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Chapter 19:Eukaryotic Genome: Organization,
Regulation, and Evolution
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• Overview: How Eukaryotic Genomes Work and Evolve• In eukaryotes, the DNA-protein complex, called
chromatin– Is ordered into higher structural levels than the DNA-
protein complex in prokaryotes
Figure 19.1
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• Both prokaryotes and eukaryotes– Must alter their patterns of gene expression in
response to changes in environmental conditions
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• Concept 19.1: Chromatin structure is based on successive levels of DNA packing
• Eukaryotic DNA– Is precisely combined with a large amount of protein
• Eukaryotic chromosomes– Contain an enormous amount of DNA relative to
their condensed length
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Nucleosomes, or “Beads on a String”• Proteins called histones– Are responsible for the first level of DNA packing in
chromatin– Bind tightly to DNA
• The association of DNA and histones– Seems to remain intact throughout the cell cycle
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• In electron micrographs– Unfolded chromatin has the appearance of beads on a
string• Each “bead” is a nucleosome
– The basic unit of DNA packing
Figure 19.2 a
2 nm
10 nm
DNA double helix
Histonetails
His-tones
Linker DNA(“string”)
Nucleosome(“bad”)
Histone H1
(a) Nucleosomes (10-nm fiber)
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Nucleosome
30 nm
(b) 30-nm fiber
Higher Levels of DNA Packing• The next level of packing– Forms the 30-nm chromatin fiber
Figure 19.2 b
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• The 30-nm fiber, in turn– Forms looped domains, making up a 300-nm fiber
Figure 19.2 c
Protein scaffold
300 nm
(c) Looped domains (300-nm fiber)
Loops
Scaffold
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• In a mitotic chromosome– The looped domains themselves coil and fold
forming the characteristic metaphase chromosome
Figure 19.2 d
700 nm
1,400 nm
(d) Metaphase chromosome
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• In interphase cells– Most chromatin is in the highly extended form called
euchromatin
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• 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
• During development of a multicellular organism– Its cells undergo a process of specialization in form
and function called cell differentiation
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Differential Gene Expression• Each cell of a multicellular eukaryote– Expresses only a fraction of its genes
• In each type of differentiated cell– A unique subset of genes is expressed
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• Many key stages of gene expression– Can be regulated in eukaryotic cells
Figure 19.3
Signal
NUCLEUSChromatin
Chromatin modification:DNA unpacking involvinghistone acetylation and
DNA demethlation
Gene
DNAGene availablefor transcription
RNA Exon
Transcription
Primary transcript
RNA processing
Transport to cytoplasm
Intron
Cap mRNA in nucleus
Tail
CYTOPLASM
mRNA in cytoplasmDegradation
of mRNA
Translation
Polypetide
CleavageChemical modificationTransport to cellular
destination
Active protein
Degradation of protein
Degraded protein
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Regulation of Chromatin Structure• Genes within highly packed heterochromatin– Are usually not expressed
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Histone Modification• Chemical modification of histone tails– Can affect the configuration of chromatin and thus
gene expression
Figure 19.4a (a) Histone tails protrude outward from a nucleosome
Chromatin changes
Transcription
RNA processing
mRNA degradation
Translation
Protein processingand degradation
DNAdouble helix
Amino acidsavailablefor chemicalmodification
Histonetails
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• Histone acetylation– Seems to loosen chromatin structure and thereby
enhance transcription
Figure 19.4 b(b) Acetylation of histone tails promotes loose chromatin structure that permits transcription
Unacetylated histones Acetylated histones
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DNA Methylation• Addition of methyl groups to certain bases in DNA– Is associated with reduced transcription in some
species
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Epigenetic Inheritance• Epigenetic inheritance– Is the inheritance of traits transmitted by
mechanisms not directly involving the nucleotide sequence
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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
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Organization of a Typical Eukaryotic Gene• Associated with most eukaryotic genes are multiple
control elements– Segments of noncoding DNA that help regulate
transcription by binding certain proteins
Figure 19.5
Enhancer(distal control elements)
Proximalcontrol elements
DNA
UpstreamPromoter
Exon Intron Exon Intron
Poly-A signalsequence
Exon
Terminationregion
Transcription
Downstream
Poly-Asignal
ExonIntronExonIntronExonPrimary RNAtranscript(pre-mRNA)
5
Intron RNA
RNA processing:Cap and tail added;introns excised andexons spliced together
Coding segment
P P PGmRNA
5 Cap 5 UTR(untranslated
region)
Startcodon
Stopcodon
3 UTR(untranslated
region)
Poly-Atail
Chromatin changes
Transcription
RNA processing
mRNAdegradation
Translation
Protein processingand degradation
Cleared 3 endof primarytransport
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The Roles of Transcription Factors• To initiate transcription– Eukaryotic RNA polymerase requires the assistance
of proteins called transcription factors
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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
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Distal controlelement
Activators
Enhancer
PromoterGene
TATAbox General
transcriptionfactors
DNA-bendingprotein
Group ofMediator proteins
RNAPolymerase II
RNAPolymerase II
RNA synthesisTranscriptionInitiation complex
Chromatin changes
Transcription
RNA processing
mRNAdegradation
Translation
Protein processingand degradation
A DNA-bending proteinbrings the bound activators
closer to the promoter.Other transcription factors,
mediator proteins, and RNApolymerase are nearby.
2
Activator proteins bindto distal control elementsgrouped as an enhancer in the DNA. This enhancer hasthree binding sites.
1
The activators bind tocertain general transcription
factors and mediatorproteins, helping them form
an active transcriptioninitiation complex on the promoter.
3
• An activator– Is a protein that binds to an enhancer and stimulates
transcription of a gene
Figure 19.6
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• Some specific transcription factors function as repressors– To inhibit expression of a particular gene
• Some activators and repressors– Act indirectly by influencing chromatin structure
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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
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Mechanisms of Post-Transcriptional Regulation• An increasing number of examples
– Are being found of regulatory mechanisms that operate at various stages after transcription
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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
Figure 19.8
Chromatin changes
Transcription
RNA processing
mRNAdegradation
Translation
Protein processingand degradation
Exons
DNA
PrimaryRNAtranscript
mRNA
RNA splicing or
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mRNA Degradation
• The life span of mRNA molecules in the cytoplasm– Is an important factor in determining the protein
synthesis in a cell– Is determined in part by sequences in the leader
and trailer regions
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• RNA interference by single-stranded microRNAs (miRNAs)
– Can lead to degradation of an mRNA or block its translation
Figure 19.9
5
Chromatin changes
Transcription
RNA processing
mRNAdegradation
Translation
Protein processingand degradation
Degradation of mRNAOR
Blockage of translation
Target mRNA
miRNA
Proteincomplex
Dicer
Hydrogenbond
The micro-RNA (miRNA)precursor foldsback on itself,held togetherby hydrogenbonds.
12 An enzymecalled Dicer movesalong the double-stranded RNA, cutting it intoshorter segments.
2 One strand ofeach short double-stranded RNA isdegraded; the otherstrand (miRNA) thenassociates with acomplex of proteins.
3 The boundmiRNA can base-pairwith any targetmRNA that containsthe complementarysequence.
4 The miRNA-proteincomplex prevents geneexpression either bydegrading the targetmRNA or by blockingits translation.
5
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Initiation of Translation• The initiation of translation of selected mRNAs– Can be blocked by regulatory proteins that bind to
specific sequences or structures of the mRNA
• Alternatively, translation of all the mRNAs in a cell– May be regulated simultaneously
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Protein Processing and Degradation• After translation
– Various types of protein processing, including cleavage and the addition of chemical groups, are subject to control
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• Proteasomes– Are giant protein complexes that bind protein
molecules and degrade them
Figure 19.10
Chromatin changes
Transcription
RNA processing
mRNAdegradation
Translation
Protein processingand degradation
Ubiquitin
Protein tobe degraded
Ubiquinatedprotein
Proteasome
Proteasomeand ubiquitinto be recycled
Proteinfragments(peptides)
Protein entering aproteasome
Multiple ubiquitin mol-ecules are attached to a proteinby enzymes in the cytosol.
1 The ubiquitin-tagged proteinis recognized by a proteasome,which unfolds the protein andsequesters it within a central cavity.
2 Enzymatic components of theproteasome cut the protein intosmall peptides, which can befurther degraded by otherenzymes in the cytosol.
3
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• Concept 19.3: Cancer results from genetic changes that affect cell cycle control
• The gene regulation systems that go wrong during cancer– Turn out to be the very same systems that play
important roles in embryonic development
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Types of Genes Associated with Cancer• The genes that normally regulate cell growth
and division during the cell cycle– Include genes for growth factors, their receptors,
and the intracellular molecules of signaling pathways
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Oncogenes and Proto-Oncogenes• Oncogenes– Are cancer-causing genes
• Proto-oncogenes– Are normal cellular genes that code for proteins that
stimulate normal cell growth and division
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• A DNA change that makes a proto-oncogene excessively active– Converts it to an oncogene, which may promote
excessive cell division and cancer
Figure 19.11
Proto-oncogene
DNA
Translocation or transposition:gene moved to new locus,under new controls
Gene amplification:multiple copies of the gene
Point mutationwithin a controlelement
Point mutationwithin the gene
OncogeneOncogene
Normal growth-stimulatingprotein in excess
Hyperactive ordegradation-resistant protein
Normal growth-stimulatingprotein in excess
Normal growth-stimulatingprotein in excess
Newpromoter
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Tumor-Suppressor Genes• Tumor-suppressor genes– Encode proteins that inhibit abnormal cell division
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Interference with Normal Cell-Signaling Pathways• Many proto-oncogenes and tumor suppressor
genes– Encode components of growth-stimulating and
growth-inhibiting pathways, respectively
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Figure 19.12a
(a) Cell cycle–stimulating pathway.This pathway is triggered by a growthfactor that binds to its receptor in theplasma membrane. The signal is relayed to a G protein called Ras. Like all G proteins, Rasis active when GTP is bound to it. Ras passesthe signal to a series of protein kinases.The last kinase activates a transcriptionactivator that turns on one or more genes for proteins that stimulate the cell cycle. If amutation makes Ras or any other pathway component abnormally active, excessive celldivision and cancer may result.
1
2
4
3
5
GTP
Ras
Ras
GTP
HyperactiveRas protein(product ofoncogene)issues signalson its own
NUCLEUS
Gene expression
Protein thatstimulatesthe cell cycle
P
P
P
P
MUTATION
P
DNA
P
• The Ras protein, encoded by the ras gene– Is a G protein that relays a signal from a growth
factor receptor on the plasma membrane to a cascade of protein kinases
2 Receptor
Transcriptionfactor (activator)
5
G protein3
Protein kinases(phosphorylationcascade)
4
1 Growth factor
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• The p53 gene encodes a tumor-suppressor protein– That is a specific transcription factor that promotes
the synthesis of cell cycle–inhibiting proteins
Figure 19.12b
UVlight
DNA
Defective ormissingtranscriptionfactor, such asp53, cannotactivatetranscription
MUTATION
Protein thatinhibitsthe cell cycle
pathway, DNA damage is an intracellularsignal that is passed via protein kinasesand leads to activation of p53. Activatedp53 promotes transcription of the gene for aprotein that inhibits the cell cycle. Theresulting suppression of cell division ensuresthat the damaged DNA is not replicated.Mutations causing deficiencies in anypathway component can contribute to thedevelopment of cancer.
(b) Cell cycle–inhibiting pathway. In this1
3
2
Protein kinases2
3 Activeformof p53
DNA damagein genome
1
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• Mutations that knock out the p53 gene– Can lead to excessive cell growth and cancer
Figure 19.12c
EFFECTS OF MUTATIONS
Proteinoverexpressed
Cell cycleoverstimulated
Increased celldivision
Cell cycle notinhibited
Protein absent
Effects of mutations. Increased cell division, possibly leading to cancer, can result if the cell cycle is overstimulated, as in (a), or not inhibited when it normally would be, as in (b).
(c)
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The Multistep Model of Cancer Development• Normal cells are converted to cancer cells
– By the accumulation of multiple mutations affecting proto-oncogenes and tumor-suppressor genes
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• A multistep model for the development of colorectal cancer
Figure 19.13
Colon
Colon wall
Normal colonepithelial cells
Small benigngrowth (polyp)
Larger benigngrowth (adenoma)
Malignant tumor(carcinoma)
2 Activation ofras oncogene
3 Loss oftumor-suppressorgene DCC
4 Loss oftumor-suppressorgene p53
5 Additionalmutations
1 Loss of tumor-suppressorgene APC (orother)
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• Certain viruses– Promote cancer by integration of viral DNA into a
cell’s genome
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Inherited Predisposition to Cancer• Individuals who inherit a mutant oncogene or tumor-suppressor allele– Have an increased risk of developing certain types of
cancer
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• Concept 19.4: Eukaryotic genomes can have many noncoding DNA sequences in addition to genes
• The bulk of most eukaryotic genomes– Consists of noncoding DNA sequences, often
described in the past as “junk DNA”
• However, much evidence is accumulating– That noncoding DNA plays important roles in the cell
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Relationship Between Genomic Composition and Organismal Complexity
• Compared with prokaryotic genomes, the genomes of eukaryotes
– Generally are larger
– Have longer genes
– Contain a much greater amount of noncoding DNA both associated with genes and between genes
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• Now that the complete sequence of the human genome is available– We know what makes up most of the 98.5% that does
not code for proteins, rRNAs, or tRNAs
Figure 19.14
Exons (regions of genes codingfor protein, rRNA, tRNA) (1.5%)
RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)
Introns andregulatorysequences(24%)
UniquenoncodingDNA (15%)Repetitive
DNAunrelated totransposableelements(about 15%)
Alu elements(10%)
Simple sequenceDNA (3%)
Large-segmentduplications (5-6%)
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Transposable Elements and Related Sequences• The first evidence for wandering DNA segments
– Came from geneticist Barbara McClintock’s breeding experiments with Indian corn
Figure 19.15
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TransposonNew copy oftransposon
Transposonis copied
DNA of genome
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
RetrotransposonNew copy of
retrotransposon
DNA of genome
RNA
Reversetranscriptase
(b) Retrotransposon movement
Insertion
Movement of Transposons and Retrotransposons• Eukaryotic transposable elements are of two types
– Transposons, which move within a genome by means of a DNA intermediate
– Retrotransposons, which move by means of an RNA intermediate
Figure 19.16a, b
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Sequences Related to Transposable Elements• Multiple copies of transposable elements and
sequences related to them– Are scattered throughout the eukaryotic genome
• In humans and other primates– A large portion of transposable element–related
DNA consists of a family of similar sequences called Alu elements
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Other Repetitive DNA, Including Simple Sequence DNA
• Simple sequence DNA– Contains many copies of tandemly repeated short
sequences– Is common in centromeres and telomeres, where it
probably plays structural roles in the chromosome
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Genes and Multigene Families• Most eukaryotic genes– Are present in one copy per haploid set of
chromosomes
• The rest of the genome– Occurs in multigene families, collections of identical
or very similar genes
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DNA RNA transcripts
Non-transcribedspacer Transcription unit
DNA18S 5.8S 28S
rRNA
5.8S28S
18S
• Some multigene families– Consist of identical DNA sequences, usually
clustered tandemly, such as those that code for RNA products
Figure 19.17a Part of the ribosomal RNA gene family
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• The classic examples of multigene families of nonidentical genes
– Are two related families of genes that encode globins
Figure 19.17b The human -globin and -globin gene families
-GlobinHeme
Hemoglobin
-Globin
-Globin gene family -Globin gene family
Chromosome 16 Chromosome 11
Embryo
Fetusand adult Embryo Fetus Adult
GA
2
1
2 1
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• Concept 19.5: Duplications, rearrangements, and mutations of DNA contribute to genome evolution
• The basis of change at the genomic level is mutation– Which underlies much of genome evolution
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Duplication of Chromosome Sets• Accidents in cell division– Can lead to extra copies of all or part of a genome,
which may then diverge if one set accumulates sequence changes
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Duplication and Divergence of DNA Segments• Unequal crossing over during prophase I of meiosis
– Can result in one chromosome with a deletion and another with a duplication of a particular gene
Figure 19.18
Nonsisterchromatids
Transposableelement
Gene
Incorrect pairingof two homologuesduring meiosis
Crossover
and
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Evolution of Genes with Related Functions: The Human Globin Genes
• The genes encoding the various globin proteins
– Evolved from one common ancestral globin gene, which duplicated and diverged
Figure 19.19
Ancestral globin gene
2 1
2 1 G A
-Globin gene familyon chromosome 16
-Globin gene familyon chromosome 11
Evo
lutio
nary
tim
e
Duplication ofancestral gene
Mutation inboth copiesTransposition todifferent chromosomes
Further duplicationsand mutations
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• Subsequent duplications of these genes and random mutations– Gave rise to the present globin genes, all of which
code for oxygen-binding proteins
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• The similarity in the amino acid sequences of the various globin proteins– Supports this model of gene duplication and mutation
Table 19.1
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Evolution of Genes with Novel Functions• The copies of some duplicated genes
– Have diverged so much during evolutionary time that the functions of their encoded proteins are now substantially different
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling
• A particular exon within a gene
– Could be duplicated on one chromosome and deleted from the homologous chromosome
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• In exon shuffling– Errors in meiotic recombination lead to the occasional
mixing and matching of different exons either within a gene or between two nonallelic genes
Figure 19.20
EGF EGF EGF EGF
Epidermal growthfactor gene with multipleEGF exons (green)
F F F F
Fibronectin gene with multiple“finger” exons (orange)
Exonshuffling
Exonduplication
Exonshuffling
K
F EGF K K
Plasminogen gene with a“kfingle” exon (blue)
Portions of ancestral genes TPA gene as it exists today
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How Transposable Elements Contribute to Genome Evolution
• Movement of transposable elements or recombination between copies of the same element– Occasionally generates new sequence combinations
that are beneficial to the organism
• Some mechanisms– Can alter the functions of genes or their patterns of
expression and regulation