BIOL 2500 - Topic 2 (part 6)

Transcription termination

Transcription continues beyond the coding region, creating the 3’-UTR, which plays a part in how termination occurs

Two types of transcription terminations

1.) Factor-independent termination (does not require any type of protein helper)

2.) Rho-dependent termination (uses rho factor as a protein helper)

Factor-independent termination characteristics

1.) A GC rich stretch is transcribed, followed by an A-rich stretch on the template strand (which makes an U-rich stretch on the transcript)

2.) The GC strand forms a stem-loop, followed by the stretch of Us

How does factor-independent termination work

The presence of the stem-loop structure and U-rich stretch causes the RNA pol to dissociate from the DNA, thereby ending transcription

Rho-dependent termination characteristics

The rho factor recognizes and binds to a specific sequence on the transcript called the rut site, which is 50-90 bp rich in C’s and poor in G’s

Rho-dependent termination vs. factor-independent termination characteristics (apart from the fact that one uses a protein helper)

Rho-dependent termination does not have a string of U’s at the 3’ end, nor does it form a stem-loop structure

How does rho-dependent termination work

1.) The rut site is upstream where the RNA pol would pause

2.) Once the the rho factor is bound to the rut site, it travels towards the 3’ end until it bumps it to the RNA pol

3.) It then unwinds the last bit of DNA-RNA complementary base-pairing, allowing the RNA pol to dissociate

Difference in transcription in eukaryotes

1.) They have larger linear genomes, with more genes that are much further apart

2.) They have 3 different RNA pols

3.) Transcription takes place in the nucleus

4.) Eukaryotic DNA is packaged into chromatin along with associated proteins

Bacterial vs. eukaryotic genomes

Bacteria have a few thousands of genes, while eukaryotes have tens to thousands of genes, but have a lot more non-coding DNA

3 different RNA pols of eukaryotes

1.) RNA pol I —> most rRNA

2.) RNA pol II —> mRNA, miRNA, and some snRNA

3.) RNA pol III —> tRNA, 5S rRNA, and some snRNAs

Additional characteristics of eukaryotic RNA pols that bacteria do not have

1.) Several general transcription factors are needed, which bind to the DNA promoters

2.) It has carboxyl-terminal domains (CTDS), which are specialized regions on the RNA pol that coordinate RNA processing

Significance of eukaryotic transcription being in the nucleus

1.) This means the RNA needs to be processed first, before it can be exported

2.) mRNA that has not been processed yet is known as pre-mRNA

Eukaryotic DNA being packaged into chromatin

It makes the DNA much more tighter compared to the bacterial DNA, making it harder to access, which affects how initiation, elongation, and termination occurs

General transcription factors

They help bind the RNA pol to the DNA promoter regions

General transcription factors binding process (i.e. eukaryotic transcription initiation)

1.) TFIID + TBP binds to the TATA box, thereby forming the initial committed complex

2.) TFIIA, B, and F, along with the RNA pol, then also bind to the initial committed complex

3.) Finally, TFIIE and H binds to form the Preinitiation complex (PIC)

What happens after the PIC is formed

Transcription starts at the +1 nucleotide on the template strand

TATA box

A eukaryotic specific sequence in the promoter, -30 upstream of the +1 start site

TFIID

The TATA-binding protein, the first transcription factor to bind to the promoter, specifically the TATA box

General transcription factors binding

1.) TFIID + TBP (thinking about transcription)

2.) TFIIA, TFIIB, TFIIF + RNA pol (actually committed to transcription)

3.) TFIIE + TFIIH (can now perform transcription)