Spatial organization of transcribed genes in mammalian cells

Knowledge pertaining to the fine molecular mechanisms of transcriptional activation and regulation, including co- and post-transcriptional processes, is rapidly expanding. Similarly, the importance of global genomic arrangement, illustrated by the spatial segregation of transcriptionally active euchromatin from inactive heterochromatin, is widely appreciated and studied. However, our knowledge regarding an intermediate level of transcriptional organization, relating to the spatial arrangement of individual transcribed genes, is surprisingly limited. 

This proposal describes my recent discovery of the phenomenon of Transcription Loops (TLs), structures formed by highly expressed and strongly decondensed genes with RNA polymerase II complexes moving along the gene axis. The phenomenon has been observed with two long genes, thyroglobulin and titin, expressed in thyrocytes and muscle cells, respectively. TLs dynamically change neighboring chromosomal loci by separating flanking sequences, modifying the structure of harboring chromosome territories and protruding into the nuclear space due to their intrinsic rigidity. I speculate that this rigidity is caused by a dense decoration of the gene axis with multiple elongating polymerases with attached voluminous nascent RNPs. The preliminary data obtained so far leads me to hypothesize that TL formation is one of the universal principles of eukaryotic gene expression that has not been appreciated until now due to the resolution limits of light microscopy and/or due to the low expression of studied genes.

To reinforce and demonstrate the generality of the above conclusions derived from the study of two genes, I plan to (i) search for more examples of TLs; (ii) experimentally inhibit or induce TLs of long genes; (iii) experimentally truncate long genes or elongate short genes thereby converting them into irresolvable or resolvable TLs, respectively; (iv) obtain more information about the fine structure of TLs on both microscopic and chromatin levels; and (v) elucidate the mechanisms of TL formation by building a polymer model based on parameters inferred from microscopy and Hi-C maps. In addition, since high thyroglobulin expression is essential for thyroid physiology and the phenomenon of the thyroglobulin TL is potentially important for medicine, I plan to further investigate the thyroglobulin TLs, performing an evolutionary study of the gene in other vertebrate groups and examining the possible regulation of thyroglobulin expression by T3/T4 hormones levels and mRNA regulation through intron retention. 

The project will (i) provide new insights into the spatial organization of expressed genes, (ii) elucidate the role of transcription in shaping the nuclear architecture, and (iii) present a new model for the spatial dynamics of transcription in eukaryotes.