chapter 18 pt. 2. concept 18.3: noncoding rnas play multiple roles in controlling gene expression...
TRANSCRIPT
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Chapter 18 Pt. 2
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Concept 18.3: Noncoding RNAs play multiple roles in controlling gene expression
• Only a small fraction of DNA codes for proteins, rRNA, and tRNA
• A significant amount of the genome may be transcribed into noncoding RNAs
• Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration
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Effects on mRNAs by MicroRNAs and Small Interfering RNAs
• MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to mRNA
• These can degrade mRNA or block its translation
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Fig. 18-13
miRNA-proteincomplex(a) Primary miRNA transcript
Translation blocked
Hydrogenbond
(b) Generation and function of miRNAs
Hairpin miRNA
miRNA
Dicer
3
mRNA degraded
5
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• The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi)
• RNAi is caused by small interfering RNAs (siRNAs)• siRNAs and miRNAs are similar but form from
different RNA precursors
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Chromatin Remodeling and Silencing of Transcription by Small RNAs
• siRNAs play a role in heterochromatin formation and can block large regions of the chromosome
• Small RNAs may also block transcription of specific genes
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Concept 18.4: A program of differential gene expression leads to
the different cell types in a multicellular organism• During embryonic development, a fertilized egg
gives rise to many different cell types• Cell types are organized successively into tissues,
organs, organ systems, and the whole organism• Gene expression orchestrates the developmental
programs of animals
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A Genetic Program for Embryonic Development
• The transformation from zygote to adult results from cell division, cell differentiation, and morphogenesis
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Fig. 18-14
(a) Fertilized eggs of a frog (b) Newly hatched tadpole
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Fig. 18-14a
(a) Fertilized eggs of a frog
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Fig. 18-14b
(b) Newly hatched tadpole
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• Cell differentiation is the process by which cells become specialized in structure and function
• The physical processes that give an organism its shape constitute morphogenesis
• Differential gene expression results from genes being regulated differently in each cell type
• Materials in the egg can set up gene regulation that is carried out as cells divide
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Cytoplasmic Determinants and Inductive Signals
• An egg’s cytoplasm contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg
• Cytoplasmic determinants are maternal substances in the egg that influence early development
• As the zygote divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression
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Fig. 18-15
(b) Induction by nearby cells(a) Cytoplasmic determinants in the egg
Two differentcytoplasmicdeterminants
Unfertilized egg cell
Sperm
Fertilization
Zygote
Mitoticcell division
Two-celledembryo
Signalmolecule(inducer)
Signaltransductionpathway
Early embryo(32 cells)
Nucleus
NUCLEUS
Signalreceptor
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Fig. 18-15a
(a) Cytoplasmic determinants in the egg
Two differentcytoplasmicdeterminants
Unfertilized egg cell
Sperm
Fertilization
Zygote
Mitoticcell division
Two-celledembryo
Nucleus
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Fig. 18-15b
(b) Induction by nearby cells
Signalmolecule(inducer)
Signaltransductionpathway
Early embryo(32 cells)
NUCLEUS
Signalreceptor
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• The other important source of developmental information is the environment around the cell, especially signals from nearby embryonic cells
• In the process called induction, signal molecules from embryonic cells cause transcriptional changes in nearby target cells
• Thus, interactions between cells induce differentiation of specialized cell types
Animation: Cell Signaling
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Sequential Regulation of Gene Expression During Cellular
Differentiation• Determination commits a cell to its final fate• Determination precedes differentiation• Cell differentiation is marked by the production of
tissue-specific proteins
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• Myoblasts produce muscle-specific proteins and form skeletal muscle cells
• MyoD is one of several “master regulatory genes” that produce proteins that commit the cell to becoming skeletal muscle
• The MyoD protein is a transcription factor that binds to enhancers of various target genes
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Fig. 18-16-1
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
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Fig. 18-16-2
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
OFFmRNA
MyoD protein(transcriptionfactor)
Myoblast(determined)
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Fig. 18-16-3
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
OFFmRNA
MyoD protein(transcriptionfactor)
Myoblast(determined)
mRNA mRNA mRNA mRNA
Myosin, othermuscle proteins,and cell cycle–blocking proteinsPart of a muscle fiber
(fully differentiated cell)
MyoD Anothertranscriptionfactor
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Pattern Formation: Setting Up the Body Plan
• Pattern formation is the development of a spatial organization of tissues and organs
• In animals, pattern formation begins with the establishment of the major axes
• Positional information, the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells
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• Pattern formation has been extensively studied in the fruit fly Drosophila melanogaster
• Combining anatomical, genetic, and biochemical approaches, researchers have discovered developmental principles common to many other species, including humans
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The Life Cycle of Drosophila
• In Drosophila, cytoplasmic determinants in the unfertilized egg determine the axes before fertilization
• After fertilization, the embryo develops into a segmented larva with three larval stages
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Fig. 18-17ThoraxHead Abdomen
0.5 mm
Dorsal
Ventral
RightPosterior
LeftAnteriorBODY
AXES
Follicle cell
(a) Adult
Nucleus
Eggcell
Nurse cell
Egg celldeveloping withinovarian follicle
Unfertilized egg
Fertilized egg
Depletednurse cells
Eggshell
FertilizationLaying of egg
Bodysegments
Embryonicdevelopment
Hatching
0.1 mm
Segmentedembryo
Larval stage
(b) Development from egg to larva
1
2
3
4
5
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Fig. 18-17a
ThoraxHead Abdomen
0.5 mm
Dorsal
Ventral
RightPosterior
LeftAnteriorBODY
AXES
(a) Adult
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Fig. 18-17bFollicle cell
Nucleus
Eggcell
Nurse cell
Egg celldeveloping withinovarian follicle
Unfertilized egg
Fertilized egg
Depletednurse cells
Eggshell
FertilizationLaying of egg
Bodysegments
Embryonicdevelopment
Hatching
0.1 mm
Segmentedembryo
Larval stage
(b) Development from egg to larva
1
2
3
4
5
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Genetic Analysis of Early Development: Scientific Inquiry
• Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus won a Nobel 1995 Prize for decoding pattern formation in Drosophila
• Lewis demonstrated that genes direct the developmental process
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Fig. 18-18
Antenna
MutantWild type
Eye
Leg
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Fig. 18-18a
Antenna
Wild type
Eye
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Fig. 18-18b
Mutant
Leg
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• Nüsslein-Volhard and Wieschaus studied segment formation
• They created mutants, conducted breeding experiments, and looked for corresponding genes
• Breeding experiments were complicated by embryonic lethals, embryos with lethal mutations
• They found 120 genes essential for normal segmentation
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Axis Establishment
• Maternal effect genes encode for cytoplasmic determinants that initially establish the axes of the body of Drosophila
• These maternal effect genes are also called egg-polarity genes because they control orientation of the egg and consequently the fly
Animation: Development of Head-Tail Axis in Fruit Flies
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• One maternal effect gene, the bicoid gene, affects the front half of the body
• An embryo whose mother has a mutant bicoid gene lacks the front half of its body and has duplicate posterior structures at both ends
Bicoid: A Morphogen Determining Head Structures
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Fig. 18-19
Tail
TailTail
Head
Wild-type larva
T1 T2T3
A1 A2 A3 A4 A5 A6A7
A8
A8A7A6A7A8
Mutant larva (bicoid)
EXPERIMENT
RESULTS
CONCLUSION
Fertilization,translationof bicoidmRNA Bicoid protein in early
embryo
Anterior endBicoid mRNA in matureunfertilized egg
100 µm
bicoid mRNA
Nurse cells
Egg
Developing egg Bicoid mRNA in mature unfertilized egg Bicoid protein in early embryo
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Fig. 18-19a
T1 T2T3
A1 A2 A3 A4 A5 A6A7
A8
A8A7 A6 A7
Tail
TailTail
Head
Wild-type larva
Mutant larva (bicoid)
EXPERIMENT
A8
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Fig. 18-19b
Fertilization,translationof bicoidmRNA Bicoid protein in early
embryo
Anterior endBicoid mRNA in matureunfertilized egg
100 µm
RESULTS
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Fig. 18-19c
bicoid mRNA
Nurse cells
Egg
Developing egg Bicoid mRNA in matureunfertilized egg
Bicoid proteinin early embryo
CONCLUSION
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• This phenotype suggests that the product of the mother’s bicoid gene is concentrated at the future anterior end
• This hypothesis is an example of the gradient hypothesis, in which gradients of substances called morphogens establish an embryo’s axes and other features
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• The bicoid research is important for three reasons:– It identified a specific protein required for some
early steps in pattern formation– It increased understanding of the mother’s role in
embryo development– It demonstrated a key developmental principle that a
gradient of molecules can determine polarity and position in the embryo
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Concept 18.5: Cancer results from genetic changes that affect cell cycle
control• The gene regulation systems that go wrong during cancer are the very same systems involved in embryonic development
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Types of Genes Associated with Cancer
• Cancer can be caused by mutations to genes that regulate cell growth and division
• Tumor viruses can cause cancer in animals including humans
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Oncogenes and Proto-Oncogenes
• Oncogenes are cancer-causing genes• Proto-oncogenes are the corresponding normal
cellular genes that are responsible for normal cell growth and division
• Conversion of a proto-oncogene to an oncogene can lead to abnormal stimulation of the cell cycle
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Fig. 18-20
Normal growth-stimulatingprotein in excess
Newpromoter
DNA
Proto-oncogene
Gene amplification:Translocation ortransposition:
Normal growth-stimulatingprotein in excess
Normal growth-stimulatingprotein in excess
Hyperactive ordegradation-resistant protein
Point mutation:
Oncogene Oncogene
within a control element within the gene
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• Proto-oncogenes can be converted to oncogenes by– Movement of DNA within the genome: if it ends up
near an active promoter, transcription may increase– Amplification of a proto-oncogene: increases the
number of copies of the gene– Point mutations in the proto-oncogene or its control
elements: causes an increase in gene expression
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Tumor-Suppressor Genes
• Tumor-suppressor genes help prevent uncontrolled cell growth
• Mutations that decrease protein products of tumor-suppressor genes may contribute to cancer onset
• Tumor-suppressor proteins– Repair damaged DNA
– Control cell adhesion
– Inhibit the cell cycle in the cell-signaling pathway
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Interference with Normal Cell-Signaling Pathways
• Mutations in the ras proto-oncogene and p53 tumor-suppressor gene are common in human cancers
• Mutations in the ras gene can lead to production of a hyperactive Ras protein and increased cell division
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Fig. 18-21
Receptor
Growthfactor
G protein
GTP
Ras
GTP
Ras
Protein kinases(phosphorylationcascade)
Transcriptionfactor (activator)
DNA
HyperactiveRas protein(product ofoncogene)issuessignalson its own
MUTATION
NUCLEUS
Gene expression
Protein thatstimulatesthe cell cycle
(a) Cell cycle–stimulating pathway
MUTATIONProtein kinases
DNA
DNA damagein genome
Defective ormissingtranscriptionfactor, suchas p53, cannotactivatetranscription
Protein thatinhibitsthe cell cycle
Activeformof p53
UVlight
(b) Cell cycle–inhibiting pathway
(c) Effects of mutations
EFFECTS OF MUTATIONS
Cell cycle notinhibited
Protein absent
Increased celldivision
Proteinoverexpressed
Cell cycleoverstimulated
1
2
3
4
5
2
1
3
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Fig. 18-21a
Receptor
Growthfactor
G protein GTP
Ras
GTP
Ras
Protein kinases(phosphorylationcascade)
Transcriptionfactor (activator)
DNA
HyperactiveRas protein(product ofoncogene)issuessignalson its own
MUTATION
NUCLEUS
Gene expression
Protein thatstimulatesthe cell cycle
(a) Cell cycle–stimulating pathway
11
3
4
5
2
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Fig. 18-21b
MUTATIONProtein kinases
DNA
DNA damagein genome
Defective ormissingtranscriptionfactor, suchas p53, cannotactivatetranscription
Protein thatinhibitsthe cell cycle
Activeformof p53
UVlight
(b) Cell cycle–inhibiting pathway
2
3
1
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Fig. 18-21c
(c) Effects of mutations
EFFECTS OF MUTATIONS
Cell cycle notinhibited
Protein absent
Increased celldivision
Proteinoverexpressed
Cell cycleoverstimulated
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• Suppression of the cell cycle can be important in the case of damage to a cell’s DNA; p53 prevents a cell from passing on mutations due to DNA damage
• Mutations in the p53 gene prevent suppression of the cell cycle
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The Multistep Model of Cancer Development
• Multiple mutations are generally needed for full-fledged cancer; thus the incidence increases with age
• At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several tumor-suppressor genes
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Fig. 18-22
EFFECTS OF MUTATIONS
Malignant tumor(carcinoma)
Colon
Colon wall
Loss of tumor-suppressor geneAPC (or other)
Activation ofras oncogene
Loss oftumor-suppressorgene DCC
Loss oftumor-suppressorgene p53
Additionalmutations
Larger benigngrowth (adenoma)
Small benigngrowth (polyp)
Normal colonepithelial cells
5
42
3
1
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Fig. 18-22a
Colon
Colon wall
Normal colonepithelial cells
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Fig. 18-22b
Loss of tumor-suppressor geneAPC (or other)
Small benigngrowth (polyp)
1
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Fig. 18-22c
Activation ofras oncogene
Loss oftumor-suppressorgene DCC
Larger benigngrowth (adenoma)
2
3
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Fig. 18-22d
Malignant tumor(carcinoma)
Loss oftumor-suppressorgene p53
Additionalmutations5
4
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Inherited Predisposition and Other Factors Contributing to Cancer
• Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes
• Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer
• Mutations in the BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers
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Fig. 18-23
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Fig. 18-UN1
Operon
Promoter
Operator
Genes
RNApolymerase
PolypeptidesA B C
CBA
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Fig. 18-UN2
PromoterGenes
Genes not expressed
Inactive repressor:no corepressor present Corepressor
Active repressor:corepressor bound
Genes expressed
Operator
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Fig. 18-UN3
Promoter
Genes
Genes not expressed
Active repressor:no inducer present
Inactive repressor:inducer bound
Genes expressed
Operator
Fig. 18-UN2
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Fig. 18-UN4
• Genes in highly compactedchromatin are generally nottranscribed.
Chromatin modification
• DNA methylation generallyreduces transcription.
• Histone acetylation seems toloosen chromatin structure,enhancing transcription.
Chromatin modification
Transcription
RNA processing
TranslationmRNAdegradation
Protein processingand degradation
mRNA degradation
• Each mRNA has acharacteristic life span,determined in part bysequences in the 5 and3 UTRs.
• Protein processing anddegradation by proteasomesare subject to regulation.
Protein processing and degradation
• Initiation of translation can be controlledvia regulation of initiation factors.
Translation
ormRNA
Primary RNAtranscript
• Alternative RNA splicing:
RNA processing
• Coordinate regulation:
Enhancer forliver-specific genes
Enhancer forlens-specific genes
Bending of the DNA enables activators tocontact proteins at the promoter, initiatingtranscription.
Transcription
• Regulation of transcription initiation:DNA control elements bind specifictranscription factors.
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Fig. 18-UN5
Chromatin modification
RNA processing
TranslationmRNAdegradation
Protein processingand degradation
mRNA degradation
• miRNA or siRNA can target specific mRNAsfor destruction.
• miRNA or siRNA can block the translationof specific mRNAs.
Transcription
• Small RNAs can promote the formation ofheterochromatin in certain regions, blocking transcription.
Chromatin modification
Translation
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Fig. 18-UN6
Enhancer Promoter
Gene 3
Gene 4
Gene 5
Gene 2
Gene 1
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Fig. 18-UN7
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Fig. 18-UN8
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You should now be able to:
1. Explain the concept of an operon and the function of the operator, repressor, and corepressor
2. Explain the adaptive advantage of grouping bacterial genes into an operon
3. Explain how repressible and inducible operons differ and how those differences reflect differences in the pathways they control
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4. Explain how DNA methylation and histone acetylation affect chromatin structure and the regulation of transcription
5. Define control elements and explain how they influence transcription
6. Explain the role of promoters, enhancers, activators, and repressors in transcription control
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7. Explain how eukaryotic genes can be coordinately expressed
8. Describe the roles played by small RNAs on gene expression
9. Explain why determination precedes differentiation
10. Describe two sources of information that instruct a cell to express genes at the appropriate time
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11. Explain how maternal effect genes affect polarity and development in Drosophila embryos
12. Explain how mutations in tumor-suppressor genes can contribute to cancer
13. Describe the effects of mutations to the p53 and ras genes