Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content
Fig 2
Hmga proteins bind to DNA in ESC as a function of DNA AT content.
(A) Genome-wide correlation heatmap for all samples (including replicate c of Hmga1) and AT content on 1kb tiling windows, illustrating both good reproducibility between replicates and the correlation of Hmga1-2 with AT content. Colors indicate the Pearson correlation coefficient. (B) Log2 enrichments over input for the depicted samples on chromosome 14. Each dot represents the enrichment of IP over input in a window of size 10kb. Gaps indicate regions with low mappability (below 80%). Top and bottom 1% of data range are not shown to enhance readability. (C) Barplot illustrating the predictive power of mono-, di-, tri- and tetranucleotide models for each individual sample. The predictive power is not substantially improved by taking into account higher-order sequence features. (D) Relationship between bioHmga samples and AT content in ES cells for two representative replicates. Scatterplots depict AT content vs. log2 Hmga1-2 input-normalized enrichment values (over 1kb tiling windows) minus the same enrichments for the respective DBD-mutant. Pearson correlation coefficients are indicated on top. (E) Hmga binding at simple repeats with very high AT content. Average profiles show log2 enrichment over the respective DBD mutants at mappable (TA)n simple repeats of a minimal length of 300nts, centered at repeat start coordinates. AT content is shown in grey (dashed line).