ICE-A: A chromatin interaction-based tool for improved annotation of distal cis-regulatory elements reveals novel regulatory functions of lineage-restricted transcription factors in lymphocytic development [ChIP-Seq]

Stage- and lineage-specific gene expression patterns are controlled by a complex interplay between transcription factors, the epigenetic landscape, and the 3-dimensional (3D) structure of the DNA. The 3D structure is of great importance because it allows for the formation of DNA loops that juxtaposition distal regulatory elements to the promoters, allowing for functional synergy and high-level transcription of a given target gene. However, chromatin loops can be highly complex and can span several megabases of genomic context and where one enhancer can interact with several promoters during cell development affecting gene regulation in a time and cell context dependent manner. Thus, our understanding of gene regulation is largely dependent upon our ability to link regulatory elements to the correct target genes. For this purpose, several approaches have been developed, including proximity annotation, linking a given regulatory element to the closest coding gene, and correlation of gene expression to changes in DNA accessibility. While these approaches are valuable, they are based on rather simplified assumptions that disregard the stage- and lineage-restricted 3D organization of the genome. To facilitate the linkage of regulatory elements to their target genes, we have developed a novel tool for easy incorporation of chromatin configuration data into the annotation process. Using this annotation procedure to explore gene regulatory networks in early lymphocyte development, we show that lineage-specific transcription factors target regulatory elements that are annotated to both lineage-specific and broadly expressed genes. Furthermore, several regulatory elements annotated to lineage-specific genes were annotated to alternative promoters in a context dependent manner. These data highlight how efficient annotation procedures for linking distal regulatory elements to target genes provide valuable insights into gene regulatory networks.