Chapter 19: Eukaryotic Genome: Organization, Regulation, and Evolution.

Chapter 19:Eukaryotic Genome: Organization,

Regulation, and Evolution

• 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

• Both prokaryotes and eukaryotes– Must alter their patterns of gene expression in

response to changes in environmental conditions

• 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

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

• 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)

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

• 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

• 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

• In interphase cells– Most chromatin is in the highly extended form called

euchromatin

• 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

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

• 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

Regulation of Chromatin Structure• Genes within highly packed heterochromatin– Are usually not expressed

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

• 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

DNA Methylation• Addition of methyl groups to certain bases in DNA– Is associated with reduced transcription in some

species

Epigenetic Inheritance• Epigenetic inheritance– Is the inheritance of traits transmitted by

mechanisms not directly involving the nucleotide sequence

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

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


Cleared 3 endof primarytransport

The Roles of Transcription Factors• To initiate transcription– Eukaryotic RNA polymerase requires the assistance

of proteins called transcription factors

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

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


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

• Some specific transcription factors function as repressors– To inhibit expression of a particular gene

• Some activators and repressors– Act indirectly by influencing chromatin structure

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

Mechanisms of Post-Transcriptional Regulation• An increasing number of examples

– Are being found of regulatory mechanisms that operate at various stages after transcription

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


Exons

DNA

PrimaryRNAtranscript

mRNA

RNA splicing or

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

• 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


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

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

Protein Processing and Degradation• After translation

– Various types of protein processing, including cleavage and the addition of chemical groups, are subject to control

• Proteasomes– Are giant protein complexes that bind protein

molecules and degrade them

Figure 19.10

Chromatin changes

Transcription

RNA processing

mRNAdegradation

Translation


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

• 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

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

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

• 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



Newpromoter

Tumor-Suppressor Genes• Tumor-suppressor genes– Encode proteins that inhibit abnormal cell division

Interference with Normal Cell-Signaling Pathways• Many proto-oncogenes and tumor suppressor

genes– Encode components of growth-stimulating and

growth-inhibiting pathways, respectively

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

• 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

• 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)

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

• 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)

• Certain viruses– Promote cancer by integration of viral DNA into a

cell’s genome

Inherited Predisposition to Cancer• Individuals who inherit a mutant oncogene or tumor-suppressor allele– Have an increased risk of developing certain types of

cancer

• 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

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

• 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%)

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

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

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

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

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

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

• 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

• 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

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

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


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

• Subsequent duplications of these genes and random mutations– Gave rise to the present globin genes, all of which

code for oxygen-binding proteins

• The similarity in the amino acid sequences of the various globin proteins– Supports this model of gene duplication and mutation

Table 19.1

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


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

• 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

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

Chapter 19: Eukaryotic Genome: Organization, Regulation, and Evolution.

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