Eukaryotic transcription
Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher order chromatin structures.
[1] More abundantly made are the so-called non-coding RNAs account for the large majority of the transcriptional output of a cell.
The transcription of rRNA genes takes place in a specialised structure of the nucleus called the nucleolus,[5] where the transcribed rRNAs are combined with proteins to form ribosomes.
[8] Crystal structures of RNA polymerases I[9] and II[10] provide an opportunity to understand the interactions among the subunits and the molecular mechanism of eukaryotic transcription in atomic detail.
[11] Long and structurally disordered, the CTD contains multiple repeats of heptapeptide sequence YSPTSPS that are subject to phosphorylation and other posttranslational modifications during the transcription cycle.
[1] Pol II-transcribed genes contain a region in the immediate vicinity of the transcription start site (TSS) that binds and positions the preinitiation complex.
[1] These factors typically have DNA-binding domains that bind specific sequence elements of the core promoter and help recruit RNA polymerase to the transcriptional start site.
General transcription factors for RNA polymerase II include TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH.
The next proteins to enter are TFIIA and TFIIB, which stabilize the DNA-TFIID complex and recruit Pol II in association with TFIIF and additional transcription factors.
One of the last transcription factors to be recruited to the preinitiation complex is TFIIH, which plays an important role in promoter melting and escape.
[17] For pol II-transcribed genes, and unlike bacterial RNA polymerase, promoter melting requires hydrolysis of ATP and is mediated by TFIIH.
Throughout abortive initiation cycles, RNA polymerase remains bound to the promoter and pulls downstream DNA into its catalytic cleft in a scrunching-kind of motion.
[1] The polymerase breaks its interactions with the promoter elements and any regulatory proteins associated with the initiation complex that it no longer needs.
[1] The former removes the incorrectly inserted ribonucleotide by a simple reversal of the polymerization reaction, while the latter involves backtracking of the polymerase and cleaving of a segment of error-containing RNA product.
Elongation factor TFIIS (InterPro: IPR006289; TCEA1, TCEA2, TCEA3) stimulates an inherent ribonuclease activity in the polymerase, allowing the removal of misincorporated bases through limited local RNA degradation.
[32] Promoter-proximal pausing during early elongation is a commonly used mechanism for regulating genes poised to be expressed rapidly or in a coordinated fashion.
Further phosphorylation of Ser-2 causes recruitment of the RNA splicing machinery that catalyzes the removal of non-coding introns to generate mature mRNA.
Just as with 5’-capping and splicing, the CTD tail is involved in recruiting enzymes responsible for 3’-polyadenylation, the final RNA processing event that is coupled with the termination of transcription.
Through a yet unknown mechanism, the 3’-end of the transcript is cleaved, generating a large primary rRNA molecule that is further processed into the mature 18S, 5.8S and 28S rRNAs.
The Pol III termination signal consists of a stretch of thymines (on the non template strand) located within 40 bp downstream from the 3' end of mature RNAs.
[1][38] Because eukaryotic genome is wrapped around histones to form nucleosomes and higher-order chromatin structures, the substrates for transcriptional machinery are in general partially concealed.
Transcription initiation is regulated by cis-acting elements (enhancers, silencers, isolators) within the regulatory regions of the DNA, and sequence-specific trans-acting factors that act as activators or repressors.
Nucleosome histone modifications could also be inherited during cell division, however, it is not clear whether it can work independently without the direction by DNA methylation.
Multiple activators can work together, either by recruiting a common or two mutually dependent components of the transcriptional machinery, or by helping each other bind to their DNA sites.
[1] These interactions can synergize multiple signaling inputs and produce intricate transcriptional responses to address cellular needs.
Repressors can indirectly repress transcription by recruiting histone modifiers (deacetylases and methylases) or nucleosome remodeling enzymes that affect the accessibility of the DNA.
[1] Repressing histone and DNA modifications are also the basis of transcriptional silencing that can spread along the chromatin and switch off multiple genes.
TFIIH causes a conformational change in the polymerase, to expose the transcription bubble trapped inside, in order for the DNA repair enzymes to gain access to the lesion.
[48] Thus, RNA polymerase serves as damage-sensing protein in the cell to target repair enzymes to genes that are being actively transcribed.
For instance, in eukaryotes the genetic material (DNA), and therefore transcription, is primarily localized to the nucleus, where it is separated from the cytoplasm (in which translation occurs) by the nuclear membrane.
