UC San Diego

Programs of gene regulation are genetically encoded by regulatory elements, which are short stretches of DNA that typically harbor one or more binding sites recognized by transcription factors. During development or cellular stimulation, activated transcription factors bind to these regulatory elements where they subsequently recruit additional factors to initiate or modulate transcription. In most cases, the precise control of gene expression is dependent on multiple regulatory elements located in the vicinity of a gene, where the prevailing theory describes transcription as being initiated through looping of DNA, physically connecting a distal regulatory element (enhancer) to its intended proximal regulatory element (promoter) thereby mediating transcription regulation. However, methods that measure nascent transcription have revealed a substantial amount of transcription activity occurs at promoter-distal regulatory elements, often far from the genes themselves. It remains unknown how these many individual distal regulatory elements communicate to drive changes in gene expression. My thesis work reveals adjacent regulatory elements are induced and repressed simultaneously upon cellular activation, forming cis regulatory domains (CRDs), spanning up to hundreds of kilobases. This observation is at odds with the current promoter-enhancer looping theory, which does not account for the behavior of all distal regulatory elements near regulated loci but only specific enhancer/promoter interactions. My thesis data suggest that communication between elements may not depend on specific pairwise regulatory element (RE) interactions but rather are mediated by mechanisms that span across the whole domain, such as enrichment in local TF concentrations or general subnuclear localization observed within CRDs. Our results identify that the loss of 3D genome structure causes a loss of synergistic transcriptional bursts within cis-regulatory domains (CRDs), demonstrating the importance of maintaining an intact genomic regulatory landscape. We report that genetic variation at TLR4 associated transcription factor binding motifs can disrupt the transcriptional landscape within CRDs at both TSS harboring the mutation as well as adjacent TSS within 50 kb of mutated sites. These results represent crucial evidence of communication between regulatory elements and identification of CRDs as genuine genomic entities. Our data supports a data mode of gene regulation that could impact how we study mechanisms governing transcription initiation and modulation of gene expression.