Combinatorial Binding Leads to Diverse Regulatory Responses: Lmd Is a Tissue-Specific Modulator of Mef2 Activity
Figure 1
A global comparison of Lmd and Mef2 activity.
(A) Schematic overview of a genomic region within an intron of the Mef2 locus: An exon (located on the antisense strand) is shown in orange. Genomic fragments on the tiling arrays are indicated as stacks of two horizontal bars in their corresponding genomic position. The top bar represents the results from the 6–8 hour (stages 10–11) ChIP-on-chip time point, the lower one corresponds to the 8–10 hour (stages 12–13) time point. Significantly enriched regions are indicated in blue for Lmd (top) and in green for Mef2 (bottom). The black bar indicates the location of the previously identified Lmd-binding site. Both Lmd and Mef2 are co-bound to genomic regions overlapping the known Lmd binding site at the 6–8 hr time point, as well as to other sites in this area. (B) Schematic overview of the genomic region upstream of the sns locus (exons show in orange): The known sns enhancer (black bar) partially overlaps with tiling array probes bound by Lmd (at both time points, blue bars) and Mef2 (at 8–10 hour time point, green bar). Additionally, Mef2 binds to other locations upstream and intronic of the sns locus. (C) Lmd and Mef2 co-occupy many genomic locations: Venn diagram displaying the number of non-overlapping regions significantly enriched in Lmd ChIPs (blue) and significantly enriched in Mef2 ChIPs at the same stages of development (green). Both factors co-occupy a large number of regions (overlap). (D) Co-regulation of common direct target genes by Lmd and Mef2: The majority of Lmd target genes (blue) are co-regulated by Mef2 (overlap), while Mef2 regulates a large number of additional genes (green). (E) Differential gene expression in lmd and Mef2 loss-of-function mutants [log2]: differences in expression between mutant and wt embryos were recorded in a timecourse for lmd (left) or Mef2 (right) mutant embryos. Shown are all direct target genes of Lmd that are significantly misregulated at one or more time points in either mutant background (fold change >1.6, q<1%). K-means clustering was used to highlight similar downregulation (top) in both mutants, similar upregulation (centre) or divergent expression changes (bottom). Color scale indicates fold changes [log2]. Genes studied in more detail are marked in grey.