1
Chapter 18
Regulation of Gene Expression
in Eukaryotes
2
Genetic Differences That Make Us
Human

While humans and chimpanzees
diverged only 5 to 7 MEA,
–

Paradoxically,
–
–

they differ in a large number of traits –
anatomical, physiological, behavioral, etc.
96% of the DNA of humans and
chimpanzees is identical
How did humans and chimpanzees
come to be so different? Where are the
genes that make us human?
Small number of genetic changes
–
in systems controlling gene expression
produce large phenotypic differences
between humans and chimpanzees
Network of interacting genes for Transcription Factors
differentially expressed in the brains of humans and
chimpanzees.
Red circles represent transcription factors
that are more highly expressed in the human brain.
Green circles represent transcription factors
that are more highly expressed in the chimpanzee brain.
3
Different Patterns of Gene
Expression

Different cells in a multicellular
organism
–

differ dramatically from one another
both in structure and function
While all cells contain the
same genome and genes,
–
–
–
–
the differences arise because cells
have different sets of genes being
actively expressed
A typical human cell express 3060% of ~25,000 genes
Some of them are common and
some are tissue specific
Each type of cells has a characteristic pattern of gene expression
1800 genes in 142 human tumor cell lines
4
Ways of Regulating Eukaryotic Gene
Expression


What level is the control of gene
expression exercised at?
Because of the way how
eukaryotic genome is structured
(chromosomes with several
levels of chromatin packaging)
and compartmentalized
(separated from cytoplasm with
the nuclear envelope),
–
the processes that regulate
gene expression in eukaryotes
are very diverse
5
Ways of Regulating Eukaryotic Gene
Expression

Expression of a gene in the eukaryotic cell includes multiple steps, each
of which could in principle be a regulatory point
1.
2.
3.
4.
5.
6.
Transcriptional control - when and where the gene is activated
RNA processing control - determines the splicing pattern
RNA transport control - determines which transcript to export
Translational control - determines which RNA will be translated
Degradation control - selectively targets RNAs for degradation
Protein activity control - selectively activates/inactivates protein molecules
6
Ways of Regulating Eukaryotic Gene
Expression
7
Alternative Splicing of RNA
(Mammalian Troponin-T Gene)
Alternative splicing of the rat
troponin T gene, which leads
to many cell-specific isoforms.
The protein encoded by this gene is
the tropomyosin-binding subunit of
the troponin complex, which regulates
muscle contraction in response to
alterations in intracellular Ca2+ ion
concentration.


Phenomenon of splicing an RNA transcript in different
ways is called alternative splicing
Alternative splicing allows for a single gene to encode
several polypeptides
–
It can serve many regulatory functions, e.g., control the variability of
muscle cell contraction in mammals, or sex determination in flies
8
Alternative Splicing of RNA
(Sex Determination in Drosophila)

A cascade of alternative RNA splicing regulates sex determination
–
–
–
–
–
It includes three genes – doublesex (Dsx), transformer (tra), and Sex-lethal (Sxl)
DsxF and DsxM are two isoforms of a transcription factor that activates femalespecific genes in females and represses the same female-specific genes in males
DsxF and DsxM are produced by alternative splicing of the dsx pre-mRNA
The Tra protein is an alternative splicing factor that regulates dsx splicing
The tra gene expression is itself regulated by alternative splicing conducted by the
Sxl protein (another splicing factor)
9
Alternative Splicing of RNA
(Sex Determination in Drosophila)

Sxl gene expression is governed by X-chromosome-encoded
activators and autosome-encoded repressors
–
In females, Sxl activation prevails: the Sxl protein is produced and regulates tra
RNA splicing, as well as, the splicing of Sxl RNA itself
10
RNA Stability
Pathways of the degradation
of eukaryotic mRNAs.

The half-life of mRNA molecules can influence gene
expression,
–

The stability of mRNA is extended by
–

as long-lived mRNAs can support multiple rounds of polypeptide synthesis
the presence of the 5’-cap and the poly(A)-tail
Among the factors decreasing stability are
the AU-rich elements (AUUUA) repeated several times in the 3’UTR of
some mRNAs
– small noncoding RNA (snRNA) molecules – siRNAs and miRNAs
–
11
Transcriptional Regulation



For most genes, transcriptional
regulation is the most important
It is mediated through regulatory
regions in DNA
–
They could be simple as a switch
–
responding to a particular signal, or
could be complex (or modular) responding and integrating a variety of signals
Transcription
Factor
Overall, transcriptional regulation
consists of two components:
–
–
Response Elements (RE) – short
stretches of DNA
Regulatory Proteins or Transcription
Factors (TF) that recognize and bind RE
Response
Element
12
Key Points
Eukaryotic gene transcripts may undergo
alternative splicing to produce mRNAs that encode
distinct, but related, polypeptides
Alternative splicing is a possible point of regulation of
gene expression
The stability of mRNA can influence the amount of
polypeptide being produced and correspondingly
the level of gene expression
Positive and negative regulatory proteins called
transcription factors (TF) interact with specific DNA
fragments (Response Elements or RE) to control
the transcription of eukaryotic genes
13
Induction of Transcriptional
Activity of Eukaryotic Genes
 Patterns
of eukaryotic gene expression
are constantly changing in response to
either environmental cues (e.g., ToC
increase) or in response to developmental
needs communicated by signaling
molecules (e.g., hormones and growth factors)
–
Both intracellular signaling and intercellular
communication are important for
transcriptional regulation in eukaryotes
14
The Heat-Shock Genes

Exposure of cells to pulses of elevated temperature
initiates the heat-shock response
–
–

A restricted subset of genes – the Hsp genes (hsp22,
hsp23, hsp26, hsp27, hsp68, hsp70, hsp83) – is activated
and the majority of transcription and translation is shut-down
The response may be elicited at all stages of the life cycle
and in cultured cells
The heat shock response (HSR) is a universal
response to a large array of stresses (e.g., hypoxia or
chemical stress)
–
–
heat-shock proteins (HSP) play a role in the protection from
these insults
HSP stabilize the internal cellular environment
15
The Heat-Shock Genes

The phenomenon of the heat-shock
response was discovered in 1960
–
–
–
–
by Italian geneticist Ritossa, when he was
studying polytene chromosomes
Due to an accidental increase in ToC of
the incubator where he was growing
Drosophila, Ritossa observed a new
pattern of “puffs” that occurs with
increased temperature
In salivary gland polytene chromosomes,
existing puffs regress and a novel group
quickly appears (33B; 63C; 64F; 67B;
70A; 87A; 87C; 93D; 95D)
“Puffs” correspond to actively transcribed
regions, as measured by radioactive
uridine incorporation
Ferruccio Ritossa (1936 – 2014)
16
Induction of the Drosophila
hsp70 Gene by Heat Shock
 The
heat shock response is very fast, within
few minutes after ToC increase, the hsp
gene encoded mRNAs can be detected
–
–
–
–
Without the heat-shock, GAGA factor binds
upstream of hsp70 gene and recruits NURF, which
keeps the promoter free of nucleosomes and allows
RNA polymerase binding
Transcription starts, but at 25oC it stalls as the CTD
of RNA Pol II is not phosphorylated enough
With a sudden rise in ToC, Heat-Shock TF (HSTF)
trimerizes and binds to heat shock element (HSE)
It then interacts with Mediator and recruits a kinase,
which phosphorylates the CTD and allows
transcription to resume
17
Gene Expression and Signaling
Molecules
 Regardless of the chemical nature,
– the response to any signaling molecule starts with
a specific receptor
are two types of receptors –
intracellular and cell-surface
 There
–
–
Some signal molecules diffuse across the plasma
membrane and activate intracellular receptors that
directly regulate the transcription of specific genes
In most cases, receptors are cell-surface or transmembrane proteins on the target cell surface; they
act as signal transducers converting the
extracellular binding into intracellular signals
18
Regulation of Gene Expression by
Steroid Hormones
 The
intracellular receptors could be activated by lipophilic
signaling molecules:
–
–
–
steroid hormones (glucocorticoids and sex steroids); thyroid
hormones; retinoids; vitamin D
Although they differ greatly in both structure and function, they all
act through a similar mechanism
Lipophilic hormones diffuse directly across the plasma membrane to
bind intracellular receptors
19
Regulation of Gene Expression by
Steroid Hormones
 In
early 1950s, while many
steroid hormones have been
characterized chemically and
physiologically, their mode of
action remained unknown
–
A breakthrough came from the
collaboration of Ulrich Clever and
Peter Karlson, when they studied
the effect of ecdysone on the
polytene chromosomes
20
Puffing of Giant Chromosomes and
Steroid Hormones
 In
1960, Ulrich Clever analyzed developmental changes of
the puffing pattern and found those that are characteristic
for metamorphosis
 Peter Karlson at the same time purified the insect steroid
hormone ecdysone, which regulates insect
metamorphosis
21
Puffing of Giant Chromosomes and
Steroid Hormones
 Together,
Ulrich Clever and Peter
Karlson found that ecdysone injection
induces the appearance of
metamorphic puffs
 These studies established a new
paradigm of steroid hormone action –
a direct interaction between the
hormone and hormone-dependent
genes
22
Regulation of Gene Expression by
Steroid Hormones
The steroid hormone enters the target
cell and binds the nuclear receptor
(NR) protein
 The hormone-receptor complex
translocates into the nucleus and binds
hormone response elements in DNA

–
Hormone response elements (HRE) are
analogous to the heat-shock response
elements (HSRE)
The bound hormone-receptor complex
(plays a role of the specific TF) stimulates
gene expression (transcription)
 mRNA is processed and transported to
the cytoplasm, where it is translated
into a protein

23
Regulation of Gene Expression by
Peptide Hormones
A peptide hormone binds to a transmembrane receptor protein of the
target cell
 The hormone-receptor complex
activates a signal transduction pathway
that brings the signal to the nucleus
 The signal induces a transcription
factor (TF) to bind to a corresponding
response element (RE) in the DNA
 The bound TF activates transcription
 mRNA is processed and transported to
the cytoplasm, where it is translated
into a protein

24
Key Points
Eukaryotic gene expression is regulated by
environmental cues or signaling molecules
Transcription of the heat-shock genes in response
to increased ToC is mediated by a heat-shock
transcription factor
Steroid hormones and their receptor proteins form
complexes that act as transcription factors to
regulate the expression of specific genes
Peptide hormones interact with membrane-bound
receptor proteins to activate a signal transduction
pathway that regulates the expression of specific
genes
25
Molecular Control of Transcription in
Eukaryotes
Transcription of eukaryotic genes is
regulated by interactions between
proteins and DNA sequences within
or near the genes
 Three sets of regulatory DNA
sequences are commonly involved in
eukaryotic gene regulation

–
The core promoter region (immediately
adjacent to the start of transcription)
contains the TATA box and related
sequences that bind RNA polymerase
II and associated general transcription
factors (TFIID, TFIIB, etc.)
– Upstream of the core promoter region (approx. few hundred base pairs) are
various proximal elements (GC box, CAAT box) that bind regulatory proteins
essential for promoter activation
– At greater distances from the core promoter are the enhancers
26
Properties of Enhancers
Tissue-specific enhancers of
the Drosophila yellow gene

Unlike core promoter and proximal promoter elements, which are
upstream and close to the gene they regulate, enhancers can be
located close to or very far from the genes they regulate
–
Enhancers can be upstream, downstream, or within the genes (e.g., introns)
– Enhancers bind regulatory proteins that interact with proteins bound to core
and proximal promoter elements
– Enhancers control the timing and location of gene transcription
– Enhancers could be simple (like HSE) or modular (composed of multiple
binding sites for different TFs)
27
Yeast Upstream Activator Sequences
(Enhancers)
 In
the yeast S. cerevisiae, transcription of genes in the
galactose utilization pathway is regulated by enhancers
–
–
When galactose is the only sugar available, yeast cells induce
transcription of enzyme-encoding genes: GAL1, GAL2, GAL7, GAL10
Together these enzymes import and then break down galactose
 Each
of the GAL genes has its own basal promoter and
similar enhancers bound by a regulatory protein, Gal4
–
The enhancer element is called the upstream activator sequence
(UAS, or UASG)
28
Yeast Upstream Activator Sequences
(Enhancers)
Galactose absent:
 Gal4
is continuously present in cells; it interacts with the
Gal80 protein (also continuously present) that binds Gal4
and keeps it inactive in the absence of galactose
–
–
–
Each UASG element contains two 17-bp repeat sequences that are
binding sites for Gal4
Gal4 functions as a homodimer with two domains – the DNA-binding
domain and the activation domain
When Gal4 is bound to Gal80, the Gal4 DNA-binding domain is unable
to bind UASG
29
Yeast Upstream Activator Sequences
(Enhancers)
Galactose present:
 When
galactose is present, galactose and Gal3 (encoded by
the GAL3 gene) form a complex and bind to Gal80
–
–
Gal80 releases Gal4, freeing the DNA-binding domain of Gal4 to
recognize and bind to the UASG sites
The transcriptional activation domain then activates transcription of the
GAL genes
30
DNA Regulatory Elements
 Regulatory
proteins are
DNA-binding transcription factors (TF)
–
–
–
They typically recognize
sequences less than 20 bp
in length, referred to as
response elements (RE)
Each TF recognizes
specific sequence of nts
Upon binding they can
change the level of gene
expression
31
Structure of Transcription Factors
 Transcription factors have modular structure
– DBD (DNA-binding domain) recognizes and binds specific response
elements adjacent to regulated genes
– TAD (transcriptional-activation domain) binds transcriptional coregulators and changes gene expression
– SSD (signal-sensing domain) senses/binds external signals (e.g.,
ecdysone) and transmits the information to other domains (optional)
 TAD
and SSD are often contained within the same domain
32
Modular Structure of Transcription Factors
The yeast-bacterial Gal4-LexA fused protein activates expression of the
reporter only when it has a corresponding response element (or binding site)
33
Structural Motifs of TFs
 Hundreds
of DNA-binding regulatory
proteins have been identified in
eukaryotes
 They are categorized into four
groups based on the structural motif
that constitutes the DNA-binding
domain
–
–
–
–
the Zinc finger motif
the helix-turn-helix motif (HTH)
the basic-leucine zipper motif (bZIP)
the basic helix-loop-helix motif (bHLH)
34
Structural Motifs of TFs
*
* Note: Homeodomain proteins constitute a
subclass of the HTH (helix-turn-helix)
group of proteins
35
Structural Motifs of TFs
(Leucine Zipper Motif)
 Most
of basic leucine zipper (bZIP)
TFs are homodimers
 Each polypeptide of the bZIP protein
–
–
–
is an α-helix composed of two regions –
the basic region that interacts with the
major groove of DNA, and the hydrophobic region responsible for dimerization
The hydrophobic region has a leucine
residue at every 7th position; every
second turn, leucine residues from two
helices interact forming the “zipper”
In the basic region, two α-helices separate to form a Y-shaped structure with two
arms bound to a specific DNA sequence
36
Structural Motifs of TFs
(Helix-loop-Helix Motif)
 A basic
helix-loop-helix (bHLH) motif
consists of two α-helices connected by
a flexible loop
 In general, bHLH type TFs are dimeric
 Each polypeptide of the bHLH protein
–
has one α-helix containing basic AA (basic
region) that facilitate DNA binding, and the
second α-helix mediate dimerization
37
Key Points
Unlike core and proximal promoter elements,
enhancers act in an orientation-independent manner
over considerable distances to regulate eukaryotic gene
expression
Transcription factors are regulatory proteins that
recognize and bind to specific DNA sequences called
response elements
Transcription factors comprise four groups, each
characterized by a structural motif in the DBD:
the zinc finger, the helix-turn-helix, the leucine zipper, and the
helix-loop-helix
38
Posttranscriptional Regulation of
Gene Expression
Short
noncoding RNAs may regulate the
expression of eukaryotic genes by interacting with the mRNAs produced by these
genes
–
The phenomenon is called RNA interference
(or RNAi)
–
RNAi occurs in plants and animals including
humans
39
Posttranscriptional Regulation of
Gene Expression

Andrew Fire and Craig Mello were investigating
–
how gene expression is regulated in the nematode worm C. elegans
Injecting ‘sense’ RNA molecules encoding a muscle protein led to no
changes in the behaviour of the worms
– Injecting ‘antisense’ RNA, which can pair with the mRNA, also had no effect
– But when Fire and Mello injected sense and antisense RNA together, they
observed that the worms displayed peculiar, twitching movements
– Thus, a double-stranded RNA molecules can specifically silence genes
whose code matches that of the injected RNA molecules
–
40
Posttranscriptional Regulation of
Gene Expression
Andrew Fire (1959)
Craig Mello (1960)
Fire and Mello published their findings in the journal Nature on
February 19, 1998
 The Nobel Prize in Physiology or Medicine 2006 was awarded jointly to
Andrew Fire and Craig Mello “for their discovery of RNA interference gene silencing by double-stranded RNA”

41
RNA Interference
 RNAi
silences gene expression
post-transcriptionally, but how?
–
–
–
Cells have a specific enzyme, Dicer
that recognizes the double stranded
RNA and chops it up into small
fragments between 21-25 bp in length
These short double stranded RNA
fragments (small interfering RNA, or
siRNA) bind to the RNA-Induced
Silencing Complex (RISC)
The RISC is activated when the siRNA
unwinds and the sense strand is
eliminated
42
RNA Interference
43
Double Stranded RNA
 Double
stranded RNA originates either from genes,
the transcription of other endogenous sequences, or
from exogenous source
–
–
In many eukaryotes, miRNA genes encode precursors of
dsRNA that are cleaved into microRNAs of 21-24 nt
Small interfering RNAs (siRNAs) are not encoded by genes;
they originate from endogenous transcription or exogenous
sources
–
Known eukaryotic siRNAs are mapped to transposons or other
genomic regions that produce transcripts capable of forming
dsRNA structures (e.g., inverted repeat structures, bidirectional
transcription and antisense transcripts)
–
The exogenous source of dsRNA could be RNA viruses
44
microRNA Biogenesis

miRNA genes are transcribed by RNA Pol
II and produce transcripts that fold back
upon themselves to produce dsRNA
–

The initial transcript is called primary
microRNA (pri-miRNA); it forms a doublestranded stem of about 65-70 nucleotides,
with free ends on one side and a singlestranded loop on the other
The pri-miRNA is processed by Drosha
enzyme complex
–
It cuts near the middle to produce a
precursor miRNA (pre-miRNA), which is a
21-25 nt stem and the terminal loop
– The pre-miRNA is transported to cytoplasm,
where it is further processed by Dicer
– RISC then binds to the remaining 21-25 bp
and separates the strands to create miRNAs
45
microRNA Biogenesis
(Summary)
46
Key Points
siRNAs and miRNAs are produced from larger
double-stranded precursors by the action of
endonucleases Dicer
siRNAs originate from transcription of sequences capable
of forming dsRNA structures, e.g. transposons
miRNAs originate from hundreds of genes present in
eukaryotic genomes
In RNA-Induced Silencing Complexes (RISC),
siRNAs and miRNAs become single-stranded so
they can target complementary sequences in
mRNAs
47
Key Points
RNA interference is used as a research tool
to knock down the expression of genes in
cells and organisms
mRNA that has been targeted by siRNA is
cleaved, and mRNA that has been targeted
by miRNA is either cleaved or prevented
from being translated
48
Chromatin Organization
 The
defining feature of
eukaryotic DNA is its
packing into chromatin
–
Electron micrograph of a
cell showing the heterochromatin localized to the
nuclear periphery.
Chromatin is a complex of
DNA and proteins representing specific levels of DNA
compactization
 Chromatin
exists in two
forms:
–
–
Euchromatin (stains lighter; gene rich) is a less condensed form of
chromatin that allows access of transcription machinery
Heterochromatin (stains darker; gene poor) is a highly condensed form
of chromatin that is typically not transcribed
49
Types of Heterochromatin
 Facultative
(or intercalary) heterochromatin exhibits variable
levels of condensation, reflecting activity of resident genes
–
Found in euchromatic environment
 Constitutive
heterochromatin is permanently condensed,
composed primarily of repetitive DNA sequences
–
Found in centromeres and telomeres, where it represses transposable
element activity and thereby ensures genome stability and integrity
50
Gene Expression and Chromatin
 The
structure of chromatin has a crucial role
in eukaryotic gene transcription
 Changes in the level of compactization
govern the accessibility of DNA by proteins
(such as, TFs and enzymes) regulating and
participating in gene expression
–
Position effect variegation (PEV) in Drosophila
illustrates the effect of chromatin compaction on
gene expression
51
Position effect variegation (PEV) in
Drosophila
 The
–
PEV was first described by Herman Muller in 1930
Muller identified mutations in flies that resulted in variegated eye color
– The X chromosomes of mutant flies had undergone inversion
– The variability in the phenotype is caused by the relocation of the white+
gene from euchromatic into heterochromatic surrounding
– The impaired ability of a gene to function at a new location is called
Position Effect Variegation (PEV)
52
Chromatin Structure and PEV
53
Chromatin Structure and PEV
 The degree of heterochromatin spreading varies
– In some cells euchromatic genes will not be affected by adjacent
heterochromatin, and in others – certain genes will be silenced
– Once heterochromatin-type structure and inactivation of neighboring
euchromatin is established, it will be inherited by all cell progeny
54
Position effect variegation (PEV) in
Drosophila
 Thus, the occurrence of PEV in Drosophila shows that
– Gene expression can be silenced by its chromosomal position
– Silencing is a feature of chromatin structure that can be transmitted
from one cell generation to the next
– This type of regulation is called epigenetic, as it is not due to
changes in the DNA base sequence
55
Molecular Organization of
Transcriptionally Active DNA
Harold Weintraub (1945-1995)
Mark Groudine
Transcriptionally active DNA is more sensitive to DNase I than inactive
 This phenomenon was discovered in 1976 by Groudine and Weintraub

–

when they compared the β-globin (active) and ovalbumin (inactive) genes
in chicken erythrocytes
Gene expression is associated with “open” chromatin structure as it
provides access to DNA by proteins involved in transcription
56
DNase I Hypersensitivity
Dubrovsky et al. (1994), J Mol Biol 241, 353-362

Regions of chromatin that are sensitive to DNase I digestion are called
DNase I hypersensitive sites (or DHS)
–

Today, mapping DNase I hypersensitive sites is a molecular approach to
identify local changes in chromatin structure
Mapping DHS is a highly accurate method for identifying promoters,
enhancers, and other transcription control sequences
57
Key Points
Heterochromatin is associated with the
repression of transcription
Position Effect Variegation is an example of
the epigenetic regulation of gene expression
Gene expression is associated with “open”
(or loosely organized) chromatin
Transcriptionally active DNA is more
sensitive to digestion with DNase I
58
Chromatin Structure and Gene
Expression
 So
far, we have established that
–
The biological role of chromatin is not purely structural (storing and
packing DNA), but it is quite a dynamic player in gene expression
–
Chromatin is not a static entity with defined regions of euchromatin
and heterochromatin, instead there are dynamic changes in levels of
compactization
–
As illustrated by PEV and DNase I hypersensitivity, dynamic changes
in chromatin organization are directly associated with regulation of
gene expression
 Still
–
questions to answer:
What defines chromatin organization? How is it established? How is it
maintained? How is it changed?
59
PEV Mutations
 Second-site
mutations
modifying PEV led to identification of proteins that
play a role in establishing
chromatin structures
–
–
Two types of mutations have
been identified – enhancers
and suppressors of positioneffect variegation
Several dozen E(var) and
Su(var) mutations have been
identified in Drosophila
60
E(var) Mutations
 E(var)
mutations, enhancers of PEV, increase the
appearance of the mutant white phenotype in flies
with a variegating allele of the white gene
–
–
E(var)s encourage the spread of heterochromatin further, and
thus restrict w+ expression to even smaller patches of cells
E(var)s produce a greater number of eye cells lacking pigment
61
Su(var) Mutations
 Su(var)
mutations, suppressors of PEV, increase the
appearance of the wild-type red phenotype in flies with
a variegating allele of the white gene
–
–
Su(var)s restrict the spread of heterochromatin or interfere with
its function, and thus leave more cells with w+ expression
Su(var)s produce a greater number of pigmented eye cells
62
Histone-Modifiers
 Analysis
–
genes encoding histone modifiers or
proteins that make epigenetic marks
on histones (e.g., adding methyl or
acetyl group)
 These
–
–
of PEV mutants led to
covalent modifications
can directly alter chromatin structure
making it more open or reverse more
condensed
Thus, histone modifiers are critical in
any process that involves accessing
DNA (e.g., activation of gene
expression)
(a) Histone tails protrude from the nucleosome core.
(b) Examples of histone tail modifications: ‘A’ represents
acetylation; ‘M’ represents methylation.
63
HP-1 and HMT
64
Histone Acetylation
 Histone acetylation is another
– post-translational modification of
histones that can alter chromatin
compaction and gene expression
 Covalent
attachment of the acetyl
(-COCH3) group is catalyzed by
–
histone acetyltransferase (HAT)
 Like
any other histone modification,
acetylation is reversible
–
Acetyl groups are removed by histone
deacetylase (HDAC)
Acetylation of lysine amino acids in histone tails
opens the chromatin, exposing DNA to the activity
of proteins that regulate transcription.
65
Histone Acetylation
 HDAC
closes the chromatin structure
 HAT opens the chromatin structure
 Activity of these and other chromatin modifiers
is under tight control
66
Histone Modifications

Lysine (K) is the most frequently targeted residue for acetylation
–

Lysine and arginine (R) are the most frequent methylation targets
Serine (S) and threonine (T) are targets for phosphorylation
67
Histone Modifications

There are now known at least 150 histone modifications that utilize a wide
variety of molecules:
–

acetyl, methyl, phosphoryl, ubiquitine, and ADP ribose
Histone modifications can affect chromatin structure in different ways (and
either activate or silence genes), but they are all reversible
68
Histone-Modifiers

The modifications of histones are conducted by
specific enzymes (histone-modifiers)
69
Histone Modifications

Specific modifications are associated with different chromatin
regions or cellular events

E.g., acetylation of lysine residues at positions 8 and 16 of H4 is
associated with chromatin regions where the start sites of the
expressed genes are located
70
Histone Modifications

Methylation of lysine residues at positions 4 and 36 of H3 typically
is associated with the expressed genes
71
Histone Modifications

On the other hand, methylation of lysine residues at positions 9 or
27 of H3 is associated with transcriptional repression