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First published online July 2, 2007
doi: 10.1242/10.1242/jcs.006007

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SUUR joins separate subsets of PcG, HP1 and B-type lamin targets in Drosophila

¹ Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
² Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
³ Imperial College London, London, SW7 2AZ, UK

View larger version (24K): [in this window] [in a new window]   Fig. 1. Localization of transfected Dam-SUUR and SUUR-Dam fusion proteins after heat shock induction in Kc cells. The average transfection efficiency was 15-30%. FITC-conjugated donkey-anti-mouse IgG was used as a secondary antibody for detection of the 9E10 mouse monoclonal anti-Myc antibody. DNA was stained with DAPI.

View larger version (14K): [in this window] [in a new window]   Fig. 2. SUUR target genes are mostly repressed and late replicated. Gene activity and replication timing data were taken from Schübeler et al. (Schübeler et al., 2002). Information was available for 1034 SUUR target and 4322 non-target genes. (A) Transcriptional activity of SUUR target and non-target genes. Active and repressed gene fractions are shown as green and red bars, respectively. (B) Density plot of log2-transformed replication timing of SUUR target (red) and non-target (black) genes.

View larger version (13K): [in this window] [in a new window]   Fig. 3. SUUR target genes are depleted with active histone marks and enriched with repressive histone mark. Density plots of histone modification of SUUR target (red) and non-target (black) genes are shown for H3-di-meK4 (A), H3-tri-meK4 (B), H3-Ac (C), H4-Ac (D), H3-di-meK79 (E), and H3-tri-meK27 (F). Histone modification data for 1034 SUUR targets and 4322 non-targets (A-E) were taken from Schübeler et al. (Schübeler et al., 2004) and for 2497 SUUR targets and 7083 non-targets (F) from Tolhuis et al. (Tolhuis et al., 2006).

View larger version (45K): [in this window] [in a new window]   Fig. 4. Degree of similarity between the binding profiles of SUUR and Pc, Esc, Sce, SU(VAR)3-9, HP1 or Lam. (A-F) Bivariate scatter plots of log2-transformed binding ratios are shown for: SUUR versus Pc (A), SUUR versus Esc (B), SUUR versus Sce (C), SUUR versus SU(VAR)3-9 (D), SUUR versus HP1 (E) and SUUR versus Lam (F). Spearman's rank correlation coefficient is denoted at the right top corner of each plot. SUUR targets are shown in yellow, targets of other proteins in blue, and co-targets in red. (G-I) SUUR shares target genes with PcG proteins, HP1 and Lam. Venn diagrams show the overlap between target genes of SUUR and Pc, Esc (G), HP1 (H) or Lam (I). The number of investigated probes is indicated at the bottom right corner of each diagram. Pc and Esc datasets were taken from Tolhuis et al. (Tolhuis et al., 2006) and the Lam dataset from Pickersgill et al. (Pickersgill et al., 2006).

View larger version (12K): [in this window] [in a new window]   Fig. 5. Correlation between the SUUR binding profile in Kc cells and the UR profile of salivary gland polytene chromosomes. An 11.3 Mb fragment of chromosomal arm 2L is shown. Cytological regions and chromosome nucleotide positions are indicated above and below the graph. A running mean algorithm (a sliding window of 10 genes, one gene per step) was applied to the UR and SUUR binding data. The UR running mean is represented by blue dots and the SUUR binding running mean by red dots. UR regions are confined by vertical dotted lines and labelled in rectangles. UR data were taken from Belyakin et al. (Belyakin et al., 2005).

View larger version (23K): [in this window] [in a new window]   Fig. 6. SUUR is associated with genes that are repressed in embryos. Average expression of 744 SUUR target genes during Drosophila development: E, embryos; L, larvae; M, metamorphosis; Am, adult male; and Af, adult female. Bars with red borders indicate developmental stages with significant difference in expression between SUUR targets and non-targets (P<0.01, Wilcoxon rank sum test, Bonferroni corrected). Gene expression data were taken from Arbeitman et al. (Arbeitman et al., 2002).