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Regulation of
Transcription in
Eukaryotes
By,
Ishaque P.K
Biochemistry & molecular biology
Pondicherry university
•INTRODUCTION
•

•

•

•

•

Although the control of gene expression is far more complex in
eukaryotes than in bacteria.
The expression of eukaryotic genes is controlled primarily at
the level of initiation of transcription, although in some cases
transcription may be attenuated and regulated at subsequent
steps.
As in bacteria, transcription in eukaryotic cells is also
controlled by proteins that bind to specific regulatory sequences
and modulate the activity of RNA polymerase.
The intricate task of regulating gene expression in the many
differentiated cell types of multicellular organisms is
accomplished primarily by the combined actions of multiple
different transcriptional regulatory proteins.
In addition, the packaging of DNA into chromatin and its
modification by methylation impart further levels of complexity
to the control of eukaryotic gene expression.
•cis-ACTING REGULATORY SEQUENCES
•

Transcription in bacteria is regulated by the binding
of proteins to cis-acting sequences (e.g., the lac operator) that
control the transcription of adjacent genes.

•

Similar cis-acting sequences regulate the expression of eukaryotic
genes.

•

These sequences have been identified in mammalian cells largely
by the use of gene transfer assays to study the activity of
suspected regulatory regions of cloned genes.

•

Biologically active regulatory regions can thus be identified,
and in vitro mutagenesis can be used to determine the roles of
specific sequences within the region.
Identification of eukaryotic regulatory sequences
The regulatory sequence of a cloned eukaryotic gene is ligated to a
reporter gene that encodes an easily detectable enzyme. The
resulting plasmid is then introduced into cultured recipient cells
by
transfection.
An
active
regulatory
sequence
directs transcription of the reporter gene, expression of which is
then detected in the transfected cells.
•PROMOTERS AND ENHANCERS
•

•

•

•

Genes transcribed by RNA polymerase II have two
core promoter elements, the TATA box and the Inr sequence,
that serve as specific binding sites for general transcription
factors.
Other cis-acting sequences serve as binding sites for a wide
variety of regulatory factors that control the expression of
individual genes.
These cis-acting regulatory sequences are frequently, though
not always, located upstream of the TATA box.
For example, two regulatory sequences that are found in many
eukaryotic genes were identified by studies of the promoter of
the herpes simplex virus gene that encodes thymidine kinase.
•

Both of these sequences are located within 100 base pairs
upstream of the TATA box: Their consensus sequences are
CCAAT and GGGCGG (called a GC box).
Specific proteins that bind to these sequences and stimulate
transcription have since been identified.

A eukaryotic promoter
The promoter of the thymidine kinase gene of herpes simplex
virus contains three sequence elements upstream of the TATA
box that are required for efficient transcription: a CCAAT box
and two GC boxes (consensus sequence GGGCGG).
•

In contrast to the relatively simple organization of CCAAT and
GC boxes in the herpes thymidine kinase promoter, many
genes in mammalian cells are controlled by regulatory
sequences located farther away (sometimes more than 10
kilobases) from thetranscription start site.

•

These sequences, called enhancers, were first identified by
Walter Schaffner in 1981 during studies of the promoter of
another virus, SV40 .

•

In addition to a TATA box and a set of six GC boxes, two 72base-pair repeats located farther upstream are required for
efficient transcription from this promoter.

•

These sequences were found to stimulate transcription from
other promoters as well as from that of SV40, and, surprisingly,
their activity depended on neither their distance nor their
orientation with respect to the transcription initiation site.
The SV40 enhancer
The SV40 promoter for early gene expression contains
a TATA box and six GC boxes arranged in three sets of
repeated sequences. In addition, efficient transcriptionrequires
an upstream enhancer consisting of two 72-base-pair (bp)
repeats.
Action of enhancers
Without an enhancer,
the gene is transcribed at a
low basal level (A). Addition
of an enhancer, E for
example, the SV40 72-bp
repeats stimulates
the transcription. The
enhancer is active not only
when placed just upstream of
the promotor (B), but also
when inserted up to several
kbp either upstream or
downstream from the
transcription start site (C and
D). In addition, enhancers
are active in either the
forward or backward
orientation (E).
•

The ability of enhancers to function even when separated by long
distances from transcription initiation sites, like promoters,
function by binding transcription factors that then regulate RNA
polymerase.

•

This is possible because of DNA looping, which allows
a transcription factor bound to a distant enhancer to interact with
RNA polymerase or general transcription factors at the
promoter.
DNA looping
Transcription factors bound at distant enhancers are able to
interact with general transcription factors at the promoter because
the intervening DNA can form loops. There is therefore no
fundamental difference between the action of transcription factors
bound to DNA just upstream of the promoter and to distant
enhancers.
The binding of specific transcriptional regulatory proteins to
enhancers is responsible for the control of gene expression
during
development
and
differentiation,
the
immunoglobulin enhancer is active in lymphocytes, but not in
other types of cells. Thus, this regulatory sequence is at least
partly responsible for tissue-specific expression of the
immunoglobulin genes in the appropriate differentiated cell type.

The immunoglobulin enhancer
The immunoglobulin heavy-chain enhancer spans about 200
bases and contains nine functional sequence elements (E, μE15, π, μB, and OCT), which together stimulatetranscription in
B lymphocytes.
Features Of Cis-acting Elements
(1) Promoter
 Core promoter
 in eukaryote: TATA-box, Initiator (Inr).
 in prokaryote: -10 region, Inr.
 Proximal elements of promoter
 in prokaryote: -35 region.
 in eukaryote: CAAT-box, GC-box.

UPE: upstream promoter element.
UAS: upstream activating sequence.
(2) Terminator
A DNA sequence just downstream of the coding
segment of a gene, which is recognized by RNA
polymerase as a signal to stop transcription.
(3) Enhancer
A regulatory DNA sequence that greatly enhances the
transcription of a gene.
(4) Silencer
A DNA sequence that helps to reduce or shut off the
expression of a nearby gene.
Transcription Regulation
(5) Insulators
No transcription
•Transcriptional Regulatory Proteins
•

One of the prototypes of eukaryotic transcription factors was initially
identified by Robert Tjian and his colleagues during studies of the
transcription of SV40 DNA.

•

This factor (called Sp1, for specificity protein 1) was found to stimulate
transcription from the SV40promoter, but not from several other
promoters, in cell-free extracts.

•

Then, stimulation of transcription by Sp1 was found to depend on the
presence of the GC boxes in the SV40 promoter: If these sequences
were deleted, stimulation by Sp1 was abolished.

•

Moreover, footprinting experiments established that Sp1 binds
specifically to the GC box sequences.
The isolation of a variety of transcriptional regulatory
proteins has been based on their specific binding
to promoter or enhancer sequences. Protein binding to these
DNA sequences is commonly analyzed by two types of
experiments. The first, footprinting. The second approach is
the electrophoretic-mobility shift assay, in which a
radiolabeled DNA fragment is incubated with a protein
preparation and then subjected to electrophoresis through a non
denaturing gel. The general approach of DNA-affinity
chromatography, has been used successfully to isolate a wide
variety of sequence-specific DNA-binding protein from
eukaryotic cells
•Structure and Function of Transcriptional
Activators

Structure of
transcriptional activators consist of two
independent domains. The DNA-binding domain recognizes a
specific DNA sequence, and the activation domain interacts with
other components of the transcriptional machinery
•

•

•

•

•

The basic function of the DNA-binding domain is to anchor
the transcription factor to the proper site on DNA; the
activation domain then independently stimulates transcription
by interacting with other proteins.
Molecular characterization has revealed that the DNAbinding domains of many of these proteins are related to one
another .
Zinc finger domains contain repeats of cysteine and histidine
residues that bind zinc ions and fold into looped structures
(“fingers”) that bind DNA.
These domains were identified in the polymerase III
transcription factor TFIIIA but are also common among
transcription factors that regulate polymerase II promoters,
including Sp1.
Other examples of transcription factors that contain zinc finger
domains are the steroid hormone receptors, which regulate
gene transcription in response to hormones such
as estrogen and testosterone.
•

The helix-turn-helix motif was first recognized in
prokaryotic DNA-binding proteins, including the E. coli
catabolite activator protein (CAP).

•

In these proteins, one helix makes most of the contacts with
DNA, while the other helices lie across the complex to
stabilize the interaction.

•

In eukaryotic cells, helix-turn-helix proteins include
the homeodomain proteins, which play critical roles in the
regulation of gene expression during embryonic
development.

•

Molecular cloning and analysis of these genes then indicated
that they contain conserved sequences of 180 base pairs
(called
homeoboxes)
that
encode
the
DNAbinding domains (homeodomains) of transcription factors
Transcription Regulation
•Gene Regulation at DNA Level
Chromatin Remodeling
DNA Methylation
 Housekeeping gene -A gene involved in basic
functions is required for the sustenance of the cell.
Housekeeping genes are constitutively expressed
 Luxury gene - are those coding for specialized
functions synthesized (usually) in large amounts in
particular cell types.
 CpG islands
- These are genomic regions that contain a high

frequency of CG dinucleotides.
- CpG islands particularly occur at or near
the transcription start site of housekeeping
genes.
TF

RNA pol
Active
transcription

Unmethylated CpG island
TF
CH3

CH3

RNA pol
CH3

Methylated CpG island

Repressed
transcription
Histone modification
 methylation

 acetylation

TF
Transcription Regulation

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Transcription Regulation

  • 1. Regulation of Transcription in Eukaryotes By, Ishaque P.K Biochemistry & molecular biology Pondicherry university
  • 2. •INTRODUCTION • • • • • Although the control of gene expression is far more complex in eukaryotes than in bacteria. The expression of eukaryotic genes is controlled primarily at the level of initiation of transcription, although in some cases transcription may be attenuated and regulated at subsequent steps. As in bacteria, transcription in eukaryotic cells is also controlled by proteins that bind to specific regulatory sequences and modulate the activity of RNA polymerase. The intricate task of regulating gene expression in the many differentiated cell types of multicellular organisms is accomplished primarily by the combined actions of multiple different transcriptional regulatory proteins. In addition, the packaging of DNA into chromatin and its modification by methylation impart further levels of complexity to the control of eukaryotic gene expression.
  • 3. •cis-ACTING REGULATORY SEQUENCES • Transcription in bacteria is regulated by the binding of proteins to cis-acting sequences (e.g., the lac operator) that control the transcription of adjacent genes. • Similar cis-acting sequences regulate the expression of eukaryotic genes. • These sequences have been identified in mammalian cells largely by the use of gene transfer assays to study the activity of suspected regulatory regions of cloned genes. • Biologically active regulatory regions can thus be identified, and in vitro mutagenesis can be used to determine the roles of specific sequences within the region.
  • 4. Identification of eukaryotic regulatory sequences The regulatory sequence of a cloned eukaryotic gene is ligated to a reporter gene that encodes an easily detectable enzyme. The resulting plasmid is then introduced into cultured recipient cells by transfection. An active regulatory sequence directs transcription of the reporter gene, expression of which is then detected in the transfected cells.
  • 5. •PROMOTERS AND ENHANCERS • • • • Genes transcribed by RNA polymerase II have two core promoter elements, the TATA box and the Inr sequence, that serve as specific binding sites for general transcription factors. Other cis-acting sequences serve as binding sites for a wide variety of regulatory factors that control the expression of individual genes. These cis-acting regulatory sequences are frequently, though not always, located upstream of the TATA box. For example, two regulatory sequences that are found in many eukaryotic genes were identified by studies of the promoter of the herpes simplex virus gene that encodes thymidine kinase.
  • 6. • Both of these sequences are located within 100 base pairs upstream of the TATA box: Their consensus sequences are CCAAT and GGGCGG (called a GC box). Specific proteins that bind to these sequences and stimulate transcription have since been identified. A eukaryotic promoter The promoter of the thymidine kinase gene of herpes simplex virus contains three sequence elements upstream of the TATA box that are required for efficient transcription: a CCAAT box and two GC boxes (consensus sequence GGGCGG).
  • 7. • In contrast to the relatively simple organization of CCAAT and GC boxes in the herpes thymidine kinase promoter, many genes in mammalian cells are controlled by regulatory sequences located farther away (sometimes more than 10 kilobases) from thetranscription start site. • These sequences, called enhancers, were first identified by Walter Schaffner in 1981 during studies of the promoter of another virus, SV40 . • In addition to a TATA box and a set of six GC boxes, two 72base-pair repeats located farther upstream are required for efficient transcription from this promoter. • These sequences were found to stimulate transcription from other promoters as well as from that of SV40, and, surprisingly, their activity depended on neither their distance nor their orientation with respect to the transcription initiation site.
  • 8. The SV40 enhancer The SV40 promoter for early gene expression contains a TATA box and six GC boxes arranged in three sets of repeated sequences. In addition, efficient transcriptionrequires an upstream enhancer consisting of two 72-base-pair (bp) repeats.
  • 9. Action of enhancers Without an enhancer, the gene is transcribed at a low basal level (A). Addition of an enhancer, E for example, the SV40 72-bp repeats stimulates the transcription. The enhancer is active not only when placed just upstream of the promotor (B), but also when inserted up to several kbp either upstream or downstream from the transcription start site (C and D). In addition, enhancers are active in either the forward or backward orientation (E).
  • 10. • The ability of enhancers to function even when separated by long distances from transcription initiation sites, like promoters, function by binding transcription factors that then regulate RNA polymerase. • This is possible because of DNA looping, which allows a transcription factor bound to a distant enhancer to interact with RNA polymerase or general transcription factors at the promoter.
  • 11. DNA looping Transcription factors bound at distant enhancers are able to interact with general transcription factors at the promoter because the intervening DNA can form loops. There is therefore no fundamental difference between the action of transcription factors bound to DNA just upstream of the promoter and to distant enhancers.
  • 12. The binding of specific transcriptional regulatory proteins to enhancers is responsible for the control of gene expression during development and differentiation, the immunoglobulin enhancer is active in lymphocytes, but not in other types of cells. Thus, this regulatory sequence is at least partly responsible for tissue-specific expression of the immunoglobulin genes in the appropriate differentiated cell type. The immunoglobulin enhancer The immunoglobulin heavy-chain enhancer spans about 200 bases and contains nine functional sequence elements (E, μE15, π, μB, and OCT), which together stimulatetranscription in B lymphocytes.
  • 13. Features Of Cis-acting Elements (1) Promoter  Core promoter  in eukaryote: TATA-box, Initiator (Inr).  in prokaryote: -10 region, Inr.  Proximal elements of promoter  in prokaryote: -35 region.  in eukaryote: CAAT-box, GC-box. UPE: upstream promoter element. UAS: upstream activating sequence.
  • 14. (2) Terminator A DNA sequence just downstream of the coding segment of a gene, which is recognized by RNA polymerase as a signal to stop transcription. (3) Enhancer A regulatory DNA sequence that greatly enhances the transcription of a gene. (4) Silencer A DNA sequence that helps to reduce or shut off the expression of a nearby gene.
  • 18. •Transcriptional Regulatory Proteins • One of the prototypes of eukaryotic transcription factors was initially identified by Robert Tjian and his colleagues during studies of the transcription of SV40 DNA. • This factor (called Sp1, for specificity protein 1) was found to stimulate transcription from the SV40promoter, but not from several other promoters, in cell-free extracts. • Then, stimulation of transcription by Sp1 was found to depend on the presence of the GC boxes in the SV40 promoter: If these sequences were deleted, stimulation by Sp1 was abolished. • Moreover, footprinting experiments established that Sp1 binds specifically to the GC box sequences.
  • 19. The isolation of a variety of transcriptional regulatory proteins has been based on their specific binding to promoter or enhancer sequences. Protein binding to these DNA sequences is commonly analyzed by two types of experiments. The first, footprinting. The second approach is the electrophoretic-mobility shift assay, in which a radiolabeled DNA fragment is incubated with a protein preparation and then subjected to electrophoresis through a non denaturing gel. The general approach of DNA-affinity chromatography, has been used successfully to isolate a wide variety of sequence-specific DNA-binding protein from eukaryotic cells
  • 20. •Structure and Function of Transcriptional Activators Structure of transcriptional activators consist of two independent domains. The DNA-binding domain recognizes a specific DNA sequence, and the activation domain interacts with other components of the transcriptional machinery
  • 21. • • • • • The basic function of the DNA-binding domain is to anchor the transcription factor to the proper site on DNA; the activation domain then independently stimulates transcription by interacting with other proteins. Molecular characterization has revealed that the DNAbinding domains of many of these proteins are related to one another . Zinc finger domains contain repeats of cysteine and histidine residues that bind zinc ions and fold into looped structures (“fingers”) that bind DNA. These domains were identified in the polymerase III transcription factor TFIIIA but are also common among transcription factors that regulate polymerase II promoters, including Sp1. Other examples of transcription factors that contain zinc finger domains are the steroid hormone receptors, which regulate gene transcription in response to hormones such as estrogen and testosterone.
  • 22. • The helix-turn-helix motif was first recognized in prokaryotic DNA-binding proteins, including the E. coli catabolite activator protein (CAP). • In these proteins, one helix makes most of the contacts with DNA, while the other helices lie across the complex to stabilize the interaction. • In eukaryotic cells, helix-turn-helix proteins include the homeodomain proteins, which play critical roles in the regulation of gene expression during embryonic development. • Molecular cloning and analysis of these genes then indicated that they contain conserved sequences of 180 base pairs (called homeoboxes) that encode the DNAbinding domains (homeodomains) of transcription factors
  • 24. •Gene Regulation at DNA Level Chromatin Remodeling DNA Methylation
  • 25.  Housekeeping gene -A gene involved in basic functions is required for the sustenance of the cell. Housekeeping genes are constitutively expressed  Luxury gene - are those coding for specialized functions synthesized (usually) in large amounts in particular cell types.  CpG islands - These are genomic regions that contain a high frequency of CG dinucleotides. - CpG islands particularly occur at or near the transcription start site of housekeeping genes.
  • 26. TF RNA pol Active transcription Unmethylated CpG island TF CH3 CH3 RNA pol CH3 Methylated CpG island Repressed transcription