Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation
Fig 3
Increasing the number of GA-dinucleotide repeats increases CLAMP occupancy.
A) A multiple linear regression to test contribution of sequence length (k-mer) and shape to overall binding. Adding dinucleotide (2mer) features to the sequence-only (1mer) model increases the performance more than adding DNA shape features, indicating the importance of dinucleotides in CLAMP-DNA recognition. Adding trinucleotide (3mer) features further increases the performance marginally. B) CLAMP PBM binding for GA-dinucleotide repeats of different lengths is plotted as box plot distributions. The y-axis is the PBM intensity score for each number of GA-repeats, which are plotted along the x-axis, e.g. 1 = GA, 2 = GAGA. C) An electrophoretic mobility shift assay to test MBP-CLAMP binding to increasing numbers of GA-repeats. The labeled probes contain GA-repeats of 4 (8-bp), 8 (16-bp), 10 (20-bp) and 15 (30-bp) centered within a 60-bp sequence. The first four lanes are reactions containing MBP control protein with DNA, and the next four are MBP-CLAMP with DNA. D) Input-normalized CLAMP ChIP-seq signal enrichments at GA-repeats of different lengths are given for the X-chromosome (red) and autosomes (blue) from male S2 (top) and female Kc cells (bottom). The x-axis shows the number of GA-repeats e.g. 1 = GA, 2 = GAGA.