UCLA

The activation of tissue specific genes relies upon the precise orchestration of a number of events that result in the initiation of transcription upon lineage specification. This process is heavily dictated by the chromatin environment both at the promoter and distal sequences, as well as by the availability of transcription factors necessary for activation. A critical role is played at distal regulatory sequences, which often are the first sites to be engaged by key regulatory proteins. This interaction often promotes a chromatin environment that is necessary for the activation of the gene and results in the recruitment of additional sequence specific factors and a direct interaction with the promoter to initiate transcription. Understanding the properties of enhancer elements for tissue specific genes is important for a clear understanding of the mechanisms of activation. A number of studies have shown that enhancers are marked long before the activation of the gene takes place, in some cases as early as the embryonic stem cell stage. A detailed study described an unmethylated window within the enhancer of the Ptcra locus. Further analysis showed the enhancer mark to be regulated by sequence specific binding factors. These studies lacked the appropriate chromatin environment, which we know to be important. Here we use bacterial artificial chromosome containing the Ptcra locus to demonstrate that the enhancer mark persists in a chromatin context but is not regulated in the manner described in a non-native chromatin context. We then expand our studies to global tissue specific gene expression in order to understand more broadly the regulatory properties the define tissue specific genes. Parsing the mechanisms that drive tissue specific gene expression is critical for an understanding of pluripotency and tissue specificity. Here we use deep chromatin RNA-sequencing to accurately quantify the transcriptome of pluripotent stem cells and four primary differentiated cell types - E14.5 cortical neurons, CD4+ CD8+ thymocytes, bone marrow-derived macrophages and hepatocytes, in mouse. We define tissue specific genes with the broadest dynamic range in expression and define the chromatin properties at their promoters. Separating tissue specific genes with the largest dynamic range in expression allowed us to uncover cell type specific differences in the fundamental promoter properties.