Eukaryotic Transcription Overall, the process of RNA synthesis in eukaryotes is similar to that of prokaryotes. There are some real differences, however. For one thing, initial transcripts in eukaryotes contain introns, which must be removed after transcription (this will be examined later). Eukaryotes also have three RNA polymerases, instead of just one. Each of these polymerases transcribes a different class of genes, as outlined in the table below: Our consideration of eukaryotic transcription will focus on genes transcribed by RNA polymerase II (known as class II genes). As with prokaryotes, the transcription process can be broken down into the steps of initiation, elongation, and termination. In eukaryotes, there is also the additional step of RNA processing, which occurs during and after transcription. Initiation Initiation in eukaryotes is much more complex than it is in prokaryotes. Eukaryotic genes must be much more carefully regulated, because many genes are only expressed in specific cells or tissues at specific times in the organism\'s life. To achieve this careful regulation, eukaryotes have evolved a more complicated initiation scheme than prokaryotes. In addition to promoters, eukaryotic genes also have regulatory regions called enhancers. Both elements (promoter and enhancer) are required for full, correct expression of eukaryotic genes. As a result of this added complexity, eukaryotic RNA polymerases do not have anything equivalent to the sigma subunit found in prokaryotic RNA polymerases. Instead, eukaryotes have groups of transcription factors, which are proteins, independent of the RNA polymerases, that recognize promoter and enhancer sequences. Eukaryotic promoters, like prokaryotic promoters, contain conserved sequences that are important for initiation. (Eukaryotes, because of their added complexity, tend to have more conserved sequences in their promoters than do prokaryotes.) One important sequence in most eukaryotic promoters is found around -30, and has the sequence TATAAA (or something close to it). This promoter element, known as the TATA Box, is analogous to the -10 element in prokaryotes. Other promoter sequences vary from gene to gene, but a common one is GGCCAATCT, otherwise known as the CCAAT Box (for the central bases in the sequence), which tends to occur around -80. A group of basal transcription factors helps to initiate transcription of class II genes. Each member of this group is named \"TFII\" for Transcription Factor, class II genes. The individual factors are assigned a separate letter designation. For example, TFIID, a factor made of multiple polypeptides, recognizes and binds to the TATA box. This factor and the other factors (TFIIA, TFIIB, TFIIE, TFIIF, TFIIH, and TFIIJ) forms a complex on the DNA that recruits RNA polymerase II to the promoter, and promotes initiation of transcription. These transcription factors are sufficient to get a basal (minimal) level of transcription. Other transcription .

1. Eukaryotic Transcription
Overall, the process of RNA synthesis in eukaryotes is similar to that of prokaryotes. There are
some real differences, however. For one thing, initial transcripts in eukaryotes contain introns,
which must be removed after transcription (this will be examined later). Eukaryotes also have
three RNA polymerases, instead of just one. Each of these polymerases transcribes a different
class of genes, as outlined in the table below:
Our consideration of eukaryotic transcription will focus on genes transcribed by RNA
polymerase II (known as class II genes). As with prokaryotes, the transcription process can be
broken down into the steps of initiation, elongation, and termination. In eukaryotes, there is also
the additional step of RNA processing, which occurs during and after transcription.
Initiation
Initiation in eukaryotes is much more complex than it is in prokaryotes. Eukaryotic genes must
be much more carefully regulated, because many genes are only expressed in specific cells or
tissues at specific times in the organism's life. To achieve this careful regulation, eukaryotes
have evolved a more complicated initiation scheme than prokaryotes. In addition to promoters,
eukaryotic genes also have regulatory regions called enhancers. Both elements (promoter and
enhancer) are required for full, correct expression of eukaryotic genes. As a result of this added
complexity, eukaryotic RNA polymerases do not have anything equivalent to the sigma subunit
found in prokaryotic RNA polymerases. Instead, eukaryotes have groups of transcription factors,
which are proteins, independent of the RNA polymerases, that recognize promoter and enhancer
sequences.
Eukaryotic promoters, like prokaryotic promoters, contain conserved sequences that are
important for initiation. (Eukaryotes, because of their added complexity, tend to have more
conserved sequences in their promoters than do prokaryotes.) One important sequence in most
eukaryotic promoters is found around -30, and has the sequence TATAAA (or something close
to it). This promoter element, known as the TATA Box, is analogous to the -10 element in
prokaryotes. Other promoter sequences vary from gene to gene, but a common one is
GGCCAATCT, otherwise known as the CCAAT Box (for the central bases in the sequence),
which tends to occur around -80.
A group of basal transcription factors helps to initiate transcription of class II genes. Each
member of this group is named "TFII" for Transcription Factor, class II genes. The individual
factors are assigned a separate letter designation. For example, TFIID, a factor made of multiple
polypeptides, recognizes and binds to the TATA box. This factor and the other factors (TFIIA,
TFIIB, TFIIE, TFIIF, TFIIH, and TFIIJ) forms a complex on the DNA that recruits RNA
polymerase II to the promoter, and promotes initiation of transcription. These transcription

2. factors are sufficient to get a basal (minimal) level of transcription. Other transcription factors
binding to other promoter and enhancer elements are necessary for higher levels of transcription
(enhancers and their transcription factors will be addressed in the module on eukaryotic gene
regulation).
Elongation
Elongation in eukaryotes is just like in prokaryotes.
Termination
Termination in eukaryotes is quite different in eukaryotes than it is in prokaryotes. Eukaryotic
genes have no strong termination sequences like prokaryotes. Instead, RNA polymerase II
continues transcribing up to 1000 to 2000 nucleotides beyond where the 3' end of the mature
mRNA will be. The actual 3' end will be determined during RNA processing.
Processing
Eukaryotic class II transcripts are processed in order to produce the final mRNA. Processing of
the initial transcript includes capping, polyadenylation, and intron removal. Ribosomal and
transfer RNAs are also processed, but differently; they are neither capped nor polyadenylated.
Capping of the RNA occurs at the 5' end. A methylated guanine nucleotide is added to the
transcript in a 5' to 5' phosphodiester linkage (it's like a nucleotide added to the 5' end in the
backwards direction). This 'cap' is important for recognition of the mRNA by ribosomes during
translation.
Polyadenylation involves cleavage of the RNA to produce the proper 3' end, and addition of a
string of adenine nucleotides. The position of the 3' end is determined by a sequence within the
RNA itself. This sequence, AAUAAA, is known as the polyadenylation signal. When this signal
is recognized by the appropriate enzymes, the RNA is cleaved 10 to 30 nucleotides downstream
of the signal, and a series of adenine nucleotides is added. This polyadenylation is done without a
template - the As are simply added one after another to the 3' end of the RNA. This poly (A)
tail, which averages about 200 nucleotides in length, helps protect the RNA from degradation,
and plays other regulatory roles that are beyond the scope of our discussion.
Introns in some RNAs (particularly mitochondrial RNAs) are capable of self-splicing (or
autocatalytic splicing). In these splicing reactions, no protein enzyme is required - the enzyme
activity resides within the intron RNA itself! Such RNA enzymes are termed ribozymes. Class II
RNAs (pre-mRNAs) from most eukaryotes, however, do require protein enzymes to remove their
introns. The splicing of these RNAs is carried out by large protein/RNA complex called
spliceosomes. Spliceosomes are made up of five different snRNPs (pronounced 'snurps'; short
for small nuclear ribonucleoprotein), called U1, U2, U4, U5, and U6. Each snRNP consists of a
specific small nuclear RNA (snRNA) molecule complexed with protein. Spliceosomes are able
to detect intron/exon boundaries, cleave the RNA at the appropriate point, and join adjacent

3. exons together to produce the mature mRNA.
Transcription: Summary of Key PointsRNA Polymerase IGenes encoding ribosomal RNARNA
polymerase IIGenes encoding messenger RNARNA Polymerase IIIGenes encoding transfer
RNA
Solution
Eukaryotic Transcription
Overall, the process of RNA synthesis in eukaryotes is similar to that of prokaryotes. There are
some real differences, however. For one thing, initial transcripts in eukaryotes contain introns,
which must be removed after transcription (this will be examined later). Eukaryotes also have
three RNA polymerases, instead of just one. Each of these polymerases transcribes a different
class of genes, as outlined in the table below:
Our consideration of eukaryotic transcription will focus on genes transcribed by RNA
polymerase II (known as class II genes). As with prokaryotes, the transcription process can be
broken down into the steps of initiation, elongation, and termination. In eukaryotes, there is also
the additional step of RNA processing, which occurs during and after transcription.
Initiation
Initiation in eukaryotes is much more complex than it is in prokaryotes. Eukaryotic genes must
be much more carefully regulated, because many genes are only expressed in specific cells or
tissues at specific times in the organism's life. To achieve this careful regulation, eukaryotes
have evolved a more complicated initiation scheme than prokaryotes. In addition to promoters,
eukaryotic genes also have regulatory regions called enhancers. Both elements (promoter and
enhancer) are required for full, correct expression of eukaryotic genes. As a result of this added
complexity, eukaryotic RNA polymerases do not have anything equivalent to the sigma subunit
found in prokaryotic RNA polymerases. Instead, eukaryotes have groups of transcription factors,
which are proteins, independent of the RNA polymerases, that recognize promoter and enhancer
sequences.
Eukaryotic promoters, like prokaryotic promoters, contain conserved sequences that are
important for initiation. (Eukaryotes, because of their added complexity, tend to have more
conserved sequences in their promoters than do prokaryotes.) One important sequence in most
eukaryotic promoters is found around -30, and has the sequence TATAAA (or something close
to it). This promoter element, known as the TATA Box, is analogous to the -10 element in
prokaryotes. Other promoter sequences vary from gene to gene, but a common one is
GGCCAATCT, otherwise known as the CCAAT Box (for the central bases in the sequence),
which tends to occur around -80.

4. A group of basal transcription factors helps to initiate transcription of class II genes. Each
member of this group is named "TFII" for Transcription Factor, class II genes. The individual
factors are assigned a separate letter designation. For example, TFIID, a factor made of multiple
polypeptides, recognizes and binds to the TATA box. This factor and the other factors (TFIIA,
TFIIB, TFIIE, TFIIF, TFIIH, and TFIIJ) forms a complex on the DNA that recruits RNA
polymerase II to the promoter, and promotes initiation of transcription. These transcription
factors are sufficient to get a basal (minimal) level of transcription. Other transcription factors
binding to other promoter and enhancer elements are necessary for higher levels of transcription
(enhancers and their transcription factors will be addressed in the module on eukaryotic gene
regulation).
Elongation
Elongation in eukaryotes is just like in prokaryotes.
Termination
Termination in eukaryotes is quite different in eukaryotes than it is in prokaryotes. Eukaryotic
genes have no strong termination sequences like prokaryotes. Instead, RNA polymerase II
continues transcribing up to 1000 to 2000 nucleotides beyond where the 3' end of the mature
mRNA will be. The actual 3' end will be determined during RNA processing.
Processing
Eukaryotic class II transcripts are processed in order to produce the final mRNA. Processing of
the initial transcript includes capping, polyadenylation, and intron removal. Ribosomal and
transfer RNAs are also processed, but differently; they are neither capped nor polyadenylated.
Capping of the RNA occurs at the 5' end. A methylated guanine nucleotide is added to the
transcript in a 5' to 5' phosphodiester linkage (it's like a nucleotide added to the 5' end in the
backwards direction). This 'cap' is important for recognition of the mRNA by ribosomes during
translation.
Polyadenylation involves cleavage of the RNA to produce the proper 3' end, and addition of a
string of adenine nucleotides. The position of the 3' end is determined by a sequence within the
RNA itself. This sequence, AAUAAA, is known as the polyadenylation signal. When this signal
is recognized by the appropriate enzymes, the RNA is cleaved 10 to 30 nucleotides downstream
of the signal, and a series of adenine nucleotides is added. This polyadenylation is done without a
template - the As are simply added one after another to the 3' end of the RNA. This poly (A)
tail, which averages about 200 nucleotides in length, helps protect the RNA from degradation,
and plays other regulatory roles that are beyond the scope of our discussion.
Introns in some RNAs (particularly mitochondrial RNAs) are capable of self-splicing (or
autocatalytic splicing). In these splicing reactions, no protein enzyme is required - the enzyme
activity resides within the intron RNA itself! Such RNA enzymes are termed ribozymes. Class II

5. RNAs (pre-mRNAs) from most eukaryotes, however, do require protein enzymes to remove their
introns. The splicing of these RNAs is carried out by large protein/RNA complex called
spliceosomes. Spliceosomes are made up of five different snRNPs (pronounced 'snurps'; short
for small nuclear ribonucleoprotein), called U1, U2, U4, U5, and U6. Each snRNP consists of a
specific small nuclear RNA (snRNA) molecule complexed with protein. Spliceosomes are able
to detect intron/exon boundaries, cleave the RNA at the appropriate point, and join adjacent
exons together to produce the mature mRNA.
Transcription: Summary of Key PointsRNA Polymerase IGenes encoding ribosomal RNARNA
polymerase IIGenes encoding messenger RNARNA Polymerase IIIGenes encoding transfer
RNA