Enhancers, which are specific DNA sequences, play a role in increasing the initiation rate of transcription by RNA polymerase II. They are typically found on the same chromosome as the gene they stimulate. Enhancers can be located upstream or downstream of the transcription start site, and they can be close to or far away from the promoter. Additionally, enhancers can occur on either strand of the DNA. These enhancers contain response elements that bind STF. By bending or looping the DNA, STF can interact with other transcription factors bound to the promoter and with RNA polymerase II, thus promoting transcription. Mediator also binds enhancers. It's worth noting that silencers, similar to enhancers, can act over long distances but actually reduce gene expression.

The α-Amanitin toxin, produced by the poisonous mushroom Amanita phalloides, is an inhibitor of RNA polymerase II. It tightly binds to RNA polymerase II, slowing its movement and inhibiting mRNA synthesis.

RNA polymerase III is responsible for synthesizing tRNA, 5S rRNA, and some snRNA and snoRNA.

The primary transcript is the initial RNA copy of a transcription unit, which is the segment of DNA between specific initiation and termination sequences. Ribonucleases posttranscriptionally modify the primary transcripts of both prokaryotic and eukaryotic tRNA and rRNA by cleaving the original transcripts. tRNA molecules are further modified to contribute to the unique identity of each species. On the other hand, prokaryotic mRNA is generally identical to its primary transcript, while eukaryotic mRNA undergoes extensive modifications both during and after transcription.

Both prokaryotic and eukaryotic rRNA are generated from long precursor molecules known as pre-rRNA. Prokaryotes produce the 23S, 16S, and 5S rRNA from a single pre-rRNA molecule, while eukaryotes produce the 28S, 18S, and 5.8S rRNA. These pre-rRNA molecules are cleaved by ribonucleases to produce intermediate-sized pieces of rRNA, which are further processed by trimming and modification at certain bases and riboses to obtain the required RNA species.

Both eukaryotic and prokaryotic tRNA are made from longer precursor molecules that require modification. Sequences at both ends of the molecule are removed, and introns present in the anticodon loop are removed by nucleases. Additional posttranscriptional modifications include the addition of a -CCA sequence at the 3' terminal end of tRNA and modification of specific bases to produce the unique bases found in tRNA.

Heterogeneous nuclear RNA (hnRNA) refers to the collection of all primary transcripts synthesized in the nucleus by RNA polymerase II. The premRNA components of hnRNA undergo extensive co- and posttranscriptional modifications in the nucleus to become mature mRNA. These modifications are usually facilitated by the recruitment of proteins by RNA polymerase II itself.
d. Role of enhancers: Enhancers are special DNA sequences that increase the rate of initiation of transcription by RNA pol II. Enhancers are typically on the same chromosome as the gene whose transcription they stimulate (Fig. 31.13B). However, they can 1) be located upstream (to the 5′-side) or downstream (to the 3′-side) of the transcription start site, 2) be close to or thousands of base pairs away from the promoter (Fig. 31.14), and 3) occur on either strand of the DNA. Enhancers contain DNA sequences called response elements that bind STF. By bending or looping the DNA, STF can interact with other TF bound to a promoter and with RNA pol II, thereby stimulating transcription (see Fig. 31.13B). Mediator also binds enhancers. [Note: Although silencers are similar to enhancers in that they also can act over long distances, they reduce gene expression.] e. RNA polymerase II inhibitor: α-Amanitin, a potent toxin produced by the poisonous mushroom Amanita phalloides (sometimes called the “death cap”), binds RNA pol II tightly and slows its movement, thereby inhibiting mRNA synthesis.
3. RNA polymerase III: This enzyme synthesizes tRNA, 5S rRNA, and some snRNA and snoRNA.
V. POSTTRANSCRIPTIONAL MODIFICATION OF RNA
A primary transcript is the initial, linear, RNA copy of a transcription unit (the segment of DNA between specific initiation and termination sequences). The primary transcripts of both prokaryotic and eukaryotic tRNA and rRNA are posttranscriptionally modified by cleavage of the original transcripts by ribonucleases. tRNA are further modified to help give each species its unique identity. In contrast, prokaryotic mRNA is generally identical to its primary transcript, whereas eukaryotic mRNA is extensively modified both co-and posttranscriptionally.
A. Ribosomal RNA rRNA of both prokaryotic and eukaryotic cells are generated from long precursor molecules called pre-rRNA. The 23S, 16S, and 5S rRNA of prokaryotes are produced from a single pre-rRNA molecule, as are the 28S, 18S, and 5.8S rRNA of eukaryotes (Fig. 31.15). [Note: Eukaryotic 5S rRNA is synthesized by RNA pol III and modified separately.] The prerRNA are cleaved by ribonucleases to yield intermediate-sized pieces of rRNA, which are further processed (trimmed by exonucleases and modified at some bases and riboses) to produce the required RNA species. [Note: In eukaryotes, rRNA genes are found in long, tandem arrays. rRNA synthesis and processing occur in the nucleolus, with base and sugar modifications facilitated by snoRNA.]
B. Transfer RNA
Both eukaryotic and prokaryotic tRNA are also made from longer precursor molecules that must be modified (Fig. 31.16). Sequences at both ends of the molecule are removed, and, if present, an intron is removed from the anticodon loop by nucleases. Other posttranscriptional modifications include addition of a –CCA sequence by nucleotidyltransferase to the 3′terminal end of tRNA and modification of bases at specific positions to produce the unusual bases characteristic of tRNA (see p. 291).
C. Eukaryotic messenger RNA
The collection of all the primary transcripts synthesized in the nucleus by RNA pol II is known as heterogeneous nuclear RNA (hnRNA). The premRNA components of hnRNA undergo extensive co-and posttranscriptional modification in the nucleus and become mature mRNA. These modifications usually include the following. [Note: Pol II itself recruits the proteins required for the modifications.] 1.