Eukaryotic Transcription

Please excuse me if the material is slightly long or beyond the scope of MCAT. But, I think, this should summarize most of eukaryotic transcription. For the purposes of this post, I’m only going to summarize RNA pol II (mRNA synthesis) mediated transcription. RNA pol I regulates rRNA synthesis and Pol III regulates 5s RNA and tRNA synthesis.

The mechanism of gene transcription by RNA pol II follows 3 general steps, initiation, elongation and termination. These 3 steps are followed by RNA processing.
Initiation
In eukaryotes initiation is regulated by the presence of regulatory regions, promoters and enhancers. Common promoter elements are the TATA and CCAAT boxes, found upstream of the transcription start site. Enhancers can be found upstream, downstream, or within the coding region
Promoters are recognized by basal transcription factors and are necessary for initiating transcription, while enhancers, as the name suggests are necessary for enhancing transcription and also for regulating and mediating cell and tissue specific transcription.
The basal transcription factors (TFs) such as TFIID, along with other TFs, recruit RNA pol II to the promoter element and initiate basal transcription.
Other enhancer elements and TFs mediate higher levels of transcription.
Elongation
During elongation, RNA pol II moves along the DNA, close to the bubble that represents separation of the two strands of DNA. As the enzyme moves forward along the bubble, RNA is synthesized in the 5’ to 3’ direction. DNA ahead of the bubble is unwound and behind it is rewound. Elontation continues until the enzyme reaches a termination point.
Termination
If I may, termination in eukaryotic genes is not very specific. Pol II continues to transcribe RNA for a few thousand (1000-2000) bases past the end of the mature mRNA. The exact end is determined during RNA processing.
Processing
RNA processing is characterized by capping at the 5’ end, polyadenylation at the 3’ end and intron splicing.
5′ Capping
A methylated guanine nucleotide is added to the 5’ end of the mRNA in a 5’ to 5’ phosphodiester linkage. This capping is essential for mRNA recognition by ribosomes during translation.
3′ Polyadenylation
A polyadenylation signal (AUAAA) is present in most of the mRNA transcripts and this signal is reconized by an enzyme that cleaves the transcript about 20 nucleotides downstream and adds a series of As (~200) to the 3’ end. These As are added without the need for a template and prevent the mRNA from degradation.
Splicing
Removal of the introns from the pre-mRNA to yield mature mRNA is called splicing. Splicing is carried out by spliceosomes that contain at least 5 known small nucleotide ribonucleoproteins (snRNPs). These snRNPs contain small nuclear RNAs (snRNAs) and together they detect intron/exon boundaries and cleave the RNA at those specific junctions. The spliced RNA is then joined together to form the mature mRNA transcript.

Salient points of eukaryotic mRNA transcription:
1) occurs in 5’ to 3’ direction
2) mRNA synthesis regulated by RNA pol II
3) mRNA synthesis involves initiation, elongation and termination followed by processing to make the mature transcript.
4) Initiation is mediated by promoters and enhancers, and elongation by the RNA pol II. Termination in eukaryotes occurs way downstream and is not very specific, unlike in prokaryotes.
5) mRNA processing to produce the mature trancript involves 5’ capping, 3’ polyadenylation and intron splicing.