Genome-wide profiling of regulatory elements is often guided by the known properties of active regulatory elements. Enhancers and promoters need to be in open chromatin and carry the correct DNA sequences to be accessible by and able to bind transcription factor proteins. These proteins must also exist in sufficient amounts in the cell. State-of-the-art methods also rely on differential post-translational modifications (PTMs) of histone proteins that have been suggested to discern enhancers from gene promoters. Search for certain histone modifications in the genome distal to gene promoters is therefore often performed to predict enhancer loci and their activities across assayed cell types. In our work, we have carefully profiled transcription initiation events at regulatory elements and the biogenesis and fate of produced RNAs. Our work shows that not only gene promoters but also enhancers initiate transcription, indicating promoter activity of enhancers. In addition, several studies have shown enhancer activities of bona fide gene promoters blurring their distinction. We have found that both enhancers and promoters initiate bidirectional transcription in a divergent manner and that the abundance and fate of produced RNAs rely not on the core regulatory regions themselves but on the flanking DNA surrounding each regulatory element. In addition, the abundances of produced RNAs reflect their proximal histone modifications. Based on these observations we conclude that histone modifications therefore should not guide the interpretation of function for a regulatory element. Rather, our results suggest that enhancers and gene promoters have many properties in common. We suggest regulatory elements to be considered to have a unified architecture and that the function of each regulatory element (enhancer or promoter activity) may be context specific. We have further shown that the unified promoter architecture of enhancers and promoters is conserved across Metazoa and that the strength of core promoter elements is related to the function (enhancer and/or promoter activity) of a transcriptional regulatory element.
Transcriptional regulation is tightly coupled with chromosomal positioning and three-dimensional chromatin architecture. However, it has been unclear what proportion of transcriptional activity is reflecting such organisation, how much can be informed by RNA expression alone, and how this organisation impacts disease. To this end, we have developed a transcriptional decomposition approach to separate the proportion of expression associated with genome organisation from independent effects not directly related to genomic positioning. We have shown that positionally attributable expression accounts for a considerable proportion of total levels and is highly informative of topological associating domain activities and organisation, revealing boundaries and chromatin compartments. Furthermore, using expression data alone we can accurately predict individual enhancer-promoter interactions, drawing features from expression strength, stabilities, insulation and distance. We have further characterised commonalities and differences across predictions in 76 human cell types, which allowed us to observe extensive sharing of domains, yet highly cell-type specific enhancer-promoter interactions and strong enrichments in relevant trait-associated variants. We have further applied this approach to investigate individual variation in regulatory activities and their associated chromatin architectures across a panel of genotyped human individuals. Our work demonstrates a close relationship between transcription and chromatin architecture, presenting a novel strategy and an unprecedented resource for investigating regulatory organisations and interpretations of disease associated genetic variants across cell types.
We have further investigated the role of regulatory elements in DNA replication and cell fates and answered an outstanding question in the field: how maintenance of chromatin epigenetic marks (histone modifications) are maintained during replication. Our work reveals regulatory elements as sites prone to sister chromatid histone modification asymmetry.
