NF-YB bound loci reside within five epigenetic domains. (A) K-means clustering of K562 NF-YB loci based on the distribution of histone PTM, RNA Pol II, NF-YB, and NF-YA ChIP-seq reads within a region spanning ±5 kbp from the summit of NF-YB peaks (centered at 0 bp). Clustering was carried out on transformed, rank normalized read counts. Raw read count intensity is depicted in red. The interpretation and classification of clusters into functional categories are shown at right. (B) NF-YB summits from clusters derived from A are annotated to genomic features: chromatin states, LTRs, dbTSS, RefSeq promoters, and FAIRE-seq regions. The percentage of peak summits within each cluster overlapping a specific feature is indicated. Overlap with LTRs is assayed within a window of ±250 bp from the ends of the LTR feature. RefSeq promoters are considered within a window of −2500:+500 bp from the TSS. A direct overlap with FAIRE-seq regions and chromatin states is used. Long poly(A) purified RNA reads were counted within a window of ±500 bp about the NF-YB peak summit, and the median value of that cluster is shown (n = size of cluster in peaks).
