CG920 Genomics
Lesson 4
Forward Genetics
Jan Hejátko
Functional Genomics and Proteomics of Plants,
CEITEC - Central European Institute of Technology
And
National Centre for Bimolecular Research,
Faculty of Science,
Masaryk University, Brno
hejatko@sci.muni.cz, www.ceitec.eu
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 Forward vs. Reverse Genetics
 Use of Libraries of Insertional Mutants in Forward Genetics
 Searching in Libraries of Insertional Mutants According to:
 anatomically or morphologically detectable phenotype
 metabolic profile
 expression of genes of interest
 Identification of the Mutated Locus
 plasmid rescue
 iPCR
 Use of Libraries of Point Mutants in Forward Genetics
 Positional Cloning
 GWAS
Outline
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 Forward vs. Reverse Genetics
Outline
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„Classical genetics“ approach
1. IDENTIFICATION OF PHENOTYPE
2. GENE MAPPING
3. GENE IDENTIFICATION
- position cloning
„Reverse genetics“ approach
1. ISOLATION OF SEQUENCE-SPECIFIC
MUTANT
2. IDENTIFICATION OF
PHENOTYPE
3. PROOF OF CAUSAL RELATIONSHIP
BETWEEN INSERTION AND
PHENOTYPE
RANDOM MUTAGENESIS
„Classical“ genetics versus „reverse genetics“
approaches in functional genomics
EMS
T-DNA
(retro)transposons
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 Forward vs. Reverse Genetics
 Use of Libraries of Insertional Mutants in Forward Genetics
 Searching in Libraries of Insertional Mutants According to:
 anatomically or morphologically detectable phenotype
Outline
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Insertional mutagenesis in
forward genetics approaches
 Use of insertional mutagenesis for study of
carcinogenesis
Mikkers et al., Nature Gen (2002)
?
 Infection of EμMyc mice by MoMuLV retrovirus leads to lymphomas
formation, which arose due to activation of Pim kinases (40 % activation
of Pim1, 15 % activation of Pim2), molecular targets of these kinases
were unknown
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 Infection of EμMyc pim1 mutants by MoMuLV retrovirus leads to
lymphomas formation, which in 90 % contain insertion nearby
(activation) Pim2
 Use of insertional mutagenesis for study of
carcinogenesis
Mikkers et al., Nature Gen (2002)
?
Insertional mutagenesis in
forward genetics approaches
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 Use of insertional mutagenesis for study of
carcinogenesis
Mikkers et al., Nature Gen (2002)
?
Insertional mutagenesis in
forward genetics approaches
 Infection of EμMyc double mutants pim1, pim2 by MoMuLV retrovirus leads to
lymphomas formation, which can be expected to activate either one of the
signalling partner of Pim proteins (Y), one of the downsteram proteins of Pim
signalling pathway (X) or to activate some of the related pathways leading to
lymphomagenesis (Z).
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 Cleavage of genomic DNA and ligation
of special linkers, so-called splincerettes
(increasing the specifity of amplification)
 Isolation of genomic regions adjacent to the insertion site
of the provirus
Mikkers et al., Nature Gen (2002)
Devon et al., Nucl Acid Res (1994)
Insertional mutagenesis in
forward genetics approaches
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 First amplification using specific primers
 Isolation of genomic regions adjacent to the insertion site
of the provirus
Mikkers et al., Nature Gen (2002)
Devon et al., Nucl Acid Res (1994)
Insertional mutagenesis in
forward genetics approaches
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 Second amplification using nested
primers (increasing the specifity)
 Isolation of genomic regions adjacent to the insertion site
of the provirus
Mikkers et al., Nature Gen (2002)
Devon et al., Nucl Acid Res (1994)
Insertional mutagenesis in
forward genetics approaches
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 Sequencing and localization of regions
adjacent to provirus by searching in
annotated databases of mouse genome
 Isolation of genomic regions adjacent to the insertion site
of the provirus
Mikkers et al., Nature Gen (2002)
Devon et al., Nucl Acid Res (1994)
Insertional mutagenesis in
forward genetics approaches
In case of splincerette, the primer is of the same sequence as the top
strand and therefore it is unable to act as a primer until the complement of
this strand has been synthesized (from the insert-specific primer at the
right-hand side).
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 Forward vs. Reverse Genetics
 Use of Libraries of Insertional Mutants in Forward Genetics
 Searching in Libraries of Insertional Mutants According to:
 anatomically or morphologically detectable phenotype
 metabolic profile
Outline
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 Automated analysis of metabolites (up to
25.000) by GC-MS techniques in libraries
of T-DNA mutants
 Metabolic profiling of plants
Metabolic profiling
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 Automated analysis of metabolites (up to
25.000) by GC-MS techniques in libraries
of T-DNA mutants
 Identification of interesting (even
comercially interesting) mutants
 Metabolic profiling of plants
Metabolic profiling
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Metabolic profiling
 Automated analysis of metabolites (up to
25.000) by GC-MS techniques in libraries
of T-DNA mutants
 Identification of interesting (even
comercially interesting) mutants
 Fast and easy isolation of genes through
identification of sequences adjacent to T-
DNA
 Metabolic profiling of plants
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 Possibility to use special techniques, e.g. microdissection
 Metabolic profiling of plants
Metabolic profiling
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 Forward vs. Reverse Genetics
 Use of Libraries of Insertional Mutants in Forward Genetics
 Searching in Libraries of Insertional Mutants According to:
 anatomically or morphologically detectable phenotype
 metabolic profile
 expression of genes of interest
Outline
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 Analysis of expression profile (pattern) of the gene and
identification of mutants with altered expression pattern
 Identification of mutants with a change in the expression profile
Expression profile
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 Analysis of expression profile (pattern) of the gene and
identification of mutants with altered expression pattern
 Identification of mutants with a change in the
expression profile
 Possibility of partial automation (virtual digital microscopy)
Expression profile
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Automated Microscopy Screening
Dobisova and Hejatko, Methods in Mol Biol, 2014
image.vsi
Tady by mohla být reference zpět na CEITEC, jaké skvělé vybavení v něm je a
jak dobře se vám s tím pracuje
Pokud tam nezůstane video, ikonu bych dala pryč
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WT
Expression profile
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 Forward vs. Reverse Genetics
 Use of Libraries of Insertional Mutants in Forward Genetics
 Searching in Libraries of Insertional Mutants According to:
 anatomically or morphologically detectable phenotype
 metabolic profile
 expression of genes of interest
 Identification of the Mutated Locus
 plasmid rescue
 iPCR
Outline
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 Identification of chromosomal rearrangements responsible
for bushy phenotype of Arabidopsis
 Description of phenotype
Identification of mutated locus
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Identification of mutant
 Crinkled leaves
 No trichomes on leaves and
stems
 Late senescence
 Bushy phenotype (branching
defective)
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 Male sterility, defects in stamen
filament elongation (A,B)
(compare with wild type C)
Identification of mutant
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 Identification of chromosomal rearrangements responsible
for bushy phenotype of Arabidopsis
 Description of phenotype
 Identification of T-DNA mutated region
Identification of mutated locus
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1. Identification of region of genomic DNA adjacent to the left
border using plasmid rescue
 Restriction digestion (EcoRI)
of mutant genomic DNA
 Religation and transformation of
E. coli
 Isolation of plasmid DNA from
positively selected clones
 Identified sequence was
identical to gene for NAD7
coded by mtDNA
Identification of mutated locus
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2. Identification of region of genomic DNA adjacent to the right
border using inversion PCR (iPCR)
 Restriction digestion
(EcoRI) of mutant genomic
DNA
 Purification, religation and
PCR using T-DNA specific
primers
 Cloning and sequencing
 Identified sequence was
not homologous to any
sequences with known
function
Identification of mutated locus
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 Identification of chromosomal rearrangements responsible
for bushy phenotype of Arabidopsis
 Description of phenotype
 Identification of T-DNA mutated region
 Localization of T-DNA insertion site in Arabidopsis genome
Identification of mutated locus
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Searching in library IGF-BAC
 Genome library containing 10.752 clones with an average size of an
insert of 100 kb
 Bacterial clones arranged in the microtiter plates
 Library loaded onto nylon filters for hybridization with the
radiolabeled probe
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I. Sequences adjacent to the left border of T-DNA
 28 positively hybridizing clones in total
 19 of them located on chromosome 2
 18 of them similar with mtDNA
II. Sequences adjacent to the right border of T-DNA
 6 positively hybridizing clones in total
 all of them located on chromosome 2
Mapping with IGF-BAC database
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left border of T-DNASequences adjacent to right and
Localization of genomic T-DNA adjacent to both left
and right T-DNA borders on chromosome 2
 There was probably an inversion of almost entire
chromosome 2
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 Forward vs. Reverse Genetics
 Use of Libraries of Insertional Mutants in Forward Genetics
 Searching in Libraries of Insertional Mutants According to:
 anatomically or morphologically detectable phenotype
 metabolic profile
 expression of genes of interest
 Identification of the Mutated Locus
 plasmid rescue
 iPCR
 Use of Libraries of Point Mutants in Forward Genetics
 Positional Cloning
Outline
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 Positional cloning
 Principle: co-segregation analysis of segregating population (mostly of
offspring of backcrosses) with molecular markers
 RFLP (Restriction Fragment Length Polymorphism)
 RAPD (Randomly Amplified Polymorphic DNA)
 SSLP (Simple Sequence Length Polymorphism)
 Polymorphism of genome (PCR products) length, amplified using
specific primers
 Detection by Southern blot (PCR after digestion of the genomic DNA
and ligation of adapters)
 Polymorphism of length of randomly amplified genome segments,
using short 8-10bp primers
 CAPS (Cleaved Amplified Polymorphic Sequence)
 Restriction fragment length polymorphism, genome segments
amplified by PCR
Identification of mutated locus
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m m
M M
Col Col
+
M
Col Ler
m
M
+
M
+
M
Ler Ler
M M
m m
Col Ler
M M
m m
Ler Ler
m +
M M
Col Ler
m
M
+
M
Ler Ler
+ +
M M
Col Col Col Ler
+
M
+
M
M M
m +
Col Ler
+ +
M M
♂
Ler Ler
♀
Col Col
mm
M M
Preparation of mapping population
M
m+
M M
Positional cloning
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Recombinant analysis – determining the percentage of
recombination between mutation and molecular marker
r [%] = number of chromosomes of Col /
number of all the chromosomes × 100
marker I – linked
5 mutants
1/10×100 = 10%
marker II - no linkage
6 mutants
7/12×100 = 58%
• Analysis of approximately 2000 mutant plants
• Determining the closest (still segregating) marker
• Identification of mutation by sequencing
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Map of DNA molecular markers
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Markers for fine mapping
CIW2
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 Forward vs. Reverse Genetics
 Use of Libraries of Insertional Mutants in Forward Genetics
 Searching in Libraries of Insertional Mutants According to:
 anatomically or morphologically detectable phenotype
 metabolic profile
 expression of genes of interest
 Identification of the Mutated Locus
 plasmid rescue
 iPCR
 Use of Libraries of Point Mutants in Forward Genetics
 Positional Cloning
 GWAS
Outline
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Genome Wide Association
Study - GWAS
https://www.ebi.ac.uk/training-beta/online/courses/gwas-catalogue-exploring-snp-
trait-associations/what-is-gwas-catalog/what-are-genome-wide-association-
studies-gwas/
A typical GWAS study collects data to find out the common variants in a number
of individuals, both with and without a common trait (e.g. a disease), across the
genome, using genome wide SNP arrays. Variants associated with the disease,
or within the same haplotype as a variant associated with a disease, will be found
at a higher frequency in cases than in controls. Statistical analysis is carried out
to indicate how likely a variant is to be associated with a trait.
As GWAS analyse common variants, usually typed on commercial SNP arrays
(Figure 3), they do not generally identify causal variants. GWAS identify common
variants which tag a region of linkage disequilibrium (LD) containing causal
variant(s). Additional or follow-on studies are usually required to narrow the
region of association and identify the causal variant
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 Forward genetics allows targeted screening for interesting
phenotypes, whose association with a given gene/locus is
unknown
 Employs both insertional mutagenes as well as point
mutations
 Inserional mutation
 (mostly) loss-of-function mutation
 Identification via
 iPCR
 plasmid rescue
 Point mutation
 Both loss-of-function as well as
 gain-of-function mutations
 Identification via
 map-based cloning
 GWAS
Key Concepts
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Discussion