Fig. 8: Classes of transcription clusters.

In a self-sustaining transcription cluster, a TF and the gene encoding that TF are both present. The inter- and intra-chromosomal examples in (a) and (b), respectively, illustrate this phenomenon where in a we see the TF of interest (orange triangle) circulating at the cluster, its binding motif present on the chromatin (orange portion), and its corresponding gene expressed (orange rectangle on Chromosome 6). The gray shapes represent additional TFs with binding motifs (gray portion of chromatin) at the cluster. Black rectangles on Chromosomes 3, 9, and 19 represent additional genes present in the cluster. c An analog-independent class of transcription clusters where we observe a TF (red square) bind at a transcription cluster (red cluster) and its corresponding gene expressed in a separate transcription cluster (grey cluster), yet not in the same cluster. d An analog-independent class of transcription clusters where we observe a TF (green circle) bind at a transcription cluster (green cluster) and its corresponding gene expressed but not within a transcription cluster. e Genome-wide cell type-specific self-sustaining transcription clusters extracted from multi-way contact data and decomposed into Hi-C contact matrices at 100 kb resolution. Contact frequencies are log-transformed for better visualization. Frequencies along the diagonal indicate interaction between two or more unique multi-way loci that fall within the same 100 kb bin. Axis labels are non-contiguous 100 kb bin coordinates in chromosomal order. Multi-way contacts that make up the self-sustaining transcription clusters are superimposed. Multi-way contacts with green-colored loci represent 'core' transcription clusters - transcription clusters containing a master regulator and its gene analog. An example read-level contact map for the inter-chromosomal FOXO3 self-sustaining transcription cluster is denoted by the orange highlighted box in the adult fibroblast contact matrix and a read-level contact map for the intra-chromosomal ZNF320 self-sustaining transcription cluster is denoted by the blue highlighted box. Values along the left axis of these read-level contact matrices are base-pair positions of the contacting loci in the genome.