Article Title: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
Figure Lengend Snippet: MIAA identifies global influence of GC-content and differentially accessible motifs. A) GC-content observed to be correlated with accessibility in both stem and endoderm cells from positive (universally opening) and negative (universally closing) control sequences. B) GC-content correlated with accessibility in random DNA phrases. The regression model was trained on MIAA Dpn proportions with GC-content, replicate, and cell type-specific effects of 20 motifs and 26 motif pairs as features, and predicts well on (C) training data (n = 21,420) and (D) held-out test data (n = 4,404). The correlation reported is the Pearson correlation coefficient (r). E) Regression weights of individual motifs and motif pairs in stem and definitive endoderm cells. Hierarchical clustering of regression weights followed by motif enrichment recovers clusters representing cell type-specific transcription factor DNA binding motifs. F) Example of individual motifs (left, middle) which alone do not differentially open chromatin, but differentially open chromatin stem cells in combination (right). Each dot represents the average DpnII read proportion of an individual phrase, compared to shuffled controls (CTRL). Significance computed by paired t-test.
Article Snippet: DpnII digest:20 ug genomic DNA + 20 uL DpnII buffer (New England Biolabs) + 4 uL DpnII 9New England Biolabs) + up to 200 uL water.
Techniques: Binding Assay