RNA polymerase

RNA polymerase refers to an enzyme that catalyzes the formation of phosphodiester bonds and polymerizes a new mRNA molecule that is exactly complementary to the DNA strand used as a template.

Before RNA synthesis begins, RNAP II must pass through the promoter clearance phase, the transition between transcription initiation and elongation. During this phase, the protein composition of the complex that supports the polymerase undergoes massive remodeling. Most of the original transcription factors are released or left on the promoter, while new auxiliary proteins attach to the polymerase, forming the RNAPII transcript elongation complex. The elongation phase is mechanistically demanding, and RNAP only achieves a successful start if a stable elongation complex is formed and the first 8-9 bases are transcribed. Serine phosphorylation at the C-terminal domain of the RNA polymerase and histone modifications control the dynamic and changing composition of the transcriptional machinery as it moves along the gene body. During elongation, RNA polymerases must be processive, and once they start an RNA molecule, they must finish it without detaching from the template.

To ensure this basic necessity, the transcription machinery contains all the factors that allow the polymerase to overcome the physical barriers created by DNA supercoiling and its complex formation in nucleosomes, the main kinetic barrier to RNA polymerase progression in eukaryotes. Within genes, nucleosomes represent a barrier to both appropriate transcription and inappropriate initiation.

The cryo-electron microscopy structures of RNAP II-nucleosome complexes show that the enzyme is stuck at four different positions around the nucleosome, corresponding to the major histone-DNA contact sites. The accessible state of upstream chromatin can be progressively converted to repressive chromatin with the passage of the transcriptional machinery to avoid parasitic transcription starts that would negatively impact efficient and finely regulated gene expression programs. These processes involve extensive processing of histone tail modifications: transcription is regulated by the dynamic epigenetic marks, with erasers and modifiers acting together with the RNAP along the gene body.