Regulation of gene expression in eukaryotes

Dr. Namrata Chhabra
Professor and Head
Department of Biochemistry
S.S.R. Medical College, Mauritius
Biochemistry for medics- Lecture notes
www.namrata.co
1Biochemistry for medics-Lecture notes

IntroductionIntroduction
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 geneLevels of regulation of gene
expressionexpression

Purpose of regulation of genePurpose of regulation of gene
Regulated expression of genes is required for
1) Adaptation- Cells of multicellular organisms
respond to varying conditions.
Such cells exposed to hormones and growth factors
change substantially in –
o shape,
o growth rate, and
o other characteristics

Purpose of regulation of genePurpose of regulation of gene
2) Tissue specific differentiation and development
The genetic information present in each somatic cell of a
metazoan organism is practically identical.
Cells from muscle and nerve tissue show strikingly
different morphologies and other properties, yet they
contain exactly the same DNA.
These diverse properties are the result of differences in
gene expression.
Expression of the genetic information is regulated during
ontogeny and differentiation of the organism and its
cellular components.

Control of gene ExpressionControl of gene Expression
• Mammalian cells possess about 1000 times more
genetic information than does the bacterium
Escherichia coli.
• Much of this additional genetic information is
probably involved in regulation of gene expression
during the differentiation of tissues and biologic
processes in the multicellular organism and in
ensuring that the organism can respond to complex
environmental challenges.

Mechanism of regulation of geneMechanism of regulation of gene
expression- An overviewexpression- 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.

expression- An overviewexpression- An overview
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 geneDifferences between gene
expression in prokaryotes andexpression in prokaryotes and
eukaryoteseukaryotes
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
o The E. coli genome consists of a single, circular
chromosome containing 4.6 Mb.
o This genome encodes approximately 2000 proteins.

1) Larger genome1) Larger genome
• 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 types2) 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 operons3) 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 structure4) 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 and5) Uncoupled transcription and
translation processestranslation 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.

expression- Detailsexpression- 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.

1) Chromatin Remodeling1) Chromatin Remodeling
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" chromatin in muscle cells.

Formation and disruption ofFormation and disruption of
nucleosome structurenucleosome 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-

nucleosome structure (contd.)nucleosome structure (contd.)
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.

i) Histone Acetylation andi) Histone Acetylation and
deacetylationdeacetylation
The amino-terminal tail
of histone H3 extends
into a pocket in
which a lysine side
chain can accept an
acetyl group from acetyl
CoA bound in an
adjacent site.

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 Repressors2) 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.

(contd.)(contd.)
• 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.

(contd.)(contd.)
• 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.

(contd.)(contd.)

3) Locus control regions and3) Locus control regions and
InsulatorsInsulators
• 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 .

3) Locus control regions and3) Locus control regions and
InsulatorsInsulators
Biochemistry for medics-Lecture notes 28

4) Gene Amplification4) 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.

4) Gene Amplification (contd.)4) Gene Amplification (contd.)
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.

4) Gene Amplification(contd.)4) Gene Amplification(contd.)
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 Rearrangement5) 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.

5) Gene Rearrangement (contd.)5) Gene Rearrangement (contd.)
These DNA coding changes are needed for generating
the required recognition diversity central to
appropriate immune function.

The IgG light chain is composed of variable (VL),
joining (JL), and constant (CL) domains or segments.
For particular subsets of IgG light chains, there are
roughly 300 tandemly repeated VL gene coding
segments, five tandemly arranged JL coding sequences,
and roughly ten CL gene coding segments.
All of these multiple, distinct coding regions are
located in the same region of the same chromosome.

However, a given functional IgG light chain
transcription unit contains only the coding sequences
for a single protein.
Thus, before a particular IgG light chain can be
expressed, single VL, JL, and CL coding sequences must
be recombined to generate a single, contiguous
transcription unit excluding the multiple nonutilized
segments.

This deletion of unused genetic information is
accomplished by selective DNA recombination that
removes the unwanted coding DNA while retaining
the required coding sequences: one VL, one JL, and one
CL sequence.

6) Alternative RNA Processing6) 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.

(contd.)(contd.)
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.

(contd.)(contd.)

(contd.)(contd.)
Alternative splicing and processing, results in the
formation of seven unique -tropomyosin mRNAs in
seven different tissues.

7) Class switching7) 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.

7) Class switching (contd.)7) Class switching (contd.)
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 “α2and 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 switched on.

7) Class switching (contd.)7) Class switching (contd.)
Gene switching is also
observed in the
formation of
immunoglobulins.
Ig M is the formed
during primary immune
response, while Ig G is
formed during
secondary immune
response.

8) mRNA stability8) 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.

8) mRNA stability (contd.)8) mRNA stability (contd.)
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 proteins9)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.

9) DNA binding proteins (contd.)9) DNA binding proteins (contd.)
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 regulatory10)Specific motifs of regulatory
proteinsproteins
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.

10) Specific motifs of regulatory10) Specific motifs of regulatory
proteins (contd.)proteins (contd.)
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.

Three unique motifs of DNAThree unique motifs of DNA
binding proteinsbinding proteins
Helix –turn- helix
Leucine zipper
Zinc finger

11) RNA Editing11) 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.

11)RNA Editing (contd.)11)RNA Editing (contd.)

SummarySummary
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
influence gene expression. 53Biochemistry for medics-Lecture notes

Regulation of gene expression in eukaryotes

Recomendados

Recomendados

Mais conteúdo relacionado

Mais procurados

Mais procurados (20)

Destaque

Destaque (20)

Semelhante a Regulation of gene expression in eukaryotes

Semelhante a Regulation of gene expression in eukaryotes (20)

Mais de Namrata Chhabra

Mais de Namrata Chhabra (20)

Último

Último (20)

Regulation of gene expression in eukaryotes