Fig. 6: Data-driven identification of transcription clusters.
From: Deciphering multi-way interactions in the human genome
a Blue shaded area: A 5 kb region before and after each locus in a Pore-C read (region between red dashed lines) is queried for chromatin accessibility and RNA Pol II binding (ATAC-seq and ChIP-seq, respectively). Multi-way contacts between accessible loci that have ≥1 instance of RNA Pol II binding are indicative of potential transcription clusters. Gray shaded area: Gene expression (RNA-seq, E1 for gene 1 and E2 for gene 2, respectively) and transcription factor binding sites (TF1 and TF2) are integrated to determine potential coexpression and coregulation within multi-way contacts with multiple genes. Transcription factor binding sites are queried ±5 kb from the gene's transcription start site (see Data-driven Identification of Transcription Clusters in Methods). Genes are colored based on the overlapping Pore-C locus, and the extended horizontal line from each gene represents the 5 kb flanking region used to query transcription factor binding sites. b Pipeline for extracting transcription clusters (Supplementary Methods). c Schematic representation of a transcription cluster.
