Capturing the chromatin interactome with Epi-Decoder.
(A) Scatter plot of ChIP/input values, which can be interpreted as binding scores, of BC_UP versus BC_DN. For some factors, only the BC_UP or BC_DN value was available. In these cases, the missing value was set to −1 in order to still visualize the remaining value. Factors are coloured based on known functions or complexes. Triangles represent histone proteins. The average values of 6 replicates are shown. (B) Enrichment plot for 3 categories: initiation (TFIID-E and GRFs), termination (Cleavage and Polyadenylation and THO complex), and replication (ORC and MCM) factors. Binders were ranked based on the BC_UP/BC_DN ratio. The top part shows the running sum enrichment for each category. Initiation factors were significantly enriched at BC_UP (p = 3.18−3) and termination and replication at BC_DN (p = 2.03−7 and p = 1.06−5). The bottom lines indicate the factors represented in the categories. (C) Illustration of the different protein complexes that Epi-Decoder identified at the barcoded KanMX gene at the HO locus. BC_DN, downstream barcode; BC_UP, upstream barcode; ChIP, chromatin immunoprecipitation; GRF, general regulatory factor; IP, immunoprecipitation; MCM, minichromosome maintenance; ORC, origin recognition complex.