This document discusses transcription and post-transcriptional modification. It begins by explaining the central dogma and gene expression. It then defines key terms like gene, transcription, RNA polymerase, template strand, and primary transcript. The document outlines the steps of transcription including initiation, elongation, and termination. It describes the transcription bubble and pre-initiation complex. Finally, it discusses post-transcriptional modification of primary transcripts, including 5' capping, 3' polyadenylation, splicing, and RNA editing. Prokaryotic and eukaryotic transcription are briefly compared.

1. TRANSCRIPTION &
POST
TRANSCRIPTIONAL
MODIFICATION
DR IFAT ARA BEGUM
Assistant Professor
(Biochemistry)
Dhaka Medical College, Dhaka

2. PART - I

3. CENTRAL DOGMA
It is an explanation of the flow of
genetic information within a
biological system
It was first stated by Francis
Crick in 1956
It deals with the detailed residue-
by-residue transfer of sequential
information.

5. CONTD
It may also be described as "DNA
makes RNA and RNA makes
protein”
It includes 3 main processes:
replication, transcription &
translation.

7. CONTD
Information cannot be transferred
back from protein to either protein
or nucleic acid.

8. GENE EXPRESSION
It is the process by which
information from a gene is used in
the synthesis of a functional gene
product.
These products are often proteins
But in non-protein coding genes
such as transfer RNA
(tRNA) or small nuclear RNA
(snRNA) genes, the product is a
functional RNA.

10. CONTD
So, there are 2 processes:
transcription & translation.
4 stages: Transcription, RNA
processing, RNA transport &
Translation.
Abnormalities in gene expression
can lead to diseases including
cancer

11. GENE
Unit of heredity / genetic
information
Defined as functional unit of DNA
consisting of coding region with its
regulatory sequences that carry
genetic information encoded within
the base sequence of coding region

12. CONTD
Regulatory sequence (transcription
control sequence): Promoter
sequence, terminator sequence,
enhancer and silencer
Regulatory sequence of gene is
flanked by leader sequence in 5’
end (5’ UTR) & trailer sequence in
3’ end (3’ UTR)

15. CONTD
Majority of gene are on
chromosome (nucleus), small
portion (37 gene) on naked loop of
mitochondrial DNA

16. TRANSCRIPTI
ON

17. DEFINITION
DNA directed RNA synthesis
which is the 1st
step in gene
expression

19. CONTD
During transcription, an RNA
polymerase reads a DNA
sequence and then produces
a complementary, antiparallel
RNA strand (primary
transcript).

20. CONTD
All eukaryotic cells have five
major classes of RNA:
i. Ribosomal RNA (rRNA)
ii.Messenger RNA (mRNA)
iii.Transfer RNA (tRNA)
iv. Small nuclear RNA (snRNA )
v. MicroRNA (miRNA).

21. CONTD
The first three are involved in
protein synthesis
 Remember, of them only mRNA
carries instruction for protein
synthesis (translation), as
genetic message is copied to
mRNA only.
 Other 2 RNA are not
translated, but help in
translation

22. CONTD
The small RNAs are involved
in mRNA splicing and
regulation of gene expression.
RIBOZYME
 Also called catalytic RNA
 These are enzymatically
active RNA molecule

23. CRITERIA OF
TRANSCRIPTION
Totally conservative process:
Because, RNA is synthesized
from parent DNA with total
conservation of parental DNA
duplex
Copying of DNA template always
occurs from 3’ to 5’ direction &
RNA synthesis occurs from 5’ to
3’ direction
No need of primer, but needs an
initiating nucleotide

24. CONTD
Asymmetric process: After
melting of parental dsDNA, only
one strand of DNA serves as
template for RNA synthesis
Highly selective process: Only
some selected portions of total
genome are copied to RNA

25. CONTD
Process of less fidelity with
high error rate : As RNAP has no
proof reading property,
transcription is a process of
less fidelity
Primary transcript needs
extensive post transcriptional
modification

26. REQUIREMENTS OF
TRANSCRIPTION
Activated NTP
Template strand (DNA template)
RNAP
RNAP associated protein &
enzymes: TATA binding protein ,
Transcription factors,
Topoisomerase
An initiating nucleotide (usually
a phosphoryl purine base like
PPP-G or PPP-A)
Magnesium ion
Manganese

27. TEMPLATE STRAND
A definite segment of ds DNA
contains gene (functional unit
of DNA consisting of coding
region with its regulatory
sequences that carry genetic
information encoded within the
base sequence of coding
region )

28. CONTD
i.e. DNA consists of one coding
strand where actually genetic
code lies in its base sequence
and one noncoding template
strand having base sequence
complementary to that of
coding strand

29. CONTD
 Coding strand synonym:
Sense strand / positive strand /
non-template strand
and
 Noncoding strand synonym:
antisense strand / anticoding
strand / noncoding strand /
template strand / negative
strand / transcribed strand

30. CONTD
Template strand of DNA may be
defined as the strand that is
transcribed or copied into an
RNA molecule

31. CONTD
The information in the template
strand is read out in the 3' to 5'
direction
And the sequence of
ribonucleotides in the RNA
molecule is complementary to
the sequence of deoxy
ribonucleotides in template
strand of the ds DNA molecule

32. CONTD
So finally, in the coding strand,
the sequence is same as that of
the sequence of nucleotides in
the primary transcript (with an
exception)

33. CONTD
With the exception of T for U
changes, coding strand
corresponds exactly to the
sequence of the RNA primary
transcript, which encodes the
(protein) product of the gene.

34. TRANSCRIPTION UNIT
The stretch of
DNA transcribed into an RNA
molecule is called
a transcription unit

35. CONTD
It may also be defined as the
segment of a gene between
promoter sequence & terminator
sequence which is transcribed

36. REMEMBER
Transcription unit includes the
signal for transcription
initiation, elongation &
termination

37. CONTD
A transcription unit in DNA
consists of the following
regions:
1) Zero or one promoter
2) A set of 1/more gene (exon
& intron)

38. TRANSCRIPTION START
SITE (TSS)
It is the 1st
nucleotide of a gene
to be transcribed
Designated as +1

39. CONTD
Nucleotide towards the 5’ end
(upstream) of TSS is designated
as minus (-)
Nucleotide towards the 3’ end
(downstream) of TSS is
designated as plus (+)
Nucleotide proceeding the TSS
(on 5’ direction) is denoted as
-1
All these designations of NTs
(+/-) refer to coding strand of
gene

40. PROMOTER SEQUENCE
It is the DNA sequence of a
gene, located towards the 5’
end of TSS of coding strand and
is needed for binding of RNAP &
TF to initiate transcription

41. CONTD
It determines the specificity of
gene transcription
Promoter sequence has 3
consensus sequences :
i. TATA box (-25 sequence): at 25
bases upstream of TSS
ii.GC box : at upstream of TSS
iii.CAAT box (-75 sequence): at 75
bases upstream of TSS

43. RNA POLYMERASE
Synonym: RNAP/ RNApol/ DNA
dependent RNA polymerase
It is an enzyme that produces
primary transcript RNA using
DNA genes as template
It polymerizes ribonucleotides
at the 3’ end of an RNA
transcript
Metalloenzyme ( contain 2 zinc
molecules)

44. CONTD
It initiates transcription at
promoters
Then it produces an RNA chain,
which is complementary to
template DNA strand

45. TYPES OF MAMMALIAN
DNA-DEPENDENT RNAP
Types of RNAP Functions
RNAP-I (A)
[nucleolus]
Transcribes rRNA
(28S, 18S & 5.8S)
RNAP-II (B)
[nucleoplasm]
Transcribes
mRNA, snRNA,
miRNA
RNAP-III (C)
[nucleoplasm]
Transcribes
tRNA, 5S rRNA

46. FUNCTIONS OF RNAP
Recognizes & binds with
promoter sequence of gene to
initiate transcription
Melting of dsDNA of gene to
expose single stranded
noncoding template DNA for
transcription
Polymerization of
ribonucleotides and synthesis of
RNA

47. CONTD
Recognizes terminator
sequences of gene to end
transcription
Regulates transcription rate by
interacting with activator &
repressor proteins

48. RNAP VS. DNAP
Points DNAP RNAP
Nucleic acid
synthesized
(5’->3’)
DNA RNA
Required
template
(copied 3’-
>5’)
DNA DNA
Required
substrates
dATP,
dGTP, dCTP,
dTTP
ATP, GTP,
CTP, UTP

49. CONTD
Points DNAP RNAP
Required
primer
RNA (or
DNA)
None
Proof
reading
activity (3’-
>5’
exonuclease)
Yes NO
Speed of
activity
High Low

50. TRANSCRIPTION BUBBLE
A transcription bubble is a
molecular structure that occurs
during the transcription of DNA
when a limited portion of the
DNA double strand is unwound.
RNA polymerase may then bind
to the exposed DNA and begin
synthesizing a new strand of
RNA.

51. TRANSCRIPTION BUBBLE
i.e. It may also be defined as
transiently melted DNA that
exposes ss DNA template for
binding of RNAP & to initiate
RNA synthesis .

53. CONTD
As RNAP moves, transcription
bubble also moves
As RNA grows longer, DNA
unwinds in the front & rewinds
at the back of the transcription
bubble

54. PRIMARY TRANSCRIPT
Immediate product of
transcription

55. CONTD
May be defined as single-
stranded RNA product,
synthesized by transcription of
DNA & processed
to yield various mature RNA
products such as
mRNAs, tRNAs, and rRNAs
It spans between the promoter
and terminator sequence
Primary transcripts of mRNA is
also known as hn mRNA or pre-
mRNA

56. CONTD
It consists of exons & introns
flanked by 5’ UTR & 3’ UTR
Its 5’ end corresponds to TSS
(+1)
The newly synthesized
primary transcripts are
modified in several ways to be
converted to their mature,
functional forms

59. PART - II

60. STEPS OF
TRANSCRIPTION
Transcription occurs in nucleus
& is divided into :
1.Formation of pre-initiation
complex & initiation of
transcription
2.Elongation of chain
3.Termination

61. INITIATION COMPLEX &
INITIATION OF
TRANSCRIPTION: ROLE
OF RNAP

62. CONTD
a) An RNA polymerase along with
the help of TBP & TF scans out
the promoter sequence of the
coding strand of the gene
& binds with it to form a closed
complex called the pre-
initiation complex
b) Melting of dsDNA (by RNAP)
exposes single strand non
coding template DNA (template
for transcription)

63. CONTD
c) Initiating nucleotide (PPP-G/A)
binds with RNAP
d) Transcription of 1st
nucleotide
(TSS) of the transcription unit
& there is beginning of
formation of nascent RNA

68. 2) ELONGATION OF CHAIN

69. CONTD
a) Transcription of the
subsequent nucleotides of the
transcription unit by RNAP
(starting from TSS) occurs.
 DNA template is read from 3’ to
5’ direction
 Growth of primary transcript
happens from 5’ to 3’ direction
by polymerization of
ribonucleotides

70. CONTD
b) Topological crisis (caused by
unwinding of dsDNA) is solved
by topoisomerase
c) Transcription progresses from
promoter sequence to
terminator sequence

72. 3) TERMINATION OF
TRANSCRIPTION

73. CONTD
a) RNAP recognizes the
terminator sequence
b) The dissociation of the
complete transcript (polarity &
base sequence of which is
same as that of coding strand
of DNA) and the release of RNA
polymerase from the template
DNA

74. POST
TRANSCRIPTIONAL
MODIFICATION OF
PRIMARY TRANSCRIPT

75. WHAT IS IT?
Also called Co-transcriptional
modification
A process in cell biology by
which, in eukaryotic
cells, primary transcript RNA is
converted into mature RNA.
A notable example is the
conversion of precursor
messenger
RNA into mature messenger
RNA (mRNA)

76. OF MESSENGER RNA
PROCESSING/
MODIFICATION
The pre-mRNA molecule
undergoes the following
modifications, which occur in
the cell nucleus before the RNA
is translated:
a.5' capping
b.3' polyadenylation
c.RNA splicing
d.RNA editing

78. 5' CAPPING
Done by addition of methyl
guanosine tri phosphate at 5’
end of pre-mRNA

79. CONTD
It protects mRNA from
degradation by exonuclease
It helps in the transport of
mRNA from nucleus to
cytoplasm
It increases the translation
efficiency by making mRNA to
be recognized easily by the
translational machineries

80. 3' POLYADENYLATION
Done by trimming at 3’ end
followed by addition of 40-350
A nucleotide

81. CONTD
It is catalyzed by poly-A-
polymerase
It protects mRNA from
degradation by exonuclease
It helps in the transport of
mRNA from nucleus to
cytoplasm
It increases the translation
efficiency by making mRNA to
be recognized easily by the
translational machineries

82. SPLICING
Introns are eliminated from
pre-mRNA which is followed by
binding together of exons

83. CONTD
After splicing , introns are
removed & destroyed in
nucleus
Done by SnRNP (small nuclear
RNA protein) & ScRNP (small
cytoplasmic RNA protein)
 SnRNP: Protein + SnRNA
 ScRNP: Protein +ScRNA
[SnRNP together with ScRNP
forms ribozyme]

84. CONTD
Ribozyme + hn mRNA =
Spliceosome
Spliceosome removes introns
from hn mRNA & splices
together the exons to make
uninterrupted genetic code

86. RNA EDITING
A molecular process through
which some cells can make
discrete changes to specific
nucleotide sequences within
a RNA molecule after it has
been generated by RNA
polymerase.
Relatively rare
Common forms of RNA
processing (e.g. splicing, 5'-
capping and 3'-polyadenylation)
are not usually included as

87. CONTD
Editing events may include the
insertion, deletion, and base
substitution of nucleotides
within the edited RNA molecule.
mRNA of apo B gene produces
apo B-100 (100 AA). Same gene
also produces apo B-48 (48 AA)
by RNA editing by changing the
49th
codon (CAA) of mRNA in to a
stop codon (UAA)

89. OF RIBOSOMAL RNA
PROCESSING/
MODIFICATION
The primary transcript of rRNA
is a big molecule composed of
3 units with sedimentation
coefficient of 45 S & it doesn’t
contain any intron
Later it is cleaved into 3
independent rRNAs (28 S, 5.8 S,
18 S)

91. OF TRANSFER RNA
PROCESSING/
MODIFICATION
The primary transcript of
tRNA is very large &
composed of multiple tRNA
Individual tRNA of primary
transcript is cleaved out to
make independent tRNA

92. CONTD
Phosphorylated guanosine is
added to 5’ end & CCA base
sequence to 3’ end of each
independent tRNA
Base modification to insert
some unusual bases like
pseudouridine

94. PROKARYOTIC
VERSUS
EUKARYOTIC
TRANSCRIPTION

95. Prokaryotic
Transcription
Eukaryotic
Transcription
Coupled
transcription-
translation process
occurs
Coupled
transcription-
translation process
doesn’t occur
Single type of RNAP
is required for
synthesis of all types
of RNA
Three different types
of RNAP is required
for synthesis of all
types of RNA

96. Prokaryotic
Transcription
Eukaryotic
Transcription
No need of any
transcription factor
for initiation
Transcription factor
is required for
initiation
Occurs in cytoplasm Occurs in nucleus

97. SIMILARITIES WITH
REPLICATION
The general steps of
initiation, elongation, and
termination
Synthesis of new strand
always occurs from 5’ to 3’
direction
Adherence to base-pairing
rules.

98. DIFFERENCES WITH
REPLICATION
POINTS REPLICATIO
N
TRANSCRIPTIO
N
Template Both strands
(whole genome
is copied)
Single strand
(small portion of
genome is
copied)
Primer Yes No
Enzyme DNAP RNAP
Substrate dNTP NTP

99. CONTD
POINTS REPLICATIO
N
TRANSCRIPTIO
N
Product dsDNA ssRNA
Base pair A-T, G-C A-U, T-A, G-C
Proof
reading
Yes No
Complem-
entary
base for
adenine
Thymine Uracil

100. CONTD
POINTS REPLICATIO
N
TRANSCRIPT
ION
Process in
terms of :
i)Fidelity
ii)Symmetry
iii)Selectivity
iv)Conservative
or not
High fidelity
Symmetric
Non-selective
Semi-
conservative
Less fidelity
Asymmetric
Highly
selective
Totally
conservative