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Introduction
Gene expression is the combined process of :

o the transcription of a gene into mRNA,
o the processing of that mRNA, and
o its translation into protein (for protein-
encoding genes).
Levels of regulation of gene expression
Mechanism of regulation of gene
expression- An overview
Gene activity is controlled first and foremost at the level of
transcription.
Much of this control is achieved through the interplay between
proteins that bind to specific DNA sequences and their DNA
binding sites.
This can have a positive or negative effect on transcription.
Transcription control can result in tissue-specific gene expression.

In addition to transcription level controls, gene expression can also
be modulated by
Gene rearrangement,
Gene amplification,
Posttranscriptional modifications, and
RNA stabilization.
Differences between gene expression in
prokaryotes and eukaryotes
Gene regulation is significantly more complex in eukaryotes than in
prokaryotes for a number of reasons:
1) First, the genome being regulated is significantly larger
oThe E. coli genome consists of a single, circular chromosome containing
4.6 Mb.
oThis genome encodes approximately 2000 proteins.
•In comparison, the genome within a human cell contains 23 pairs of
chromosomes ranging in size from 50 to 250 Mb.
•Approximately 40,000 genes are present within the 3000 Mb of human
DNA.
•It would be very difficult for a DNA-binding protein to recognize a unique
site in this vast array of DNA sequences.
•More-elaborate mechanisms are required to achieve specificity
2) Different cell types
Different cell types are present in most eukaryotes.
Liver and pancreatic cells, for example, differ dramatically in the
genes that are highly expressed.

Different mechanisms are involved in the regulation of such genes.
3) Absence of operons
The eukaryotic genes are not generally organized into operons as are
there in prokaryotes
Instead, genes that encode proteins for steps within a given pathway
are often spread widely across the genome.

4) Chromatin structure
The DNA in eukaryotic cells is extensively folded and packed into the
protein-DNA complex called chromatin.

Histones are an important part of this complex since they both form
the structures known as nucleosomes and also contribute

significantly into gene regulatory mechanisms.
5) Uncoupled transcription andtranslation processes
•In prokaryotes, transcription and translation are coupled processes,
the primary transcript is immediately translated.
•The transcription and translation are uncoupled in eukaryotes,
eliminating some potential gene- regulatory mechanisms.
•The primary transcript in eukaryotes undergoes modifications to
become a mature functional m RNA.
Mechanism of regulation of gene expression- Details
1) Chromatin Remodeling
•Chromatin structure provides an important level of control of
gene transcription.
•With few exceptions, each cell contains the same complement
of genes (antibody-producing cells are a notable exception).
•The development of specialized organs, tissues, and cells and
their function in the intact organism depend upon the
differential expression of genes.
•Some of this differential expression is achieved by having
different regions of chromatin available for transcription in
cells from various tissues.
Large regions of chromatin are transcriptionally inactive in
some cells while they are either active or potentially active in
other specialized cells
For example, the DNA containing the -globin gene cluster is
in "active" chromatin in the reticulocytes but in "inactive"
Formation and disruption of Nucleosome structure
• The presence of nucleosomes and of complexes of histones and DNA provide a
barrier against the ready association of transcription factors with specific DNA
regions.
• The disruption of nucleosome structure is therefore an important part of
eukaryotic gene regulation and the processes involved are as follows-
i) Histone acetylation and deacetylation
Acetylation is known to occur on lysine residues in the amino terminal tails of
histone molecules.
This modification reduces the positive charge of these tails and decreases the
binding affinity of histone for the negatively charged DNA.
Accordingly, the acetylation of histones could result in disruption of nucleosomal
structure and allow readier access of transcription factors to cognate regulatory
DNA elements.
ii) Modification of DNA
Methylation of deoxycytidine residues in DNA may effect gross changes in
chromatin so as to preclude its active transcription.
Acute demethylation of deoxycytidine residues in a specific region of the tyrosine
aminotransferase gene—in response to glucocorticoid hormones— has been
associated with an increased rate of transcription of the gene.
iii) DNA binding proteins
The binding of specific transcription factors to certain DNA elements may result
in disruption of nucleosomal structure.
Many eukaryotic genes have multiple protein-binding DNA elements.
The serial binding of transcription factors to these elements may either directly
disrupt the structure of the nucleosome or prevent its re-formation.
These reactions result in chromatin-level structural changes that in the end
increase DNA accessibility to other factors and the transcription machinery.
2) Enhancers and Repressors
• Enhancer elements are DNA sequences, although they
have no promoter activity of their own but they greatly
increase the activities of many promoters in eukaryotes.
• Enhancers function by serving as binding sites for
specific regulatory proteins.
• An enhancer is effective only in the specific cell types in
which appropriate regulatory proteins are expressed.
• Enhancer elements can exert their positive influence on
transcription even when separated by thousands of base
pairs from a promoter;
• they work when oriented in either direction; and they
can work upstream (5') or downstream (3') from the
promoter.
• Enhancers are promiscuous; they can stimulate any
promoter in the vicinity and may act on more than one
promoter.
• The elements that decrease or repress the expression of specific genes have
also been identified.
• Silencers are control regions of DNA that, like enhancers, may be located
thousands of base pairs away from the gene they control.
• However, when transcription factors bind to them, expression of the gene they
control is repressed.
• Tissue-specific gene expression is mediated by enhancers or enhancer-like
elements.
3) Locus control regions and Insulators
•Some regions are controlled by complex DNA elements called locus control
regions (LCRs).
•An LCR—with associated bound proteins—controls the expression of a cluster of
genes. The best-defined LCR regulates expression of the globin gene family over a
large region of DNA.
• Another mechanism is provided by insulators. These DNA elements, also
in association with one or more proteins, prevent an enhancer from acting on a
promoter .
4) Gene Amplification
The gene product can be increased by increasing the number of genes available
for transcription of specific molecules
Among the repetitive DNA sequences are hundreds of copies of ribosomal

RNA genes and tRNA genes.
During early development of metazoans, there is an abrupt increase in the

need for ribosomal RNA and messenger RNA molecules for proteins that
make up such organs as the eggshell.
Such requirements are fulfilled by amplification of these specific genes.
 Subsequently, these amplified genes, presumably generated by a process of
repeated initiations during DNA synthesis, provide multiple sites for gene
transcription.
Gene amplification has been demonstrated in patients receiving methotrexate
for cancer.
The malignant cells can develop drug resistance by increasing the number of
genes for dihydrofolate reductase, the target of Methotrexate.
5) Gene Rearrangement
Gene rearrangement is observed during immunoglobulins synthesis.
Immunoglobulins are composed of two polypeptides, heavy (about 50 kDa) and light
(about 25 kDa) chains.
The mRNAs encoding these two protein subunits are encoded by gene sequences that
are subjected to extensive DNA sequence-coding changes.
These DNA coding changes are needed for generating the required recognition
diversity central to appropriate immune function.
6) Alternative RNA Processing
Eukaryotic cells also employ alternative RNA processing to control gene expression.
This can result when alternative promoters, intron- exon splice sites, or
polyadenylation sites are used.
Occasionally, heterogeneity within a cell results, but more commonly the same primary
transcript is processed differently in different tissues.
Alternative polyadenylation sites in the immunoglobulin (Ig M) heavy

chain primary transcript result in mRNAs that are either 2700 bases long (m) or
2400 bases long (s).
This results in a different carboxyl terminal region of the encoded proteins such
that the (m ) protein remains attached to the membrane of the B
lymphocyte and the (s) immunoglobulin is secreted.
7) Class switching
In this process one gene is switched off
and a closely related gene takes up the

function.
During intrauterine life embryonic Hb is
the first Hb to be formed.

It is produced by having two “Zeta” and two
“Epsilon” chains.
By the sixth month of intrauterine life,
embryonic Hb is replaced by HbF consisting of
“α2 and y2 chains.
After birth HbF is replaced by adult type of Hb

A 1(97%) and HbA2(3%).
Thus the genes for a particular class of Hb are
switched off and for another class are
8) mRNA stability
Although most mRNAs in mammalian cells are very stable (half-lives measured in
hours), some turn over very rapidly (half-lives of 10–30 minutes).
In certain instances, mRNA stability is subject to regulation.
This has important implications since there is usually a direct relationship

between mRNA amount and the translation of that mRNA into its cognate
protein.
Changes in the stability of a specific mRNA can therefore have major effects on
biologic processes.
The stability of the m RNA can be influenced by hormones and certain other
effectors.
The ends of mRNA molecules are involved in mRNA stability.
The 5' cap structure in eukaryotic mRNA prevents attack by 5' exonucleases, and
the poly(A) tail prohibits the action of 3' exonucleases.
9)DNA binding proteins
Steroids such as estrogens bind to eukaryotic transcription factors called nuclear
hormone receptors. These proteins are capable of binding DNA whether or not
ligands are bound.
The binding of ligands induces a conformational change that allows the

recruitment of additional proteins called co activators.
Among the most important functions of co-activators is catalysis of the addition of
acetyl groups to lysine residues in the tails of histone proteins.
 Histone acetylation decreases the affinity of the histones for DNA, making additional
genes accessible for transcription.
10)Specific motifs of regulatory proteins
Certain DNA binding proteins having specific motifs bind
certain region of DNA to influence the rate of transcription.
The specificity involved in the control of transcription
requires that regulatory proteins bind with high affinity to the

correct region of DNA.
Three unique motifs—the helix-turn-helix, the zinc

finger, and the leucine zipper—account for many of these
specific protein-DNA interactions.
The motifs found in these proteins are unique; their
presence in a protein of unknown function suggests that the
protein may bind to DNA.
The protein-DNA interactions are maintained by hydrogen
bonds and van der Waals forces.
Helix –turn- helix
Leucine
zipper
Zinc
finger
11) RNA Editing
Enzyme- catalyzed deamination of a specific cytidine residue in the mRNA of
apolipoprotein B-100 changes a codon for glutamine (CAA) to a stop codon
(UAA).
Apolipoprotein B-48, a truncated version of the protein lacking the LDL receptor-
binding domain, is generated by this posttranscriptional change in the mRNA
sequence.
Summary
The genetic constitutions of nearly all metazoan
somatic cells are identical.
Tissue or cell specificity is dictated by differences in
gene expression of this complement of genes.
Alterations
in gene expression allow a cell to adapt
to environmental changes.
Gene expression can be controlled at multiple levels
by chromatin modifications ,changes in
transcription, RNA processing, localization, and
stability or utilization.
Gene amplification and rearrangements also

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Introduction

Gene expression is the combined process of :

Transcription control can result in tissue-specific gene expression.

Posttranscriptional modifications, and

genes that are highly expressed.

are often spread widely across the genome.

protein-DNA complex called chromatin.

the structures known as nucleosomes and also contribute

Among the repetitive DNA sequences are hundreds of copies of ribosomal

During early development of metazoans, there is an abrupt increase in the

Gene rearrangement is observed during immunoglobulins synthesis.

Alternative polyadenylation sites in the immunoglobulin (Ig M) heavy

and a closely related gene takes up the

the first Hb to be formed.

After birth HbF is replaced by adult type of Hb

In certain instances, mRNA stability is subject to regulation.

This has important implications since there is usually a direct relationship

The ends of mRNA molecules are involved in mRNA stability.

The binding of ligands induces a conformational change that allows the

requires that regulatory proteins bind with high affinity to the

Three unique motifs—the helix-turn-helix, the zinc

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