Regulation of gene expression in eukaryotes and
cell signaling
https://www.khanacademy.org/science/biology/gene-regulation/gene-regulation-in-eukaryotes/a/overview-of-eukaryotic-gene-
regulation
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Gene regulation is the process of controlling which
genes in a cell will be expressed.
• Different cells of a multicellular organism may
express very different sets of genes, even if they
contain the same DNA.
• A set of genes expressed in a cell identifies the set
of proteins and functional RNAs it contains, giving it
its unique properties.
• In eukaryotes, such as humans, gene expression
involves many steps, and gene regulation may occur
in any of these steps. However, many genes are
regulated primarily at the transcriptional level.
Relationship between cell expression and signaling.
Regulation of gene expression - in
general
https://www.khanacademy.org/science/biology/gene-regulation/gene-regulation-in-eukaryotes/a/overview-of-eukaryotic-gene-
regulation
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Products of all genome genes are not necessary
at every point in a cell's life
conditions and variability of the environment play
a significant role
the complexity of the gene expression process is
mostly energetic
cell variability during the cell cycle
- in unicellular: reactions to environmental changes (temperature, osmotic pressure, nutrient
availability, etc.)
- - in multicellular: reactions to changes in the environment + communication between cells of
the same organism + developmental processes within the organism
Constitutive and regulatable genes
• there are different types of genes (constitutive, regulated)
• constitutive genes are expressed in most cells
• ensure stable (continuous) expression of genes that encode the components of cells
necessary to maintain normal - operational - functions ("housekeeping functions")
• eg expression of genes for rRNA, tRNA, ribosome proteins, RNA polymerases,
proteins involved in proteosynthesis, enzymes catalyzing operational functions
• the expression of regulatable (inducible / repressible) genes increases or
decreases as needed
• refers to (inducible / repressible) genes whose products
• they are only needed under certain conditions
• the synthesis of these genes is under the control of special regulatory systems
• constitutive expression of these genes would mean an unnecessary energy load on
the cell,
• evolutionary advantages - regulation
• common for both prokaryotes and eukaryotes
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Regulation of expression in
eukaryotes:
complicated process of many
factors acting depending on time
and place
Products of the same gene have a
different function in different
tissues
At different stages of ontogenetic
development, different genes
coding for similar products are
expressed
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Our amazing body contains hundreds of different types of cells, from immune cells to skin cells to neurons.
Almost all of your cells contain the same set of instructions for DNA – so why do they look so different and do
such a different job? Answer: different gene regulation!
Regulation in eukaryotes more complex than in prokaryotes
high number of genes that are variously expressed in different tissues
- inaccessibility of heterochromatin DNA by transcription
- gene expression requires the presence of several activators
- problem: DNA in the nucleus, transcription factors and protein
regulators are formed in the cytoplasm
• positive: the gene can be expressed if it receives a certain positive signal-activator
• negative: gene expression is suppressed by a repressor and can only be initiated
after its removal – dependent on the reception of the signal
• Positive and negative regulation is thus dependent on a small molecule – an inducer
that binds to the regulatory protein
• signals affecting the expression of a particular gene may be greater
• Common to both prokaryotes and eukaryotes
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- positive and negative regulation
DNA and
chromosome
levels
level of
transcription
level of
transcript
editing
translation
initiation
level
Proteins
Transcription
factors
Regulatory levels
6_regulation eukaryotic cells 1 6TEST
https://employees.csbsju.edu/hjakubowski/classes/ch331/bind/olbindtransciption.html
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TEST
1. DNA and chromosome levels
2. Transcription level
3. Level of transcript editing
4. Translation initiation level
TEST
➢Regulatory levels:
http://www.discoveryandinnovation.com/BIOL202/notes/lecture19.html
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•there are many changes in the chromatin structure at the
transcription site
•positive mechanisms regulate transcription much more often
than negative ones.
•transcription and translation occur at spatially and
temporally different places and times.
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Regulation of gene transcription availability - chromatin
Chromatine in nucleus:
• Condensed (heterochromatin) genes
are inactive
• Diffuse (euchromatin) genes
produce mRNA
In cells of differentiated
tissues, only those genes that
play a role in a given cell are
manifested
During development, there are changes in
the activity of genes, chromatin changes
from the condensed form to the diffuse
and vice versa. 6_regulation eukaryotic cells 1 9
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Influencing gene expression at the level of chromosome
structure
➢DNA accessibility in chromatin
➢ histone acetylation regulators
➢chromatin remodeling complexes
➢ DNA methylation
➢ gene DNA rearrangement
➢ gene amplification
➢ gene deletion
Epigenetic modifications
they regulate genome function by altering the
local structure of chromatin - primarily by
regulating availability and compactness
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•densely composed DNA in chromatin cannot be transcribed;
RNA polymerase does not have access to the promoter
• histone acetylation affects chromatin compactness: nonacetylated
histones form highly condensed chromatin,
acetylated histones - less condensed chromatin
• the degree of acetylation is determined by the enzymes:
histone acetlytransferases (HAT) and histone deacetylases
(HDAC) a change in chromatin status that leads to the
activation of transcription
•release of the nucleosome from the chromatin
• Development of a section of DNA from a nucleosome using
ATP cleavage
• Covalent modification of histone ends by acetylation
(acetylation of the g -amino group in the lysine side chain at
the N-termini of histones H2A, H2B, H3 and H4).
DNA accessibility in chromatin, chromatin remodeling
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Regulators chnges acetylation of histones
• coactivators of transcription are HAT (histone
acetyltransferases) eg CBP / p300 proteins
• transcription corepressors are HDAC (histone
deacetylase)
• coactivators and corepressors do not bind to DNA,
but interact with transcription factors
• - binding of the transcription factor to DNA
• - HAT binding to transcription factor
• - HAT acetylates surrounding histones and
releases them
• binding of nucleosomes to DNA
• - chromatin remodeling complexes change
• nucleosome organization - accessibility
• DNA is elevated
• - binding of other transcription factors
• - RNA polymerase binding to DNA
Complexes for
chromatin remodeling
they complement nucleosome changes
resulting from histone acetylation
they move nucleosomes across
Activation of eukaryotic transcription
gene - sequence of events
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ATP-dependent chromatin remodeling
complexes
multiprotein complexes that alter the conformation of
histones and DNA (in promoter regions) use energy from
ATP hydrolysis
• the substrate is not a mononucleosome, but rather a
chain of nucleosomes - it changes the position of
nucleosomes on DNA and forms "nucleosome-free"
regions
• SWI / SNF, RSC, NURF, CHRAC, ACF, FACT
• classification according to ATPase subunit:
SWI2 / SNF2
ISWI
Mi-2 (+ deacetylase subunit) (CHD complexes)
• their cooperation necessary for activators and
repressors
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Gene expression in eukaryotes is affected by DNA methylation
- methylation of cytosine residues in DNA 5-methylcytosine
- catalyzed by methyltransferase
recognition sequences are short: GC in animals and GNC in plants
(GC islands)
- methylation of DNA weakens gene expression
- constitutive operational genes do not have GC methylated
islands
- tissue-specific genes do not have GC islands methylated only if
their products are needed in that tissue
-methyl groups protrude into a large groove of DNA and thus
prevent proper binding of transcription factors
Ex .: genes for globin are methylated in non-erythroid cells
(hemoglobin synthesis does not take place here), in erythroblasts
and reticulocytes (erythrocyte precursors) these genes are not
methylated
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covalent modification of cytosine at position 5´ in the
CpG dinucleotide
• cytosine methylation takes place by transfer of a methyl
group from the donor: S-adenosylmethionine with the
participation of DNA methyltransferases
• DNMT1 - "maintenance" - 10x higher affinity for
semimethylated DNA, much more active than DNMT3a and
3b
• DNMT3a and DNMT3b - de novo - methylate
unmethylated DNA
• Deletion of DNMT in mice is embryonally lethal
• The pattern of DNA methylation is relatively stable in
adult cells, significant changes are described in connection
with aging
. gene silencing
The DNA methylation landscape of vertebrates is very
particular compared to other organisms. In mammals,
around 75% of CpG dinucleotides are methylated in somatic
cells,[15] and DNA methylation appears as a default state
that has to be specifically excluded from defined
locations.[12][16] By contrast, the genome of most plants,
invertebrates, fungi, or protists show “mosaic” methylation
patterns, where only specific genomic elements are
targeted, and they are characterized by the alternation of
methylated and unmethylated domains.[17][18]
DNA methylation
Methylation patterns can account for gene silencing (in
which one gene in a pair of identical chromosomes is
not expressed) and inactivation of one entire X
chromosome in a female (who has 2 X
chromosomes). In general, transcription from genes that
are methylated is inhibited.
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olbindtransciption.html6_regulation eukaryotic cells 1 15
CpG DNA methylation is associated with
repression of transcription - with maintaining
a more stable state of chromatin
methylated DNA regions are recognized by
the MeCP2 protein (its methyl-DNA binding
domain) and specifically interact
(transcriptional repressor domain) with the
Sin3 corepressor, which brings HDACs to the
methylated regions
DNA methylation and histone deacetylation
transient repression stable repression
Other histone modifications:
-phosphorylation of histones is functionally linked to acetylation
- methylation of histones (lysines and arginines can be methylated; H2B,
H3 (lys 4, 9, 27, 36) and H4 (lys 20))
- monoubiquitination, at the C-terminus of histones: lysine 119 histone
H2A and lysine 123 histone H2B
- associated with a transcriptionally active or, conversely, repressed
(H2A K119) chromatin state
- Histone polyubiquitination is also an integral part of DNA repair
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Gene amplification
In gene amplification, a region of a chromosome undergoes repeated
cycles of DNA replication
Newly synthesized DNA is excised to form small, unstable chromosomes
(double minutes)
These integrate into other chromosomes and the corresponding gene is
thus amplified
Normally, amplification is caused by errors in DNA replication and cell
division - under certain circumstances, they may be encoded in the
genome.
Ex .: Patients treated with methotrexate (a dihydrofolate reductase
inhibitor) developed drug resistance (the drug ceased to be effective).
The reason is an increase in the number of dihydrofolate reductase
genes due to amplification.
Gene
rearrangement
DNA segments can
rearrange and associate
with other genes within
the genome
Ex .: Gene rearrangement
in antibody-producing cells
(immunoglobulins)
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II. Regulation at the transcriptional level
Basic regulation of transcription (common to all
genes)
Regulation by components of the "basal
transcription complex" (RNA polymerase
binding to the TATA box, TATA binding
proteins and other "basal" transcription
factors binding to the RNA polymerase or in
the promoter region)
Genes regulated only in this way:
Constitutively expressed genes
Specific effects on gene expression:
Through regulatory sequences in DNA and
specific transcription factors.
promoter in eukaryotes
- binding of basal transcription factors
- regulatory sequences in DNA and
specific transcription factors.
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