Transcription in Eukaryotes

Transcription is how cells make RNA using DNA as a guide. In eukaryotes, it happens inside the nucleus. The RNA either helps build proteins or has other important functions. RNA may

Act as messenger RNA (mRNA) for protein synthesis
Function as structural and regulatory RNAs such as rRNA, tRNA, snRNA, etc

This process includes starting (initiation), growing the RNA strand (elongation), and finishing (termination). It’s generally more complicated than in simpler organisms.

RNA Polymerases in Eukaryotes

Eukaryotic cells use three types of RNA polymerase enzymes:

RNA Polymerase I - transcribes 28S, 18S, and 5.8S rRNA genes.
RNA Polymerase II - transcribes pre-mRNA and most snRNA genes
RNA Polymerase III - transcribes tRNA, 5S rRNA, and U6 snRNA genes.

Each RNA polymerase is a large multi-subunit enzyme complex. It consists of 12 core subunits along with additional associated factors. They operate in different nuclear regions and transcribe different gene types.

RNA Polymerase II is responsible for producing mRNA.

Initiation Phase

Initiation begins at a promoter region, often containing a TATA box. This box is located about 25–35 base pairs upstream from the start site.

RNA Polymerase II can’t bind DNA without help from general transcription factors. The key transcription factors include TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH.

TFIID binds through its subunit called TBP (TATA-binding protein). The other factors assemble step-by-step to form the initiation complex.

TFIIH unwinds the DNA using ATP and phosphorylates the polymerase. This allows RNA Polymerase II to break free and begin elongation.

Elongation Phase

RNA Polymerase II moves along the template DNA strand (3′ to 5′ direction). It adds RNA nucleotides in the 5′ to 3′ direction of the new strand.

The enzyme forms a transcription bubble by unwinding about 17 base pairs. At any given time, about 8–9 RNA nucleotides remain base-paired to the DNA template within the bubble.

Behind the bubble, the DNA rewinds and RNA detaches from the template.

Eukaryotic DNA is tightly packed into nucleosomes, which are made of histone proteins.

This wrapping slows down the transcription process.

A protein called FACT helps RNA Polymerase II move through nucleosomes. FACT removes H2A–H2B dimers from histones ahead of the polymerase.

After transcription passes, FACT helps restore the nucleosome structure. This process allows transcription to continue without permanently altering chromatin.

3. Termination Phase

Termination works differently for the three types of RNA polymerase:

RNA Polymerase I - terminates transcription with the help of transcription termination factor-1 (TTF-1) in mammals.
RNA Polymerase III - terminates when it encounters a stretch of thymidines (T) in the DNA template (results in a string of uracils (U) in the RNA).
RNA Polymerase II has no fixed stop signal in the DNA.

In Polymerase II, RNA is cleaved after a polyadenylation signal (AAUAAA). Proteins CPSF and CstF bind the signal and the nearby GU-rich region.

The RNA is then cut 10–30 nucleotides downstream from the AAUAAA site. The free RNA is processed as pre-mRNA or hnRNA.

A 5′ exonuclease called Xrn2 digests leftover RNA still being transcribed. When Xrn2 catches up to RNA Polymerase II, it ends transcription.

Post-Transcriptional Processing

Eukaryotic pre-mRNA is not ready for translation without modification:

A 5′ cap of 7-methylguanosine (7mG) is added.
A poly-A tail is added at the 3′ end.
Splicing removes introns and joins exons using the spliceosome, a complex of snRNPs and proteins that requires ATP.
Other nucleotide modifications like methylation and deamination may occur.

This turns the primary transcript into a functional mRNA molecule.

Importance of Eukaryotic Transcription

In cells, transcription controls gene activity.
It makes proteins when needed. The process is precise and well-regulated.
Transcription helps in development, stress handling, and fighting disease.

Summary

The cell’s nucleus of an eukaryote is the site of transcription. Three RNA polymerases (Pol I, Pol II, Pol III) help make different classes of RNA in eukaryotes. RNA Polymerase II reads DNA to make mRNA. The mRNA gets modified through capping, splicing, etc.

Frequently Asked Questions (FAQs)

Q1. What is the main function of RNA Polymerase II?

A. RNA Polymerase II makes messenger RNA (mRNA). mRNA carries instructions to make proteins.

Q2. What is a promoter region in transcription?

A. A promoter is a DNA sequence where general transcription factors come together along with RNA Polymerase II. It signals the start site for RNA synthesis.

Q3. What is the purpose of adding a 5′ cap to mRNA?

A. The 5′ cap protects mRNA from damage. It also helps mRNA leave the nucleus for protein making.