al. [37]; (b) our cdc28 dataset with the other Cdc28 datasets of Spellman et al. [30] and Cho et al. [28]; (c) our alpha-factor dataset with the existing alpha-factor datasets of Spellman et al. [30] and Pramila et al. [29]. The fraction of the B1 benchmark set genes identified by the various datasets is plotted as a function of gene rank. (a) Comparison of the method of de Lichtenberg et al. applied to our data (red line) with the comprehensive integrated dataset of Gauthier et al. (black line) [35]. The cross indicates our combined list, obtained by the combination of two computational methods of analyses, and curated manually. (b) Comparison of Cdc28 datasets. (c) Comparison of alpha factor-induced growth arrest datasets. The color code displays: light brown, Cho et al.; green, Spellman et al.; cyan and blue, Pramila et al.; black, Gauthier et al.; red, this study. The dotted line indicates random selection of genes.

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Additional file 5:

A table listing periodic protein-coding genes, antisense and unannotated intergenic transcripts. Excel sheet 1 lists 598 periodic ORFs identified in our dataset, sheet 2 lists 37 cycling antisense transcripts, and sheet 3 lists 11 periodic unannotated intergenic transcripts.

Format: XLS Size: 218KB Download file

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Additional file 6:

A Word document providing supplemental data. The file provides additional information on the following sections: 1, Determination of the boundaries of the cell cycle phases; 2, Conservation analysis of non-coding RNAs; 3, Analysis of upstream regulatory elements for periodic unannotated transcripts; 4, UTR lengths; 5, Divergently transcribed periodic transcripts.

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Additional file 7:

A table listing the categories of 37 periodic and 43 non-periodic antisense transcripts. Excel table sheet 1 lists 37 periodic antisense transcripts and sheet 2 lists 43 non-periodic antisense transcripts, each characterized by genomic position, length, overlapping sense feature, function of the opposite sense counterpart according to the Saccharomyces Genome Database, and peak time of expression (cycling 37 antisense transcripts only).

Format: XLS Size: 41KB Download file

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Additional file 8:

A figure showing a comparison of the relative timing of expression within 13 periodic SAPs. We calculated the peak-time difference for the periodic sense and antisense transcripts within each of the 13 cycling SAPs for the alpha-factor and Cdc28 experiments separately. A difference of 0 corresponds to in-phase expression, whereas a difference of 50 corresponds to opposite-phase expression (180 degree phase shift). We observe a good correlation between the two experiments. The shape of the symbol shows how the sense-antisense counterparts overlap.

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Additional file 9:

A table listing pairs of pairs of divergent transcripts from a bidirectional promoter. Each transcript in a pair is characterized by the genomic location, category and gene name.

Format: XLS Size: 22KB Download file

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Additional file 10:

A figure showing GO categories of the ORFs opposite cell-cycle-regulated antisense transcripts. The x-axis displays the number of genes and the y-axis shows the names of GO categories.

Format: PDF Size: 11KB Download file

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Additional file 11:

A figure showing GO categories of 443 non-periodic ORFs opposite non-periodic antisense transcripts. The x-axis displays the number of genes and the y-axis shows the names of GO categories.

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Additional file 12:

A contingency table for sense-antisense transcript overlap.

Format: XLS Size: 17KB Download file

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Additional file 13:

A figure showing heatmaps of bi-directional expression of neighboring cell cycle-regulated genes that share transcription regulatory elements. (a) Two neighboring ORFs: TEL2 and ESP1. (b) ORF and an antisense transcript of the upstream protein-coding gene: SPT21 and antisense counterpart of YMR178W. (c) ORF and cycling unannotated intergenic transcript: MCD1and upstream cycling novel transcript. The heatmap plot is explained in the caption of Figure 3.

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Additional file 14:

A table listing the 109 periodic ORFs identified in our study.

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Additional file 15:

A figure showing GO categories of 109 periodic ORFs unique to our dataset. The x-axis displays the number of genes and the y-axis shows the names of GO categories.

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Additional file 16:

A figure showing Hoechst nuclear staining of dividing cdc28-ts mutant cells. Control data displaying synchronous division of the yeast cells along with the cell cycle progression. Each image represents a gallery of approximately 10 to 20 representative cells that were chosen, for the respective time-point, from different fields of view. Criteria of choice were sharpness of the image and visibility of the bud; besides these, we aimed for random selection.

Format: PDF Size: 2.6MB Download file

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