Transcription is the first step in the process of gene expression, in which an enzyme RNA polymerase (RNA Pol) copies a particular segment of DNA into RNA (especially mRNA) to produce a functional unit called protein. The polymerases are large enzymes formed with a dozen of subunits, which are complexed with other factors called as transcription factors, which usually helps in signaling the gene which is to be transcribed. During transcription, a single strand of DNA template is used to synthesis a complementary strand of RNA. Basically, The RNA polymerase read the 3’ to 5’ DNA template to produce a 5’ to 3’ RNA by adding new nucleotide in the 3’-end of the RNA, which is being synthesized.
Transcription of the gene takes place in three steps: initiation, elongation and termination
1) Initiation: RNA polymerase attaches to a specific sequence of DNA called the promoter region usually found near the beginning of a gene but sometimes can also be seen in the end of a gene. Each gene (group of genes, in bacteria) has its own promoter. Once bound, RNA polymerase separates the DNA strands, providing the single-stranded template needed for transcription.
2) Promoter region: In prokaryotes, the promoter region is completely defined unlike eukaryotes. The promoter region in the bacteria has two specific region called as -10 region or Pribnow box and a -35 TTGCCA region upstream from the transcription start site (+1 in the DNA). The RNA polymerase bound this region in the promoter and unwinds the DNA for transcription.
In eukaryotes, the promoter region has a specific region called as TATA box like region at -10 upstream, which are recognized by various transcription factors, and thus signaling the RNA polymerase to bind with the specific region, a number of transcription factors, and one of these, TFIID, recognizes the TATA box and ensures that the correct start site is used for binding to the promoter and another cofactor, TFIIB, which recognizes a different common consensus sequence TTGCCA in -35 upstream of the initiation point. The “TATA box” is composed of 5’- TATAAT-3’ nucleotide, which becomes easy for the polymerase to separate the two strand as “AT” bond is comparatively weaker then the “GC” bond.
Enhancer sequences are regulatory DNA sequences that, which binds with specific proteins called transcription factors to enhance the transcription of the associated gene. The enhancer could be present in thousands of nucleotide away from the promoter region but are brought into close proximity with the promoter by looping due to interaction between the proteins binding to the promoter and enhancer. The proteins which promote the gene transcription are called as Activators and the proteins which inhibit this are called as Repressor.
2) Elongation : As the transcription get initiated, the DNA double strand get unwind and RNA polymerase read the template strand of the DNA by adding nucleotide complementary to the template strand nucleotide in the 3’-end of the growing nucleotide chain.
The RNA transcript is almost identical to the coding strand of the DNA, except in place of thymine (T) the rna has uracil (U)
3) Termination : Terminator sequences are found close to the ends of template sequence. There are two types of termination strategies found in bacteria: Rho-dependent and Rho-independent.
a) In rho-independent terminators, as the RNA polymerase reaches the end, it transcribe a GC rich region or inverted repeat sequences, which are then fold back on themselves in hairpin loops, thus causing RNA polymerase to pause and resulting in release of the transcript.
In eukaryotes, termination of transcription depends upon the polymerase utilized.
For pol I, transcription is stopped using a termination factor similar to the rho-dependent termination in bacteria.
Transcription of genes by the pol III ends after transcribing a termination sequence that includes a polyuracil stretch resembling a hairpin loop formation like rho-independent prokaryotic termination.
Transcription of genes by the pol II can continue for thousands of nucleotides beyond the non-coding sequence. The RNA strand is detached by cleaving with a complex protein associated with the polymerase. Cleavage occurs when a mature RNA pol II polyadenylated the mRNAs at the 3′-end, resulting in a poly(A) tail, this process helps in cleavage and thus termination.
- What is the difference between a coding strand and a template strand?
- Which of the following enzymes are involved in the transcription?
a) RNA polymerase
b) DNA polymerase
c) DNA polymerase I
d) DNA Topoisomerase
- What is the nucleotide sequence for the TATA box?
- How does transcription help in gene expression?
- Explain Rho-independent termination.