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. 2014 Dec 15;3:e04506. doi: 10.7554/eLife.04506

Figure 2. Set1 localizes to lowly expressed and repressed loci.

(A and B) Enrichment of Set1 and RNA polymerase II (Pol II) determined by chromatin immunoprecipitation (ChIP)–chip displaying significant Set1 enrichment at highly transcribed genes (A) and repressed genes (B). Positions of genomic features on forward (top) and reverse strands (bottom), top panel. Black bars denote protein coding gene open reading frames (ORFs); white, associated untranslated regions (UTRs); orange, noncoding RNAs. Pol II ChIP–chip data was derived from Chen et al. (2008). (C) Set1 enrichment relative to transcript abundance and Pol II occupancy. Comparisons of RNA-seq expression levels (blue), Pol II ChIP-seq enrichment (green) and Set1 ChIP–chip enrichment (red) at loci showing significant Set1 enrichment (N = 290 transcripts with nonoverlapping annotated features). Processed RNA-Seq FPKM data were obtained from Rhind et al. (2011) and Pol II ChIP-seq data from Zaratiegui et al. (2010). The horizontal red line denotes mean expression for all Schizosaccharomyces pombe transcripts (Rhind et al., 2011). (D) Gene ontology (GO) analysis of Set1-bound transcripts by expression level quintile. Representative GO terms were significantly enriched (p ≤ 1 × 10−5, hypergeometric test) and found exclusively in quintiles of highly expressed (top panel) versus lowly expressed genes (bottom panel). See Figure 2—source data 1 for a complete list of all significantly enriched GO terms/quintile.

DOI: http://dx.doi.org/10.7554/eLife.04506.005

Figure 2—source data 1. Gene ontology (GO) enrichment of Set1-localized transcripts (ChIP-chip) by target expression level.
Set1-targeted transcripts (see Figure 2C) were rank ordered by absolute expression level and divided into quintiles. GO analysis of each quintile was performed as for Figure 1—source data 1.
DOI: http://dx.doi.org/10.7554/eLife.04506.006
elife04506s003.xlsx (68KB, xlsx)
DOI: 10.7554/eLife.04506.006

Figure 2.

Figure 2—figure supplement 1. Set1 localization at active and repressed loci.

Figure 2—figure supplement 1.

Localization of FLAG-set1 or Set1 mutants deficient in H3K4me (set1FH3K4me−), or lacking the catalytic domain (set1-SETΔ) at (A) the housekeeping gene act1, (B and C) repressed genes scr1 and ste11, (D) pericentromeric (cen), or (E) rDNA array was assessed by chromatin immunoprecipitation (ChIP) followed by qPCR. Relative ChIP fold enrichment to input (whole cell extract) was calculated using the 2−ΔΔCt method after normalization by primers corresponding to mitochondrial DNA (Lorenz et al., 2012). (SD, error bars; n = 3 qPCR replicates.) Untagged corresponds to a wild-type strain that did not express any FLAG tagged protein.
DOI: http://dx.doi.org/10.7554/eLife.04506.007
Figure 2—figure supplement 2. Distribution of Set1-localized versus all Schizosaccharomyces pombe transcripts by absolute expression level.

Figure 2—figure supplement 2.

Histogram showing number of genes by expression level (green bars), overlaid with Set1-bound transcripts (red bars). The red vertical line denotes mean log2 FPKM, all S. pombe transcripts; black lines denote quintiles of Set1-bound genes with RNA-Seq transcripts. Processed RNA-Seq FPKM data were obtained from (Rhind et al., 2011).
DOI: http://dx.doi.org/10.7554/eLife.04506.008