Lewin Benjamin (ed.) Genes IX
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ChromosomaI Segregation
May Require Site-Specific
Recombination
41.5
Partitioni ng Involves Separation
of the Chromosomes
417
Singte-Copy
Plasmids Have a
Partitioning
System
479
Plasmid
Incompatibitity Is Determined
by the
Rep[icon 421
The CotEr Compatibitity
System Is Controtled
by an RNA
Regutator 422
How
Do Mitochondria Replicate and Segregate?
424
Summary 425
18 DNA Replication 428
Introduction 429
DNA Polymerases
Are
the
Enzymes That
Make DNA 430
DNA Polymerases Have Various
Nuctease Activities
431'
DNA Potymerases Control the
Fidel.ity of Reptication
432
DNA
Potymerases Have a Common Structure
433
DNA Synthesis
Is
Semidiscontinuous
434
The <pX Model System Shows
How Single-Stranded
DNA
Is
Generated
for
Reolication
435
Priming
Is Required to Start
DNA
Synthesis
437
DNA
Potymerase Hotoenzyme
Has Three
Subcomptexes 439
The Ctamp Controls
Association of Core
Enzyme
with
DNA
440
Coordinating
Synthesis ofthe
Lagging and
Leading
Strands 442
0kazaki
Fragments Are Linked by
Ligase 443
Separate
Eukaryotic
DNA Potymerases Undertake
Initiation and
Elongation 444
Phage
T4 Provides lts Own Reptication
Apparatus 445
Creating
the Replication
Forks at an 0rigin
448
Common
Events
jn
Priming Replication
at the
0rigin 450
The
Primosome Is
Needed
to
Restart Reptication
451
Summary
453
19
Homologous and Site-Specific
Recombination
457
Introduction 459
Homotogous
Recombination Occurs
between
Synapsed
Chromosomes
460
Breakage and
Reunion
Involves Heteroduptex
DNA 462
Doubte-Strand
Breaks Initiate Recombination
464
Recombining
Chromosomes
Are Connected
by the
Synaptonema[
ComP[ex
465
The
SynaptonemaI
Complex
Forms after
Doubte-Strand
Breaks
467
Pairing
and
Synaptonemal
Complex
Formation
Are
Indeoendent
469
The Bacterial
RecBCD
System
Is Stimutated
by
chi Sequences
470
Strand-Transfer
Proteins
Catalyze
Single-Strand
Assimilation
471'
The Ruv
System
Resolves
Hol.l.iday
Junctions
473
Gene Conversion
Accounts
for
Intera[[e[ic
Recombination
475
Supercoiting
Affects
the
Structure
of
DNA
476
Topoisomerases
Relax or
Introduce
Supercoits
in DNA
478
Topoisomerases
Break
and
Reseal
Strands
480
Gyrase
Functions
by
Coi[
Inversion
481'
Specialized
Recombination
Invo[ves
Specific
Sites
482
Site-Specific
Recombination
Involves
Breakage
and
Reunion
484
Site-Specific
Recombination
Resembles
Topoisomerase
Activity
484
Lambda
Recombination
0ccurs
in an
Intasome
486
Yeast Can
Switch
Sitent
and
Active
Loci for
Mating
Type
488
Ihe
MAT Locus
Codes
for Regulator
Proteins
490
Sitent
Cassettes
at
HML
and
HMR
Are Repressed
492
UnidirectionaI
Transposition
Is
Initiated
by the
Recipient
MAT
Locus 493
Regulation
of
H0
Expression
Controts
Switching
494
Summary
496
20
Repair
Systems
499
Introduction
500
Repair
Systems
Correct
Damage
to
DNA
502
Excision
Repair
Systems
in E. coli
503
Excision-Repair
Pathways
in
Mammalian
Celts 504
Base
Flipping
Is Used
by
Methytases
and
Gtycosytases
506
Error-Prone
Repair
and
Mutator
Phenotypes
507
Controlling
the
Direction
of
Mismatch
Repair 507
Recombination-Repair
Systems
in E. coli
510
Recombination
Is an
Important
Mechanism
to
Recover
from
Replication
Errors
51'1'
RecA
Triggers
the
S0S
SYstem
513
Contents
xi
Eukaryotic
Cetls
Have
Conserved
Repair
Systems
515
A
Common
System
Repairs
Doub[e-Strand
Breaks
51,6
Summary
518
21
Transposons
521
introduction
5Zz
Insertion
Sequences
Are
Simpte Transposition
Modutes
524
Composite
Transposons
Have
IS Modutes
525
Transposition
0ccurs
by Both
Repticative
and Nonrepticative
Mechanisms
527
Transposons
Cause
Rearrangement
of DNA
5Zg
Common
Intermediates
for
Transposition
530
Repticative
Transposition
proceeds
through
a Cointegrate
531
]Zl.Fl
Nonrepticative
Transposition
proceeds
by
Breakage
and Reunion
533
TnA
Transposition
Requires
Transposase
and Resolvase
534
Transposition
ofTn10
Has Muttiple
Controls
536
Controlting
Etements
in
Maize
Cause Breakaqe
and
Rearrangements
538
Controtling
Etements
Form
Families
of Transposons
540
Spm Elements
Inftuence
Gene Expression
542
The
Ro[e
of Transposable
Elements
in Hybrid
Dysgenesis
544
P E[ements
Are
Activated
in
the Germline
545
Summary
546
22
Retroviruses
and
Retroposons
550
Introduction
551
The
Retrovirus
Life
Cycte Involves
Transposition-Like
Events
557
Retroviral
Genes
Code for
potyproteins
552
Virat
DNA Is
Generated
by Reverse
Transcription
554
Viral. DNA
Integrates
into
the
Chromosome
556
Retroviruses
May
Transduce
Cetlular
Sequences
559
Yeast
Iy
Elements
Resemble
Retroviruses
559
Many Transposable
Etements
Reside in
Drosophilo
melanogoster
567
Retroposons
Fat[
into
Three
Ctasses
562
The
Atu
Family
Has
Many
Widety
Dispersed
Members
564
Processed
Pseudogenes
0riginated
as Substrates
for
Transposition
565
LINES
Use an Endonuclease
to Generate
a
Priming
End
566
Summary
567
23 Immune
Diversity
570
Introduction
572
C[onaI
Se[ection Amplifies
Lymphocytes
That
Respond
to
IndividuaI
Antigens
574
Immunogtobulin
Genes Are Assembted
from
Their
parts
in Lymphocytes
575
Light
Chains Are
Assembled
by a
Singte
Recombination
577
Heavy
Chains Are Assembled
by Two
Recombinations
579
Recombination
Generates Extensive
Diversity
580
Immune
Recombination
Uses Two Types
of Consensus
Sequence
581
Recombination
Generates Deletions
or Inversions
582
Attetic
Exclusion
Is Triggered
by
Productive
Rearrangement
582
The
RAG Proteins
Catalyze Breakage
and
Reunion
594
Earty Heavy
Chain Expression
Can Be
Changed
by RNA
Processing
586
Class
Switching
Is Caused
by DNA
Recombination
587
Switching
0ccurs
by a Nove[
Recombination
Reaction
589
Somatic Mutation
Generates Additionat
Diversitv
in
Mouse
and Human
Being
590
Somatic Mutation
Is Induced
by Cytidine
Deaminase
and Uraci[
Glycosytase
597
Avian Immunogtobulins
Are
Assembled
from
Pseudogenes
593
B Ce[[ Memory
Altows
a Rapid
Secondary
Response
594
T
Cet[
Receptors Are
Related
to Immunogtobulins
595
The T
Cet[
Receptor Functions
in
Conjunction
with
the MHC
597
The
Major Histocompatibitity
Locus
Codes
for Many
Genes
of the Immune
System
599
Innate Immunity
Utitizes
Conserved
Signating
Pathways
602
Summary
604
24
Promoters
and Enhancers
609
Introduction
610
Eukaryotic
RNA Potymerases
Consist
of
Many
Subunits
61.2
xii
Contents
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Some Group
I Introns
Code for
Endonucteases
That
Sponsor Mobil.ity
71.5
Group II Introns
May
Code for Multifunction
Proteins
71.6
Some Autospticing
Introns
Require Maturases
717
The
Catatytic
Activity
of RNAase P Is Due
to RNA
71.8
Viroids Have
Catatytic
Activity
7tB
RNA Editing
0ccurs
at Individual
Bases
720
RNA Editing
Can Be Directed
by Guide RNAs
721.
Protein
Spticing
Is Autocatatytic
724
Summary
725
28
Chromosomes
729
Etrl
Introduction
730
]I*,
Viral
Genomes
Are Packaged
into
Their
Coats 731.
The Bacterial
Genome
Is
a
Nucteoid
734
The Bacterial
Genome
Is
Supercoiled
135
Eukaryotic
DNA
Has Loops
and
Domains
Attached
to
a Scaffotd
736
Specific
Sequences
Attach
DNA
to an Interphase
Matrix
737
Chromatin Is
Divided
into Euchromatin
andHeterochromatin
138
Chromosomes
Have Banding
Patterns
740
Lampbrush
Chromosomes
Are
Extended
747
Polytene
Chromosomes
Form
Bands
742
Polytene
Chromosomes
Expand
at
Sites of
Gene
Expression
743
The
Eukaryotic
Chromosome
Is
a
Segregation Device
744
Centromeres
May
Contain
Repetitive DNA
746
Centromeres
Have
Short DNA
Sequences
in
S. cerevisiae
747
The
Centromere
Binds
a
Protein
Comotex
748
Tetomeres
Have
Simpte
Repeating
Sequences
748
Tetomeres
Sea[ the
Chromosome
Ends
749
Te[omeres
Are
Synthesized
by a Ribonucteoprotein
Enzyme
750
Tetomeres
Are
Essential
for
Survival
752
Summary
753
29 Nucleosomes
757
Introduction
758
The
Nucteosome
Is
the Subunit
of At[
Chromatin
759
DNA Is
Coited
in Arrays
of Nucleosomes
161.
Nucteosomes
Have
a Common
Structure
l62
DNA
Structure Varies
on the
Nucleosomal
Surface 763
The Periodicity
of DNA
Changes on the Nucteosome
766
Organization
of the Histone
Octamer 767
The Path
of
Nucleosomes
in the
Chromatin Fiber
769
Reproduction
of Chromatin
Requires Assemb[y
of Nucleosomes
777
Do
Nucteosomes Lie
at Specific Positions?
774
Are Transcribed
Genes
Organized in Nucleosomes?
177
Histone
0ctamers Are Disptaced
by Transcription
779
Nucteosome
Disptacement
and Reassem
bty Requi re
SpeciaI Factors
781.
Insutators Block
the Actions
of
Enhancers
and Heterochromatin
781.
Insulators
Can
Define
a Domain 783
Insulators May Act
in One Direction
784
Insutators
Can Vary in
Strength 785
DNAase Hypersensitive
Sites Reflect Changes
in
Chromatin
Structure 786
Domains
Define
Regions That Contain Active
Genes 788
An LCR
May
Contro[ a Domain 789
What Constitutes
a Regutatory Domain?
790
Summary 797
30 ControLLing
Chromatin
Structure
796
Introduction
797
Chromatin
Can
Have
Alternative
States 797
Chromatin
Remodeting is
an
Active
Process
798
Nucteosome
0rganization May Be
Changed
at the
Promoter
801
Histone Modification
Is
a
Key
Event
802
Histone
Acetylation
0ccurs in Two
Circumstances
805
Acetytases
Are Associated
with Activators
806
Deacetytases
Are Associated
with Repressors
808
Methytation
of
Histones
and
DNA
Is
Connected
808
Chromatin States Are
Interconverted
by Modification
809
Promoter Activation
Invotves
an 0rdered
Series
of Events
809
Histone
Phosphorylation
Affects
Chromatin
Structure
810
Some Common Motifs
Are Found
in Proteins
That
Modifv
Chromatin
811
Summary
81.2
xtv
Contents
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Preface
Science is
a wonderfully
resilient
venture.
There are
new
and interesting
developments
to
report
in
each revision
of
this
book, and
this
revision
includes
much
updated
mate-
rial
to account
for
new
findings
in molecular
research.
The
general
organization
of
material
in
this edition
has been
revised
along
the same
lines
as Essential
Genes, making
it
easier
to use
the
two books
in
conjunction.
With
increas-
ing
size becoming
a
problem,
the content
has
been more
sharply focused
on
genes
and
their
expression
by
eliminat-
ing
the chapters
dealing
with
the consequences
of
gene
ex-
pression
for
cell
biology.
Striking
changes
occur in
the first
part
of the
book,
dealing
with
genomes,
resulting
from
the
success
of many
genome
sequencing projects.
The
impor-
tance
of RNA
as a
regulator
has
become
increasingly
evi-
dent and now
can
be
seen
to extend
across
all levels
of
gene
expression
in
both
prokaryotes
and
eukaryotes.
Somewhat
of a
"missing
link,"
it casts
further
light
on how
the
current
apparatus
for
gene
expression
must
have
evolved from
the
early RNA world.
My
policy
in
this
book
has
been
to cire research
and
review
articles
that
I believe
readers
will
reasonably
be abte
to access.
My
preference
is for
articles
that
are free after
six
months;
where
that is
not
possible,
the
publication
should
be
widely
available.
I
thank
the following
individuals
who served
as
proof-
readers
and
consultants
for
this revision:
Elliott
Goldstein
University
of Arizona,
Tempe
Jocelyn
Iftebs
University
of Alaska,
Anchorage
I(athleen
Matthews
Rice
Universitv.
Houston
Benjamin
Lewin
January 2007
0rganization
The
new
organization
of GENES
IX
allows
instructors
and
students
to focus
more
sharply
on
genes
and
their
expres-
sion
with expanded
coverage
of key
topics.
The
number
of
chapters
and the
order
of
topic
coverage
remains
the
same;
however,
several
chapters
were
expanded
into
two
or more
chapters.
These
changes
are
as follows:
Chapter I in
GENES 7111,
Genes are DNA,
is
expanded
to
two
chaptersinGENES
IX. Basic information
on DNA
struc-
ture, replication,
and mutation
remains
in
Chapter 1,
whereas
the discussion
of the
gene's
function
as the
unit of
heredity
appears
in the new
Chapter 2,
Genes
Code for
Proteins.
Chapter
3 in GENES WII,The
Content of
the Genome,
be-
comes two
chapters in
GENES IX.
Chapter
4, The
Content of the
Genome, includes
informa-
tion on DNA
sequences,
genome
mapping,
and DNA
in
organelles.
Chapter 5,
Genome
Sequences and
Gene
Numbers,
now
contains
genome
size and
expression information
for
a
number
of organisms,
as well
as new
material
on
genes
in
the Y chromosome.
The new
Chapter 12,
The
Operon, comprises
GENES
WII
Chapter I0, as
well information
on regulation
of transcrip-
tion and translation
from
GENES WIIChapter
I I, Regulatory
Circuits.
Material
on regulatory
RNA
is now
found
in
Chapter 13.
The
material in
GENES
VIII Chapter
13, The
Replicon,
is
expanded
in three
chapters in
GENES IX.
Chapter
15,
The
Replicon,
covers
the structure
and function
of the replicon,
as well
as
replication
origins.
Chapter 16,
Extrachromosomal
Replicons,
contains material
on terminal
proteins,
rolling
circle replication, plasmids,
and T-DNA.
Information
on
how
bacterial replication
is connected
to
the cell
cycle
is
found in
Chapter 17.
Recombination
and Repair,
Chapter l5 in
GENE
S
VIil,
is
now covered
in
two chapters
inGENES
IX.
Chapter
l9
cov-
ers
homologous
and
site-specific
recombination,
and
Chapter
20
covers
the repair
systems,
including
new
information
on excision-repair pathways
in mammalian
cells.
Chapter 23,
Controlling
Chromatin
Structure,
in
GENES
VIII
is now
Chapter
30,
discussing
the relation
between
chromatin
structure
and
gene
expression.
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IX
