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. 2008 Oct 28;6(10):e261. doi: 10.1371/journal.pbio.0060261

Figure 3. PREs with Conserved Position Show Motif Turnover.

Figure 3

(A) bxd PRE. Motif occurrence is independent of sequence conservation. The core D. melanogaster bxd PRE and the orthologous regions from the other three species are shown. Coordinates of sequences shown from left to right of the figure are as follows: D. melanogaster:12590182–12589368, D. simulans: 8886059–8886877, D. yakuba: 12487238–12488017, and D. pseudoobscura: 485021–483926. Black bar below D. melanogaster diagram indicates minimal PRE fragment [48]. Conservation between D. melanogaster and D. pseudoobscura is marked on the diagrams for these two species: Dark grey: regions of over 70% identity. Light grey: 50%–70% identity. D. simulans and D. yakuba conservation to D. melanogaster is indicated (the D. melanogaster, D. simulans, and D. yakuba sequences are over 90% identical). Motif positions are indicated above the figure. Motifs shown in red on D. simulans, D. yakuba, and D. pseudoobscura are not present in the D. melanogaster PRE. D, Dsp1 [44]; G, GAF (FBgn0013263); P, PHO extended site (PF or PM as in [18]; p, PHO core site (GCCAT) (FBgn0002521); Z, Zeste (FBgn0004050). Underlined motifs indicate overlapping runs of motif separated by two bases. G5 indicates five consecutive GAs.

(B) PRE prediction score plots for spalt major (salm) PRE at orthologous regions of the four genomes. The salm transcription unit is indicated. Grey bars at the top of each score plot indicate the regions shown in detail in (D). Black boxes indicate PCR fragments used for real time PCR detection in ChIP analysis in (C).

(C) ChIP enrichments at salm PRE in embryos of four species (see also legend to Figure 1).

(D) Motif occurrences in salm PREs, annotation as in (A). Coordinates of sequences shown from left to right of the figure are as follows: D. melanogaster: 11446402–11445612, D. simulans: 11255943–11256747, D. yakuba: 7893940–7893140, and D. pseudoobscura: 6845260–6844154 .