MODULE:
Genetics III
MODULE NUMBER:
BIO00033I
JACS CODE:
C400
STAGE / YEAR:
2
CREDITS:
10
ORGANISER:
Dr Michael Schultze
PROGRAMME COMMITTEE: BCH
VERSION:
August 2013
TERMS TAUGHT:
Autumn 2013
RECOMMENDATIONS/PREREQUISITES: 1st year Biology/Biochemistry Programme
SUMMARY:
This module will introduce the fundamental mechanisms of recombination, genome stability and
maintenance. Living organisms face the apparent conflict of having to keep their genome stable
to survive, and of the need for genetic change to allow for adaptation and evolution. Accurate
genome replication in conjunction with repair mechanisms guarantees genome stability,
whereas recombination, chromosome rearrangements, and mutations occur either at low
frequency or in a tightly controlled manner.
The module will start with details on recombination and discuss classic experimental
approaches that led to an understanding of the mechanisms. In a workshop, mechanisms of
mutation and DNA repair that were introduced in the first year will be expanded upon through
problem-based questions. This will be combined with lectures that integrate mutational
mechanisms and the specific types of DNA repair required to minimize the occurrence of
mutations. Also, the coordination of DNA replication and repair will be discussed, e.g. what
happens when the replication fork is stalled at sites of DNA damage.
A lot of genetic variability is caused by mobile genetic elements, including viruses, and here we
will introduce the actual mechanisms by which different types of transposable elements excise
from and integrate into the genome. In relation to this, the way viruses such as HIV integrate
into their host genome will be discussed. Mechanisms of site-specific recombination, such as
seen in bacteriophage integration and excision, integration of F plasmids, phase variation in
Salmonella will be discussed.
Emphasis will be given in discussing the relationship and regulation of recombination,
transpositions, DNA repair and replication; that DNA repair tools can be used by specific cell
types to enhance rather than suppress genetic variation, e.g. in the generation of antibody
diversity through somatic recombination and hypermutation.
Finally, the module will discuss how our knowledge on mutations and recombination can be
exploited to identify gene functions, and how precise in vivo genome-editing is possible through
the design of site-specific endonucleases.
Practical sessions/workshops will cover the main themes of this module: Recombination, sitespecific recombination, mutation and DNA repair.
1
AIMS:
To introduce to the mechanisms by which genome integrity is maintained. How recombination,
replication and repair are integrated to achieve a delicate balance between a stable and
dynamic genome. How these mechanisms can be exploited in genetic analysis and genetic
engineering.
LEARNING OUTCOMES:
 Gain an understanding of fundamental genetic processes that govern genome stability and
genome change.
 What the X and XX in recombination actually mean.
 Understand the basic molecular mechanisms of recombination and genome rearrangements.
 Understand the molecular mechanisms of transposition and site-specific recombination.
 Compare and contrast the properties of mobile genetic elements and their role in genome
stability (transposons, insertion elements, retroviruses, plasmids).
 Learn how DNA damage leads to mutations.
 Appreciate the importance of DNA repair mechanisms in genome maintenance and genome
change.
 Understand how DNA replication and DNA repair act in concert.
 Appreciate how mutation and recombination can be exploited in genetic research.
 How the knowledge of recombination and repair have provided the tools for specific genome
editing.
 Appreciate experimental approaches leading to key discoveries.
2
SYNOPSIS OF TEACHING:
Event
Duration
Topic
Staff
Room type
Timing
Lectures 1-3
3 x 1 hr
Homologous recombination
The first three lectures will be devoted to a detailed introduction to homologous recombination,
the mechanisms involved, and key experiments that have given important insights.
Haploid genetics (yeast, Neurospora) in the context of recombination. Demonstration that meiotic
recombination occurs at the four-chromatid stage (octad analysis). The concept of gene
conversion. Yeast mating type switch. Mitotic crossover. Centromere mapping.
Mechanisms of recombination. Strand invasion, heteroduplex formation and Holliday junction.
Movement of crossover point. Key proteins involved.
Accuracy and control of homologous recombination. Discussion of experimental evidence on
mechanisms. Mechanisms of deletions, insertions and inversions. F plasmids.
MS
Lecture room
Week 2,3
Lectures 4-5
2 x 1 hr
Mechanisms of transposition
Different types of mobile genetic elements, their life cycles and mechanisms of transposition.
Insertion (IS) elements from all kingdoms of life including DNA transposons, retroelements,
retroviruses. Examples will include HIV integration, movement of Tn5 in bacteria, Ty elements in
Yeast, P1 in Drosophila, RAG proteins in antibody switching. Mechanisms of transposition;
replicative versus conservative transposition. DNA sequence specificity of transposases.
M Smith
Lecture room
Week 3,4
Lecture 6
1 hr
Site-specific recombination
Site-specific integration, deletion and inversion of DNA. Bacteriophage integration and excision,
mechanisms of resolvases from replicative transposons, role and mechanism of inversion
elements. DNA editing by Cas-CRISPR and acquired immunity to phage infection.
M Smith
Lecture room
Week 4
Lecture 7
1 hr
Applications and uses I: Transposons and site-specific recombinases
Use of transposition and site-specific recombination in gene analysis and genetic engineering.
Transposon mutagenesis in studies of gene function. Recombination systems such as Cre/loxP,
phiC31 integrase/attP/attB, Gateway cloning vectors and their uses in DNA assembly, genome
engineering and biosensors.
M Smith
Lecture room
Week 5
Lectures 8-9
2 x 1 hr
Fidelity of DNA replication and DNA repair mechanisms
How DNA replication is completed in an orderly manner. Merging of replication forks. Replication
at sites of DNA damage. Maintenance of telomeres. The role of the major types of DNA damage
repair pathways. Transcription-coupled repair, global genomic repair. Mismatch repair. Doublestrand break repair mechanisms.
MS
Lecture room
Week 6,7
Lecture 10
1 hr
Genome stability versus genome flexibility
Relationship and regulation of recombination, transpositions, DNA repair and replication.
Discussion of common themes. Somatic recombination and hypermutation in the generation of
antibody diversity.
MS
Lecture room
Week 8
3
Lecture 11
1 hr
Applications and uses II: Induced mutations to study gene function
Positional cloning. Heteroduplex mapping.
MS
Lecture room
Week 9
Lecture 12
1 hr
Applications and uses III: Gene targeting and genome editing
Use of programmable nucleases (homing endonucleases, zinc finger nucleases, TALE
nucleases, RNA-guided DNA cleavage).
MS
Lecture room
Week 9
Workshop 1
2 hrs
Problem-based workshop on mutation and DNA repair. This will reinforce concepts introduced in
the first year.
MS
Biolabs
W5 after
L7
Practicals/
workshops
1-3
3 x 3 hrs
Practicals/workshops on Recombination, site-specific recombination, mutation and DNA repair.
Each of these practicals will comprise a 1.5-hour lab session followed by a 1.5-hour workshop of
data analysis and problem solving.
P1: MS
Biolabs
Week 6-8
Contents of practicals:
(provisional, depending on time constraints, we may not do all of these)
 P1: Octad analysis in Neurospora crassa, concepts of homologous recombination, gene
conversion
 P1-P3: Gene replacement in yeast (transformation, selection, counterselection, visualisation
through reporter gene expression).
 P1-P3: Yeast mating type switch
 P2-P3: Effects of mutagens on test strains (similar to Ames test): UV, peroxide, heat,
Ethidium
 P2-P3: Sensitivity of yeast and bacterial DNA repair mutants to mutagens, comparison with
the extremely damage-resistant Deinococcus radiodurans.
Lecturers:
L1-L3, L8-L12, W1, P1: Michael Schultze
L4-L7: Maggie Smith
P2-P3: Michael Schultze and Peter McGlynn
4
P2-P3:
MS + PM
Not on
Mondays
KEY TEXTS: These are available in EARL which is accessible through the VLE module site.
ASSESSMENT:
Formative:
Yes, via VLE
Summative:
Closed exam (1.5 h) in the January assessment period
Re-assessment: Closed exam (1.5 h) in the August resit period
DEMONSTRATING REQUIREMENTS:
Depends on class size. Most likely two required for practical sessions.
MAXIMUM NUMBERS: To capacity of lecture theatre/Biolabs
STUDENT WORKLOAD: students’ workload totalling 100 hours per 10 credit module
Lectures:
Practicals/workshops:
Total Contact hours:
Private study:
12 h
11 h
23
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