Transcript Eukaryotic Gene Regulation

Overview: How Eukaryotic Genomes Work and
Evolve
• Two features of eukaryotic genomes are a major
information-processing challenge:
– First, the typical eukaryotic genome is much
larger than that of a prokaryotic cell - can
impact efficiency of gene expression
– Second, cell specialization limits the
expression of many genes to specific cells
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Concept 19.1: Chromatin structure is based on
successive levels of DNA packing
• Eukaryotic DNA is precisely combined with a large
amount of protein
• The DNA-protein complex, called chromatin, is
ordered into higher structural levels than the DNAprotein complex in prokaryotes
• Eukaryotic chromosomes contain an enormous
amount of DNA relative to their condensed length
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Nucleosomes, or “Beads on a String”
• Proteins called histones are responsible for the
first level of DNA packing in chromatin
• The association of DNA and histones seems to
remain intact throughout the cell cycle
• In electron micrographs, unfolded chromatin has
the appearance of beads on a string
• Each “bead” is a nucleosome, the basic unit of
DNA packing
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-2a
2 nm
DNA double helix
Histones
Histone
tails
Histone H1
Linker DNA
(“string”)
Nucleosome
(“bead”)
Nucleosomes (10-nm fiber)
10 nm
Higher Levels of DNA Packing
• The next level of packing forms the 30-nm
chromatin fiber
• Interactions between histone tails, linker DNA, and
other nucleosomes cause the 10-nm fiber to coil
and fold, forming a chromatin fiber approximately
30 nm in diameter
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-2b
30 nm
Nucleosome
30-nm fiber
• In turn, the 30-nm fiber forms looped domains,
making up a 300-nm fiber
• During prophase of mitosis or meiosis, the 30-nm
fiber forms looped domains by attaching to a nonhistone protein scaffold, giving rise to a 300-nm
fiber
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LE 19-2c
Protein scaffold
Loops
300 nm
Looped domains (300-nm fiber)
Scaffold
• In a mitotic chromosome, the 300-nm looped
domains coil and fold, forming the metaphase
chromosome
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LE 19-2d
700 nm
1,400 nm
Metaphase chromosome
• Interphase chromatin is usually much less
condensed than that of mitotic chromosomes
• Much of the interphase chromatin is present as a
10-nm fiber, and some is 30-nm fiber, which in
some regions is folded into looped domains
• Interphase chromosomes have highly condensed
areas, called heterochromatin, and less
compacted areas, called euchromatin
Animation: DNA Packing
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Concept 19.2: Gene expression can be regulated at
any stage, but the key step is transcription
• All organisms must regulate which genes are
expressed at any given time
• A multicellular organism’s cells undergo cell
differentiation which is a specialization in form and
function
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Differential Gene Expression
• Differences between cell types result from
differential gene expression, the expression of
different genes by cells possessing the same
genome
• In each type of differentiated cell, a unique subset
of genes is expressed
• Many key stages of gene expression can be
regulated in eukaryotic cells
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-3
Signal
NUCLEUS
Chromatin
Chromatin
modification
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intro
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Degraded protein
Check-points where
gene expression can
be regulated
Regulation of Chromatin Structure
• Genes within highly packed heterochromatin are
usually not expressed
• Chemical modifications to histones and DNA of
chromatin influence both chromatin structure and
gene expression
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Histone Modification
• In histone acetylation, acetyl groups are attached
to positively charged lysines in histone tails
• This process seems to loosen chromatin structure,
thereby promoting the initiation of transcription
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-4
Histone
tails
DNA
double helix
Amino acids
available
for chemical
modification
Histone tails protrude outward from a nucleosome
Unacetylated histones
Acetylated histones
Acetylation of histone tails promotes loose chromatin
structure that permits transcription
DNA Methylation
• DNA methylation, the addition of methyl groups to
certain bases in DNA, is associated with reduced
transcription in some species
• In some species, DNA methylation causes longterm inactivation of genes in cellular differentiation
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Regulation of Transcription Initiation
• Chromatin-modifying enzymes provide initial
control of gene expression by making a region of
DNA either more or less able to bind the
transcription machinery
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Organization of a Typical Eukaryotic Gene
• Associated with most eukaryotic genes are control
elements, segments of noncoding DNA that help
regulate transcription by binding certain proteins
• Control elements and the proteins they bind are
critical to the precise regulation of gene
expression in different cell types
• Control elements are loosely analogous (similar in
concept) to the operator of the prokaryotic operon
in that binding of certain factors will influence the
levels of transcription
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-5
Enhancer
(distal control elements)
Proximal
control elements
Exon
Intron
Exon
Poly-A signal Termination
sequence
region
Intron Exon
DNA
Upstream
Downstream
Promoter
Primary RNA
transcript
5
(pre-mRNA)
Transcription
Exon
Intron
Intron RNA
Poly-A signal
Exon
Intron Exon
Cleaved 3 end
of primary
transcript
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Coding segment
mRNA
3
5 Cap
5 UTR
(untranslated
region)
Start
codon
Stop
codon
Poly-A
3 UTR
(untranslated tail
region)
The Roles of Transcription Factors
• To initiate transcription, eukaryotic RNA
polymerase requires the assistance of proteins
called transcription factors
• General transcription factors are essential for the
transcription of all protein-coding genes
• In eukaryotes, high levels of transcription of
particular genes depend on control elements
interacting with specific transcription factors
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Enhancers and Specific Transcription Factors
• Proximal control elements are located close to the
promoter
• Distal control elements, groups of which are called
enhancers, may be far away from a gene or even
in an intron
• An activator is a protein that binds to an enhancer
and stimulates transcription of a gene
Animation: Initiation of Transcription
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-6
Distal control
element
Activators
Promoter
Gene
DNA
TATA
box
Enhancer
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
Initiation complex
RNA synthesis
• Some transcription factors function as repressors,
inhibiting expression of a particular gene
• Some activators and repressors act indirectly by
influencing chromatin structure - recruiting
proteins that will affect levels of histone
acetylation:
Will activators tend to recruit proteins that
acetylate or de-acetylate histone? What about
repressors?
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-7
Liver cell
nucleus
Available
activators
Enhancer
Control
elements
Lens cell
nucleus
Available
activators
Promoter
Albumin
gene
Crystallin
gene
Albumin
gene not
expressed
Albumin
gene
expressed
Crystallin gene
not expressed
Liver cell
Crystallin gene
expressed
Lens cell
Coordinately Controlled Genes
• Unlike the genes of a prokaryotic operon,
coordinately controlled eukaryotic genes each
have a promoter and control elements
• The same regulatory sequences are common to
all the genes of a group, enabling recognition by
the same specific transcription factors
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Mechanisms of Post-Transcriptional Regulation
• Transcription alone does not account for gene
expression
• More and more examples are being found of
regulatory mechanisms that operate at various
stages after transcription
• Such post-transcriptional mechanisms allow a cell
to fine-tune gene expression rapidly in response to
environmental changes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
RNA Processing
• In alternative RNA splicing, different mRNA
molecules are produced from the same primary
transcript, depending on which RNA segments are
treated as exons and which as introns
Animation: RNA Processing
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-8
Exons
DNA
Primary
RNA
transcript
RNA splicing
mRNA
or
mRNA Degradation
• The life span of mRNA molecules in the cytoplasm
is a key to determining the protein synthesis
• The mRNA life span is determined in part by
sequences in the leader and trailer regions
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Initiation of Translation
• The initiation of translation of selected
mRNAs can be blocked by regulatory proteins that
bind to sequences or structures of the mRNA,
usually found in either the 5´ or 3´ UTR
• Additionally, a poly-A tail of insufficient length can
inhibit efficient translation of a transcript
• Alternatively, translation of all mRNAs
in a cell may be regulated simultaneously by mass
activation or inactivation of translation initiation
factors
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Protein Processing and Degradation
• After translation, various types of protein
processing, including cleavage and the addition of
chemical groups (such as phosphate groups), are
subject to control
• Proteasomes are giant protein complexes that
bind protein molecules and degrade them
Animation: Protein Processing
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 19-10
Proteasome
and ubiquitin
to be recycled
Ubiquitin
Proteasome
Protein to
be degraded
Ubiquitinated
protein
Protein entering a
proteasome
Animation: Protein Degradation
Protein
fragments
(peptides)