I will first briefly discuss our evolving understanding of transcriptional regulation, starting with proximal promoters to distal enhancers aided by chromatin structure. I will then summarize our recent work that exploits the current biological understanding of distal enhancers to better infer regulatory polymorphisms and how that can aid in a mechanism-based model for GWAS. Finally, especially relevant to the symposium, I will report unpublished work in the lab showing a substantial usage of distal CpG islands as an alternative promoter by genes whose proximal promoter is silenced via methylation. Time permitting, I will also present our observation of crowdsourcing of transcription factor occupancy in vivo aided by spatially clustered homotypic binding sites.
I will briefly go through the history of the CCAAT signal, as an important promoter element, and of the protein(s) that have been associated to it. I will focus on the NF-Y transcription factor, the major CCAAT binder, a trimer with Histone Fold Domain (HFD) subunits. I will discuss (i) the unique properties of sequence-specificity via NF-YA minor groove binding, coupled to histone/DNA interactions of the HFD dimer; (ii) the genomic locations, as per ENCODE, in relationship with its many partner TFs. I will then specifically report on the USF-NF-Y duo, in terms of spatial constraints of genomic sites, synergistic DNA-binding, cooperativity in transcriptional activation, matched by 3D visualization of interactions through a USF1 activation domain. Finally, I will go through the complexity of NF-Y complexes in plants, and detail a new complex composed of the HFDs and the NF-YA-like CCT protein CONSTANS (CO), conferring sequence-specificity to the trimer. I relate the deviance in the DNA matrix of the CO complex in terms of structural differences with NF-YA.
Analysis of changes in the epigenetic landscape using the ChIP-seq technique can show extremely useful to get insights into the mechanisms of cancer development and progression. In my talk, I will present our unpublished results on the analysis of epigenetic profiles of 22 neuroblastoma cell lines and tumors, where we characterized the most potent de novo super-enhancers and associated them with neuroblastoma development via the process of rewiring of the core transcriptional regulatory networks.