Web supplement to
"A gene-specific requirement of RNA polymerase II CTD phosphorylation on serine 2 for sexual differentiation in fission yeast"

BACKGROUND: The switch from cellular proliferation to differentiation occurs to a large extent through specific programs of gene expression. In fission yeast, the master regulator of sexual differentiation, ste11, is induced by environmental conditions leading to mating and meiosis. RESULTS: We show that phosphorylation of serine 2 (S2P) in the C-terminal domain of the largest subunit of the RNA polymerase II (PolII) enzyme by the Lsk1 cyclin-dependent kinase has only a minor impact on global gene expression during vegetative growth but is critical for the induction of ste11 transcription during sexual differentiation. The recruitment of the Lsk1 kinase initiates in the vicinity of the transcription start site of ste11, resulting in a marked increase of S2P on the ste11 unit, including an extended 5' untranslated region (5'UTR). This pattern contrasts with the classical gradient of S2P toward the 3' region. In the absence of S2P, both PolII occupancy at the ste11 locus and ste11 expression are impaired. This results in sterility, which is rescued by expression of the ste11 coding sequence from the adh1 promoter. CONCLUSION: Thus, the S2P polymerase plays a specific, regulatory role in cell differentiation through the induction of ste11.

The ChIP-on-chip and microarray data have been deposited in the Gene Expression Omnibus (NCBI-GEO) database under accession GSE16498

• Genome-wide binding profiles for ChIP-chip data
  Tab-delimited files containing binding ratios for each assayed position in the genome. Column format: chromosome, position and binding ratios.
  
  The binding ratios above can be visualized using the integrated genome browser (IGB). Click here to download and launch IGB. When IGB is running, select "Schizosaccharomyces pombe" as species in the "Data access" tab and "S_pombe_Sep_2007" as the genome version. After selecting the tracks "sanger-genes" and "transcript-boundaries" in the "Data sources" panel, the binding ratios can be loaded using the File->Open menu. The following screenshot shows the IGB configuration details with loaded data tracks.
  
  
• Probe-specific P-values for ChIP-chip data
  Tab-delimited files containing probe-specific p-values for each assayed position in the genome. Column format: chromosome, position and binding ratios.
  
  
• Fold-change and p-values for expression arrays
  Tab-delimited files containing log2 expression ratios between the lsk1::ura1 or rpb1(S2) mutants and wild-type strains for all genes. Associated P-values calculated using Limma and corrected for multiple testing by controlling the false-discovery rate using the Benjamini and Yekutieli step-up procedure are also included.

The raw data files used to make the heat maps in figure 2 are listed below. The treeview files can be visualized in the treeview program which can be found here.

• Cluster diagram for figure 2A. (Treeview) (Tab-delimited text)
• Cluster diagram for figure 2C. (Treeview) (Tab-delimited text)

The raw data files used to make the heat maps in figure S1 are listed below. The treeview files can be visualized in the treeview program which can be found here.

• Cluster diagram for figure S1A. (Treeview) (Tab-delimited text)
• Cluster diagram for figure S1C. (Treeview) (Tab-delimited text)