Question

Question 19: What sequences are important for the initiation of transcription in eukaryotes, and how does this compare to prokaryotic initiation? What sequence is important for the termination of transcription in eukaryotes, and how does this compare to prokaryotic termination? (There are very specific answers for each of these!)

Answer 1

Inititation of transcription: A promoter is a regulatory sequence or region of DNA, located upstream of a gene (towards 5' end). It provides a control for regulated gene transcription. A promoter has specific DNA sequences that bind to transcription factors, thus recruiting RNA polymerase which initiates mRNA synthesis from the coding region of the gene.

Sequences important for inititation of transcription in prokaryotes:

The promoter consists of two short sequences at -10 and -35 positions upstream from transcription start site

1. Sequence at -10 is called the Pribnow box and consists of 6 nucleotides TATAAT. (Absolutely essential to start transcription in prokaryotes)
2. Sequence at -35 usually consists of the 6 nucleotides TTGACA. (Its presence allows a very high transcription rate)

Sequences important for inititation of transcription in eukaryotes:

1. Unlike prokaryotes, eukaryotic promoters are extremely diverse and are difficult to characterize. They typically lie upstream of the gene and can have regulatory elements several kilobases away from the transcriptional start site.
2. In eukaryotes, the transcriptional complex can cause the DNA to bend back on itself allowing the placement of regulatory sequences far from the actual site of transcription.
3. Many eukaryotic promoters contain a TATA box (sequence TATAAA) which inturn binds a TATA binding protein which assists in the formation of RNA polymerase transcriptional complex
4. The TATA box typically lies very close to the transcriptional start site (often within 50 bases)

Termination of transcription:

Sequences important for termination of transcription in prokaryotes:

Two classes of transcription terminators, Rho-dependent and Rho- independent

1. Rho dependent transcription terminators: require a protein called Rho factor, which exhibits RNA helicase activity, to disrupt the mRNA-DNA-RNA polymerase transcriptional complex. They occur downstream of translational stop codons and consists of an unstructured, cytosine-rich sequence on mRNA known as Rho utilization site (rut) and a downstream transcription stop point (tsp)
2. Rho independent terminators: require formation of a self annealing hairpin structure on the elongating transcript, thus resulting in disruption of mRNA- DNA- RNA polymerase ternary complex.The terminator sequence in DNA contains a 20 basepair GC-rich region of dyad symmetry followed by a short poly-T tract or "T stretch" which is transcribed to form terminating hairpin and a 7-9 nucleotide "U tract respectively"

Sequences important for termination of transcription in eukaryotes:

Termination mechanism of transcription in case of eukaryotes is not completely known. It may be directed by the poly A signal or by the presence of termination sequence in the DNA or the terminator

1. Transcription of pre rRNA genes by RNA polymerase I is terminated by a mechanism that requires a polymerase specific termination factor
2. Purified RNA polymerase III terminates after polymerizing a series of U residues; unlike rho independent termination in Bacteria
3. In most protein coding genes, RNA polymerase II can terminate at multiple sites located over a distance of 0.5 to 2 kb beyond the poly(A) addition site