Molecular features underlying functional and structural interactions between diverse transcription regulatory elements in a chromosomal context

Abstract

Transcription is modulated by interactions among transcription regulatory elements (TREs), including promoters and enhancers, but their underlying interaction specificities remain opaque. Here, we develop a Chromatin-Integrated, landing-pad-based Enhancer Reporter Assay, CIERA-seq, that interrogates regulatory interactions between target promoters and distal TREs (dTREs) in a controlled genomic and chromatin context. We found both promoter-derived (pdTREs) and enhancer-derived-dTREs (edTREs) exhibit enhancer activities on target promoters with a specificity that depends on factors that dTREs recruit. pdTREs are generally enriched for factors involved in the core transcription process, whereas edTREs are enriched for pioneer factors, SWI/SNF chromatin remodelers, and histone acetyltransferase EP300. To further leverage the chromatin integration system, we applied deaminase-based footprinting to profile chromatin accessibility across individual fibers containing distinct target promoter-dTRE pairs. We found that different target promoters and dTREs exhibited distinct accessibility profiles, and that dTREs could modulate the accessibility of their cognate target promoters in a transcription factor and cofactor-dependent manner. Moreover, promoter accessibility was positively associated with transcriptional activity, linking dTRE-mediated changes in local chromatin accessibility to functional transcriptional output. Overall, our CIERA-seq assays and deamination-based footprinting assays support a model where dTREs activate target promoters constrained at different rate limiting steps in transcription by supplying complementary components of the transcription regulatory machinery.