Pan-cell type continuous chromatin state annotation of all IHEC epigenomes

Understanding the mechanistic basis of genetic disease requires annotating the regulatory elements in the human genome. To this end, the International Human Epigenome Consortium (IHEC) has generated thousands of epigenomic datasets—including ChIP-seq, DNase-seq, and ATAC-seq—that measure various biochemical activities in the genome, including transcription factor binding, histone modification, and DNA accessibility. Currently, the predominant methods for integrating these data sets to annotate regulatory elements are segmentation and genome annotation (SAGA) algorithms such as ChromHMM and Segway. The majority of annotations generated by these methods are cell type-specific. However, as the number of profiled cell types has grown into the thousands, using thousands of cell type-specific chromatin state annotations proves undesirable for many applications. Therefore, recently, researchers have sought a single unified annotation of regulatory elements across all cell types, known as a “pan-cell type” annotation. Here, we present a pan-cell type annotation that summarizes all IHEC epigenomes using the recently-developed method, epigenome-ssm. This pan-cell type annotation comprises 33 genome-wide chromatin state feature signal tracks, each of which captures a regulatory program driving genomic activity in one or more cell types. We show that these feature maps constitute an intuitive and visualizable summary of epigenomic data.