TRIP reporters measure position effects. (A) The pie chart shows observed over expected percentage of insertions in promoters, exons, and introns for active and silent Drosophila genes. The observed frequency of insertion is close to the expected for each class. (B) Chromatin protein binding on the reporters is assayed simultaneously by DamID. If the protein binds the integrated reporter, Dam methylates the DNA nearby the barcode (locus 2); otherwise, it does not (locus 1). After digestion with the methylation-sensitive enzyme DpnII, only the methylated barcodes can be amplified by PCR, revealing which insertions were bound by the chromatin protein. (C) The violin plots show the DamID score for HP1 or Brahma (markers of Green and Red chromatin, respectively) when the promoter II is inserted in different regions of the Drosophila genome. HP1 is more bound when the reporters are inserted in Green chromatin and Brahma is more bound when they are inserted in Red chromatin. (D) Chromosomal structure at two loci with and without inserted reporters. The left panel shows the 4C profile with the barcode as a viewpoint; the right panel shows the corresponding slice of the Hi-C matrix (virtual 4C) without the reporter.
