There is accumulating evidence for a new gene expression paradigm, in which genes and transcription factors cooperate to create specialized nuclear hotspots (from here on called transcription bodies) optimized for transcription. How transcription bodies form, and how they impact transcription, however, is unclear. This is mostly because mechanistic and functional approaches have been limited by the large number of transcription bodies per nucleus, their small size, and their transient nature.
We take advantage of two transcription bodies that precede all other transcription during zebrafish embryogenesis. The hotspots are large, isolated, and relatively long-lived, and we can interfere with their formation specifically. They therefore provide an excellent opportunity to study transcription bodies. The stereotyped activation of transcription during embryogenesis further provides the opportunity to determine the effect of hotspots on gene expression.
In Aim 1, we will determine what triggers transcription body formation, identify the components of hotspots and the order in which they come together, and determine the enrichment of components in hotspots compared to nucleoplasm.
In Aim 2, we turn our attention to the genes in these hotspots. We will develop a method to visualize single copy genes live and use this to determine how genes come together in transcription hotspots to be activated.
Together, the work we propose will reveal how stable gene expression programs can emerge from the self-organizing interactions between chromatin, transcription factors and emergent properties of transcribed sites.
