Lecture 18

Transcription
 Transcription

The synthesis of RNA molecules using

DNA strands as the templates so that
the genetic information can be
transferred from DNA to RNA.
 Similarity between
replication and transcription

• Both processes use DNA as the

template.
• Phosphodiester bonds are formed in
both cases.
• Both synthesis directions are from 5´
to 3´.
 Differences between
replication and transcription

replication transcription

template double strands single strand

substrate dNTP NTP

primer yes no

Enzyme DNA polymerase RNA polymerase

product dsDNA ssRNA

base pair A-T, G-C A-U, T-A, G-C

 Section 1

Template and Enzymes

• The whole genome of DNA needs to
be replicated, but only small portion
of genome is transcribed in response
to the development requirement,
physiological need and
environmental changes.
• DNA regions that can be transcribed
into RNA are called structural genes.
§1.1 Template

The template strand is the strand

from which the RNA is actually
transcribed. It is also termed as
antisense strand.
The coding strand is the strand
whose base sequence specifies the
amino acid sequence of the encoded
protein. Therefore, it is also called as
sense strand.
5' GCAGTACATGTC 3' coding
strand
3' CGTCATGTACAG 5' template
strand

transcription

5' GCAGUACAUGUC 3' RNA

 Asymmetric transcription
• Only the template strand is used for the
transcription, but the coding strand is
not.
• Both strands can be used as the
templates.
• The transcription direction on different
strands is opposite.
• This feature is referred to as the
asymmetric transcription.
5' 3'
3' 5'
Organization of coding information in
the adenovirus genome
§1.2 RNA Polymerase
• The enzyme responsible for the RNA
synthesis is DNA-dependent RNA
polymerase.
– The prokaryotic RNA polymerase is a
multiple-subunit protein of ~480kD.
– Eukaryotic systems have three kinds of
RNA polymerases, each of which is a
multiple-subunit protein and responsible
for transcription of different RNAs.
 Holoenzyme
The holoenzyme of RNA-pol in E.coli
consists of 5 different subunits: 2  
.


holoenzyme
core enzyme  


 RNA-pol of E. Coli

subunit MW function
Determine the DNA to be
 36512
transcribed

 150618 Catalyze polymerization

 155613 Bind & open DNA template

Recognize the promoter
 70263
for synthesis initiation
• Rifampicin, a therapeutic drug for
tuberculosis treatment, can bind
specifically to the  subunit of RNA-
pol, and inhibit the RNA synthesis.
• RNA-pol of other prokaryotic
systems is similar to that of E. coli in
structure and functions.
 RNA-pol of eukaryotes

RNA-pol I II III

5S rRNA
products 45S rRNA hnRNA tRNA
snRNA

Sensitivity
No high moderate
to Amanitin

Amanitin is a specific inhibitor of RNA-pol.

§1.3 Recognition of Origins
• Each transcriptable region is called
operon.
• One operon includes several structural
genes and upstream regulatory
sequences (or regulatory regions).
• The promoter is the DNA sequence that
RNA-pol can bind. It is the key point
for the transcription control.
 Promoter

regulatory
structural gene
sequences
5' 3'
promotor
RNA-pol
3' 5'
 Prokaryotic promoter

5' 3'
-50 -40 -30 -20 -10 1 10
3' 5'
-35
region -10 start
TTGACA region
AACTGT
TATAAT
ATATTA
(Pribnow box)

Consensus sequence
 Consensus Sequence

Frequency in 45 samples 38 36 29 40 25 30
37 37 28 41 29 44
• The -35 region of TTGACA sequence
is the recognition site and the
binding site of RNA-pol.
• The -10 region of TATAAT is the
region at which a stable complex of
DNA and RNA-pol is formed.
 Section 2

Transcription Process
 General concepts

• Three phases: initiation, elongation,

and termination.
• The prokaryotic RNA-pol can bind to
the DNA template directly in the
transcription process.
• The eukaryotic RNA-pol requires co-
factors to bind to the DNA template
together in the transcription process.
§2.1 Transcription of Prokaryotes

• Initiation phase: RNA-pol recognizes

the promoter and starts the
transcription.
• Elongation phase: the RNA strand is
continuously growing.
• Termination phase: the RNA-pol stops
synthesis and the nascent RNA is
separated from the DNA template.
a. Initiation

• RNA-pol recognizes the TTGACA

region, and slides to the TATAAT
region, then opens the DNA duplex.
• The unwound region is about 171 bp.
• The first nucleotide on RNA transcript
is always purine triphosphate. GTP is
more often than ATP.
• The pppGpN-OH structure remains on
the RNA transcript until the RNA
synthesis is completed.
• The three molecules form a
transcription initiation complex.

RNA-pol (2) - DNA - pppGpN- OH 3

• No primer is needed for RNA
synthesis.
• The  subunit falls off from the RNA-
pol once the first 3,5 phosphodiester
bond is formed.
• The core enzyme moves along the
DNA template to enter the elongation
phase.
b. Elongation

• The release of the  subunit causes

the conformational change of the
core enzyme. The core enzyme slides
on the DNA template toward the 3
end.
• Free NTPs are added sequentially to
the 3 -OH of the nascent RNA strand.
(NMP)n + NTP (NMP)n+1 + PPi
elongated
RNA strand substrate RNA strand
• RNA-pol, DNA segment of ~40nt and
the nascent RNA form a complex
called the transcription bubble.
• The 3 segment of the nascent RNA
hybridizes with the DNA template, and
its 5 end extends out the
transcription bubble as the synthesis
is processing.
Transcription bubble
RNA-pol of E. Coli
RNA-pol of E. Coli
 Simultaneous
transcriptions and
translation
c. Termination

• The RNA-pol stops moving on the

DNA template. The RNA transcript
falls off from the transcription
complex.
• The termination occurs in either  -
dependent or  -independent manner.
 The termination function of  factor

The  factor, a hexamer, is a ATPase

and a helicase.
 -independent termination

• The termination signal is a stretch of

30-40 nucleotides on the RNA
transcript, consisting of many GC
followed by a series of U.
• The sequence specificity of this
nascent RNA transcript will form
particular stem-loop structures to
terminate the transcription.
 rplL protein
DNA
5TTGCAGCCTGACAAATCAGGCTGATGGCTGGTGACTTTTTAGGCACCAGCCTTTTT... 3
5TTGCAGCCTGACAAATCAGGCTGATGGCTGGTGACTTTTTAGTCACCAGCCTTTTT... 3

RNA

UUUU...…

UUUU...…
 Stem-loop disruption
• The stem-loop structure alters the
conformation of RNA-pol, leading to
the pause of the RNA-pol moving.
• Then the competition of the RNA-
RNA hybrid and the DNA-DNA hybrid
reduces the DNA-RNA hybrid stability,
and causes the transcription
complex dissociated.
• Among all the base pairings, the
most unstable one is rU:dA.
§2.2 Transcription of Eukaryotes
a. Initiation
• Transcription initiation needs
promoter and upstream regulatory
regions.
• The cis-acting elements are the
specific sequences on the DNA
template that regulate the
transcription of one or more genes.
 Cis-acting element

cis-acting element
structural gene
GCGC CAAT TATA
exon intron exon

start
TATA box (Hogness box)

enhancer CAAT box

GC box
TATA box
 Transcription factors
• RNA-pol does not bind the promoter
directly.
• RNA-pol II associates with six
transcription factors, TFII A - TFII H.
• The trans-acting factors are the
proteins that recognize and bind
directly or indirectly cis-acting
elements and regulate its activity.
TF for eukaryotic transcription
 Pre-initiation complex (PIC)

• TBP of TFII D binds TATA

• TFII A and TFII B bind TFII D
• TFII F-RNA-pol complex binds TFII B
• TFII F and TFII E open the dsDNA
(helicase and ATPase)
• TFII H: completion of PIC
Pre-initiation complex (PIC)

RNA pol II

TF II F TF II E
TF II TBP TAF
TF II
A TATA B
TF II H DNA
 Phosphorylation of RNA-pol

• TF II H is of protein kinase activity to

phosphorylate CTD of RNA-pol. (CTD
is the C-terminal domain of RNA-pol)
• Only the p-RNA-pol can move toward
the downstream, starting the
elongation phase.
• Most of the TFs fall off from PIC
during the elongation phase.
b. Elongation

• The elongation is similar to that of

prokaryotes.
• The transcription and translation do
not take place simultaneously since
they are separated by nuclear
membrane.
 nucleosome

RNA-Pol

moving
direction

RNA-Pol

RNA-Pol
c. Termination

• The termination sequence is AATAAA

followed by GT repeats.
• The termination is closely related to
the post-transcriptional modification.
 Section 3

Post-Transcriptional
Modification
• The nascent RNA, also known as
primary transcript, needs to be
modified to become functional tRNAs,
rRNAs, and mRNAs.
• The modification is critical to
eukaryotic systems.
§3.1 Modification of hnRNA
• Primary transcripts of mRNA are called as
heteronuclear RNA (hnRNA).
• hnRNA are larger than matured mRNA by
many folds.
• Modification includes
– Capping at the 5- end
– Tailing at the 3- end
– mRNA splicing
– RNA edition
 a. Capping at the 5- end
OH OH
O
N
NH
O O O
O 5'
H2N N N H2C O P O P O P O CH2 N NH2
N
5' O
O O O
HN
N
O
CH 3
O OH
Pi
O P O AAAAA-OH 3'
O

m7GpppGp----
 ppp5'NpNp
removing
Pi phosphate group
pp5'NpNp
GTP forming 5'-5'
triphosphate group
PPi
G5'ppp5'NpNp

methylating at G7

7
m GpppNpNp
methylating at C2' of the
first and second
nucleotides after G
7
m Gpppm2'Npm2'Np
• The 5- cap structure is found on
hnRNA too.  The capping process
occurs in nuclei.
• The cap structure of mRNA will be
recognized by the cap-binding protein
required for translation.
• The capping occurs prior to the
splicing.
b. Poly-A tailing at 3 - end
• There is no poly(dT) sequence on the
DNA template.  The tailing process
dose not depend on the template.
• The tailing process occurs prior to the
splicing.
• The tailing process takes place in the
nuclei.
c. mRNA splicing

mRNA

DNA

The matured mRNAs are much shorter than

the DNA templates.
 Split gene

The structural genes are composed of

coding and non-coding regions that
are alternatively separated.

7 700 bp
L 1 2 3 4 5 6 7
A B C D E F G

A~G no-coding region 1~7 coding region

 Exon and intron

Exons are the coding sequences that

appear on split genes and primary
transcripts, and will be expressed to
matured mRNA.

Introns are the non-coding sequences

that are transcripted into primary
mRNAs, and will be cleaved out in the
later splicing process.
mRNA splicing
Splicing mechanism
lariat
Twice transesterification
intron

5'exon 3'exon
5' U pA G pU 3'

first transesterification
pG-OH
pGpA

5' U OH G pU 3'

second transesterification
5' pGpA

5' U pU 3'

GOH 3'
d. mRNA editing

• Taking place at the transcription

level
• One gene responsible for more than
one proteins
• Significance: gene sequences, after
post-transcriptional modification,
can be multiple purpose
differentiation.
 Different pathway of apo B

Human apo B
gene

hnRNA (14 500 base)

CAA to UAA
At 6666
liver
apo B100
intestine
（500 kD）
apo B48
（240 kD）
§3.2 Modification of tRNA
 Precursor transcription

DNA

TGGCNNAGTGC GGTTCGANNCC

RNA-pol III

tRNA precursor
Cleavage

RNAase P
endonuclease

ligase
Addition of CCA-OH

tRNA nucleotidyl
transferase

ATP ADP
 Base modification

1. Methylation
（2） （1） A→mA, G→mG
（1）
2. Reduction
U→DHU
3. Transversion
U→ψ
（3） 4. Deamination
（4） A→I
§3.3 Modification of rRNA

• 45S transcript in nucleus is the

precursor of 3 kinds of rRNAs.
• The matured rRNA will be assembled
with ribosomal proteins to form
ribosomes that are exported to
cytosolic space.
 rRNA

18S 5.8S 28S 45S-rRNA

transcription

splicing
18S-rRNA
5.8S and 28S-rRNA
§3.4 Ribozyme
• The rRNA precursor of tetrahymena
has the activity of self-splicing (1982).
• The catalytic RNA is called ribozyme.
• Self-splicing happened often for
intron I and intron II.
• Both the catalytic domain and the
substrate locate on the same
molecule, and form a hammer-head
structure.
• At least 13 nucleotides are conserved.
Hammer-head
 Significance of ribozyme

• Be a supplement to the central

dogma
• Redefine the enzymology
• Provide a new insights for the origin
of life
• Be useful in designing the artificial
ribozymes as the therapeutical
agents
 Artificial
ribozyme
• Thick lines:
artificial ribozyme
• Thin lines:
natural ribozyme
• X: consensus
sequence
• Arrow: cleavage
point