The Human Genome Project (HGP) is an international
cooperative effort to investigate the
human genome in its entirety. It consists of
different approaches, each directed toward a
different goal. Many countries participate. Five
major centers, four in the United States and
one in the United Kingdom, contribute about
85% of the data.
Sunday, April 12, 2009
The Human Genome Project (HGP) and related information online
Information about the Human Genome Project
is best gleaned from the internet. Here, several
websites provide access to detailed information
much beyond the limited space available here.
The opposite page (p. 249) provides information
about the main areas, the HGP itself, genes
and disease, gene maps, networks of databases,
education, and the genomes of other organisms
than man.
is best gleaned from the internet. Here, several
websites provide access to detailed information
much beyond the limited space available here.
The opposite page (p. 249) provides information
about the main areas, the HGP itself, genes
and disease, gene maps, networks of databases,
education, and the genomes of other organisms
than man.
(ELSI) of the Human Genome Project
From the outset, the ethical, legal, and social
implications of the human genome project have
been an important consideration. About 3% of
the total funding is directed to the ELSI Research
program. ELSI covers a wide range of issues.
These include confidentiality and fairness in the
use of individual genetic information, prevention
of genetic discrimination, use of genetic
methods in clinical diagnostics, public and professional
education, and other related issues.
implications of the human genome project have
been an important consideration. About 3% of
the total funding is directed to the ELSI Research
program. ELSI covers a wide range of issues.
These include confidentiality and fairness in the
use of individual genetic information, prevention
of genetic discrimination, use of genetic
methods in clinical diagnostics, public and professional
education, and other related issues.
Medical implications
The human genome project carries important
implications for the theory and practice of
medicine. Complete knowledge of human
genes will lead to better understanding of disease
processes. This, in turn, will lead to improved
precision of diagnosis, correct assessment
of genetic risk, and the development of
therapy.
implications for the theory and practice of
medicine. Complete knowledge of human
genes will lead to better understanding of disease
processes. This, in turn, will lead to improved
precision of diagnosis, correct assessment
of genetic risk, and the development of
therapy.
Important information
Important information about disease-causing
human genes is derived from studying the
genomes of model organisms such as yeast, C.
elegans, Drosophila, and the mouse. The recently
published sequence of the Drosophila
genome (Adams et al., 2000) revealed that of a
set of 289 human genes involved in causing diseases,
177 (62%) appeared to have an orthologue
in Drosophila
human genes is derived from studying the
genomes of model organisms such as yeast, C.
elegans, Drosophila, and the mouse. The recently
published sequence of the Drosophila
genome (Adams et al., 2000) revealed that of a
set of 289 human genes involved in causing diseases,
177 (62%) appeared to have an orthologue
in Drosophila
Identification of a Coding DNA Segment
Numerous methods are available to identify a
gene of interest that do not require large segments
of DNA to be sequenced. Some examples
are presented here.
gene of interest that do not require large segments
of DNA to be sequenced. Some examples
are presented here.
Microdissection of metaphase chromosomes
If the chromosomal location of a gene of interest
is known, this region can be cut out of a
metaphase chromosome bymeans of microdissection
(arrow). As first applied by B. Horsthemke
and co-workers (Lüdecke et al., 1989)
this method has the advantage that all other
chromosomal segments are eliminated. (Photo
from Buiting et al., 1990).
is known, this region can be cut out of a
metaphase chromosome bymeans of microdissection
(arrow). As first applied by B. Horsthemke
and co-workers (Lüdecke et al., 1989)
this method has the advantage that all other
chromosomal segments are eliminated. (Photo
from Buiting et al., 1990).
Artificial yeast chromosomes (YACs)
Large DNA fragments (200–300 kb) can be replicated
in yeast cells. They are inserted into artificial
yeast chromosomes (YAC, see p. 110) and
replicated with them. A photograph of a transverse
alternating field electrophoresis (TAFE)
with nine lanes after ethidium bromide staining
shows fragments of different sizes. These correspond
to the naturally occurring yeast chromosomes.
Six of the lanes (2–7) contain an additional
band, which corresponds to an artificial
yeast chromosome. They are marked with a yellow
point: the lowest band in lane 2 (YAC9), the
third band from the bottom in lanes 3, 4, and 6
(YAC41, YAC45, YAC51), and the lowest band in
lane 7 (YAC52). In lane 5, YAC50 is masked by a
yeast chromosome (third fragment from
below).
in yeast cells. They are inserted into artificial
yeast chromosomes (YAC, see p. 110) and
replicated with them. A photograph of a transverse
alternating field electrophoresis (TAFE)
with nine lanes after ethidium bromide staining
shows fragments of different sizes. These correspond
to the naturally occurring yeast chromosomes.
Six of the lanes (2–7) contain an additional
band, which corresponds to an artificial
yeast chromosome. They are marked with a yellow
point: the lowest band in lane 2 (YAC9), the
third band from the bottom in lanes 3, 4, and 6
(YAC41, YAC45, YAC51), and the lowest band in
lane 7 (YAC52). In lane 5, YAC50 is masked by a
yeast chromosome (third fragment from
below).
Exon trapping
In an unidentified segment of DNA, a gene can
be recognized by the occurrence of coding segments
(exons). To find and isolate an exon, the
genomic fragment can be cloned in a vector that
consists of a strong promoter gene and a reporter
gene. An exon that is present is cut out by
means of the donor and acceptor splice signals
and expressed together with the genomic fragment
(exon trapping). cDNA is produced from
the mRNA and replicated by means of PCR. Finally,
the trapped exon can be sequenced
be recognized by the occurrence of coding segments
(exons). To find and isolate an exon, the
genomic fragment can be cloned in a vector that
consists of a strong promoter gene and a reporter
gene. An exon that is present is cut out by
means of the donor and acceptor splice signals
and expressed together with the genomic fragment
(exon trapping). cDNA is produced from
the mRNA and replicated by means of PCR. Finally,
the trapped exon can be sequenced
Single-strand conformation polymorphism (SSCP)
This procedure helps establish a difference in
the nucleotide base sequence due to mutation
or polymorphism. Whether DNA segments
(single-stranded DNA) of common origin differ
from each other is determined by their speed of
migration in a polyacrylamide gel electrophoresis
under different conditions, such as changes
in temperature, in pH, etc. A base substitution
may lead to a difference in spatial arrangement
(conformation) and in mobility (lane 4, arrow).
(Polyacrylamide gel electrophoresis and silver
staining,
the nucleotide base sequence due to mutation
or polymorphism. Whether DNA segments
(single-stranded DNA) of common origin differ
from each other is determined by their speed of
migration in a polyacrylamide gel electrophoresis
under different conditions, such as changes
in temperature, in pH, etc. A base substitution
may lead to a difference in spatial arrangement
(conformation) and in mobility (lane 4, arrow).
(Polyacrylamide gel electrophoresis and silver
staining,
“Zoo blot”
The cross hybridization of DNA across species
boundaries (“zoo blot”) is an indication for
coding sequences, since genes have similar
structures in different organisms. A zoo blot is a
Southern blot of genomic DNA from different
species. Owing to evolutionary relationship,
coding DNA sequences will hybridize to the
same probe. This can be taken as evidence that
the DNA probed is part of a functioning gene.
boundaries (“zoo blot”) is an indication for
coding sequences, since genes have similar
structures in different organisms. A zoo blot is a
Southern blot of genomic DNA from different
species. Owing to evolutionary relationship,
coding DNA sequences will hybridize to the
same probe. This can be taken as evidence that
the DNA probed is part of a functioning gene.
The Dynamic Genome:
Mobile Genetic Elements
In the 1950s Barbara McClintock observed an
unusual phenomenon during her genetic investigations
of Indian corn (maize, Zea mays),
namely, “jumping genes” (mobile genetic elements).
A mobile element causes a break in a
chromosome at the site of an insertion and
causes a gene locus to move to a different location
in the chromosome (transposition). During
the last 25 years, mobile elements have been
found in every organism in which they have
been sought: in bacteria, in Drosophila, in the
nematode C. elegans, and in mammals, including
man. These observations have resulted in
the concept of a dynamic genome that is by no
means fixed and unchangeable. Mutations due
to mobile elements inserted into genes have
also been demonstrated in man.
In the 1950s Barbara McClintock observed an
unusual phenomenon during her genetic investigations
of Indian corn (maize, Zea mays),
namely, “jumping genes” (mobile genetic elements).
A mobile element causes a break in a
chromosome at the site of an insertion and
causes a gene locus to move to a different location
in the chromosome (transposition). During
the last 25 years, mobile elements have been
found in every organism in which they have
been sought: in bacteria, in Drosophila, in the
nematode C. elegans, and in mammals, including
man. These observations have resulted in
the concept of a dynamic genome that is by no
means fixed and unchangeable. Mutations due
to mobile elements inserted into genes have
also been demonstrated in man.
Stable and unstable mutations in Indian corn
McClintock observed not only stable mutations
(e.g., violet corn kernels) but also fine or somewhat
coarser pigment spots (variegation) in
some kernels due to unstable mutations.
(e.g., violet corn kernels) but also fine or somewhat
coarser pigment spots (variegation) in
some kernels due to unstable mutations.
Effect of mutation and transposition
A gene at the C locus produces a violet pigment
of the aleurone in cells of Indian corn. When a
mobile element (Ds) inactivates this gene locus,
the corn is colorless. If Ds is removed by transposition,
C-locus function is restored and small
pigmented spots appear.
of the aleurone in cells of Indian corn. When a
mobile element (Ds) inactivates this gene locus,
the corn is colorless. If Ds is removed by transposition,
C-locus function is restored and small
pigmented spots appear.
Insertion and removal (Ds)
As defined by McClintock, an activator (Ac
locus) is an element that can activate another
locus, dissociation (Ds), and cause a break in the
chromosome (1). While Ac can move independently
(autonomous transposition), Ds can only
move to another location of the chromosome
under the influence of Ac (nonautonomous
transposition). The C locus is inactivated by the
insertion of Ds (2). Under the influence of Ac, Ds
is then removed from some of the cells, and the
C locus is returned to normal function. Since the
cells of corn are of clonal origin, the time of
transposition influences the phenotype. If
transposition occurs early in development, the
pigmented spots are relatively large; if it occurs
late, the spots are small.
locus) is an element that can activate another
locus, dissociation (Ds), and cause a break in the
chromosome (1). While Ac can move independently
(autonomous transposition), Ds can only
move to another location of the chromosome
under the influence of Ac (nonautonomous
transposition). The C locus is inactivated by the
insertion of Ds (2). Under the influence of Ac, Ds
is then removed from some of the cells, and the
C locus is returned to normal function. Since the
cells of corn are of clonal origin, the time of
transposition influences the phenotype. If
transposition occurs early in development, the
pigmented spots are relatively large; if it occurs
late, the spots are small.
Transposons in bacteria
Mobile genetic elements are classified according
to their effect and molecular structure:
simple insertion sequences (IS) and the more
complex transposons (Tn). A transposon contains
additional genes, e.g., for antibiotic resistance
in bacteria.
Transposition is a special type of recombination
by which a DNA segment of about 750 bp to
10kb is able to move from one position to
another, either on the same or on another DNA
molecule. The insertion occurs at an integration
site (1) and requires a break (2) with subsequent
integration (3). The sequences on
either side of the integrated segment at the integration
site are direct repeats. At both ends,
each IS element or transposon carries inverted
repeats whose lengths and base sequences are
characteristic for different IS and Tn elements.
The expression “direct” signifies that two copies
of a sequence are oriented in the same direction
(e.g., TTAG on each side of the integrated
transposon). Direct and inverted repeats are
evidence of the presence of amobile genetic element.
One E. coli cell contains on average
about ten copies of such sequences. They have
also been demonstrated in yeast, drosophila,
and other eukaryotic cells.
to their effect and molecular structure:
simple insertion sequences (IS) and the more
complex transposons (Tn). A transposon contains
additional genes, e.g., for antibiotic resistance
in bacteria.
Transposition is a special type of recombination
by which a DNA segment of about 750 bp to
10kb is able to move from one position to
another, either on the same or on another DNA
molecule. The insertion occurs at an integration
site (1) and requires a break (2) with subsequent
integration (3). The sequences on
either side of the integrated segment at the integration
site are direct repeats. At both ends,
each IS element or transposon carries inverted
repeats whose lengths and base sequences are
characteristic for different IS and Tn elements.
The expression “direct” signifies that two copies
of a sequence are oriented in the same direction
(e.g., TTAG on each side of the integrated
transposon). Direct and inverted repeats are
evidence of the presence of amobile genetic element.
One E. coli cell contains on average
about ten copies of such sequences. They have
also been demonstrated in yeast, drosophila,
and other eukaryotic cells.
Evolution of Genes and Genomes
Genes and genomes existing today are the cumulative
result of events that have taken place
in the past. The classical theory of evolution as
formulated by Charles Darwin in 1859 states
that (i) all living organisms today have descended
from organisms living in the past; (ii)
the organisms living during earlier times
differed from those living today; (iii) the
changes were more or less gradual, with only
small changes at a time; (iv) the changes usually
led to divergent organisms, with the number of
ancestral types of organisms being much
smaller than the number of types today; and (v)
all changes result from causes that continue to
exist today and can thus be studied today.
result of events that have taken place
in the past. The classical theory of evolution as
formulated by Charles Darwin in 1859 states
that (i) all living organisms today have descended
from organisms living in the past; (ii)
the organisms living during earlier times
differed from those living today; (iii) the
changes were more or less gradual, with only
small changes at a time; (iv) the changes usually
led to divergent organisms, with the number of
ancestral types of organisms being much
smaller than the number of types today; and (v)
all changes result from causes that continue to
exist today and can thus be studied today.
Gene evolution by duplication
Observations on different genomes indicate
that different types of duplication must have
occurred: of individual genes, of parts of genes
(exons), subgenomic duplications, and rare duplications
of the whole genome. Duplication of
a gene relieves the selective pressure on this
gene. After a duplication event, the gene can accumulatemutations
without compromising the
original function, provided the duplicated gene
attains a separate regulatory control.
that different types of duplication must have
occurred: of individual genes, of parts of genes
(exons), subgenomic duplications, and rare duplications
of the whole genome. Duplication of
a gene relieves the selective pressure on this
gene. After a duplication event, the gene can accumulatemutations
without compromising the
original function, provided the duplicated gene
attains a separate regulatory control.
Gene evolution by exon shuffling
The exon/intron structure of eukaryotic genes
lends great evolutionary versatility. New genes
can be created by placing parts of existing genes
into a new context, using functional properties
in a new combination.
lends great evolutionary versatility. New genes
can be created by placing parts of existing genes
into a new context, using functional properties
in a new combination.
Evolution of chromosomes
Evolution occurs also by structural rearrangements
of the genome at the chromosomal level.
Related species, e.g., mammals, differ by the
number of their chromosomes and chromosomal
morphology, but not by the number of
genes, which often are conserved to a remarkable
degree. The human chromosomes 2 and 5
are shown in comparison with the corresponding
chromosomes in three closely related primates,
chimpanzee, gorilla, and orangutan. The
human chromosome 2 appears to have evolved
from fusion of the two primate chromosomes.
The differences in chromosome 5 are much
more subtle. The orangutan chromosome 5
differs from that of man and the other primates
by a pericentric inversion. The banding pattern
of all primate chromosomes is remarkably similar.
This reflects their close evolutionary relationship.
of the genome at the chromosomal level.
Related species, e.g., mammals, differ by the
number of their chromosomes and chromosomal
morphology, but not by the number of
genes, which often are conserved to a remarkable
degree. The human chromosomes 2 and 5
are shown in comparison with the corresponding
chromosomes in three closely related primates,
chimpanzee, gorilla, and orangutan. The
human chromosome 2 appears to have evolved
from fusion of the two primate chromosomes.
The differences in chromosome 5 are much
more subtle. The orangutan chromosome 5
differs from that of man and the other primates
by a pericentric inversion. The banding pattern
of all primate chromosomes is remarkably similar.
This reflects their close evolutionary relationship.
Molecular phylogenetics and evolutionary tree reconstruction
A convincing evolutionary relationship can be
established by reconstructing past events. A
phylogenetic tree may be based on different
types of evidence: on fossils, on differences in
proteins, on immunological data, on DNA–DNA
hybridization, and on DNA sequence similarity.
One determines the number of events that must
have taken place to explain the diversity observed
today. In the path from an ancestral gene
(1), different events of divergence can be distinguished
(two events are shown schematically
here). However, trees are not always as simple
as shown here. Since the term homology does
not distinguish whether the common evolutionary
origin is within or between species, the
terms paralogy and orthology are used (2).
Genes or nonallelic chromosomal segments or
DNA sequences are called paralogous if they
have evolved within a species (for example the
two !-globin loci in humans). If they evolved
between species prior to diversion, they are
called orthologous (for example the !-globin
and the "-globin genes).
established by reconstructing past events. A
phylogenetic tree may be based on different
types of evidence: on fossils, on differences in
proteins, on immunological data, on DNA–DNA
hybridization, and on DNA sequence similarity.
One determines the number of events that must
have taken place to explain the diversity observed
today. In the path from an ancestral gene
(1), different events of divergence can be distinguished
(two events are shown schematically
here). However, trees are not always as simple
as shown here. Since the term homology does
not distinguish whether the common evolutionary
origin is within or between species, the
terms paralogy and orthology are used (2).
Genes or nonallelic chromosomal segments or
DNA sequences are called paralogous if they
have evolved within a species (for example the
two !-globin loci in humans). If they evolved
between species prior to diversion, they are
called orthologous (for example the !-globin
and the "-globin genes).
Comparative Genomics
In comparing the genomes of different organisms
it is interesting to determine the minimal
set of gene families required to encode all
proteins required for the overall function of the
organism, the so-called core proteome. This is
one of the goals of comparative genomics. An
example for four different organisms is given in
the following table.
it is interesting to determine the minimal
set of gene families required to encode all
proteins required for the overall function of the
organism, the so-called core proteome. This is
one of the goals of comparative genomics. An
example for four different organisms is given in
the following table.
Comparison of gene loci in man, mouse, cat, and cow
The conservation of certain groups of genes
during mammalian evolution can be demonstrated
by comparing reference loci in four
different orders of mammals.Many of the loci of
humans (representing the order Primates) are
found in the same order, although often on
different chromosomes, in the house mouse
(Mus musculus, representing Rodentia), the
house cat (representing Carnivora), and the cow
(representing Artiodactyla).
during mammalian evolution can be demonstrated
by comparing reference loci in four
different orders of mammals.Many of the loci of
humans (representing the order Primates) are
found in the same order, although often on
different chromosomes, in the house mouse
(Mus musculus, representing Rodentia), the
house cat (representing Carnivora), and the cow
(representing Artiodactyla).
The X chromosomes of man and mouse
Many chromosomal segments with the same
sequences of two or more homologous loci are
syntenic (on the same chromosome) in mouse
and man. Gene loci sequences on the X chromosomes
of eutherian mammals are especially
similar owing to the conserving effect of X inactivation.
In the X chromosomes of humans and
mice, there are five blocks of gene loci that have
the same sequences, although they are in different
regions and in part oriented in different
directions;
sequences of two or more homologous loci are
syntenic (on the same chromosome) in mouse
and man. Gene loci sequences on the X chromosomes
of eutherian mammals are especially
similar owing to the conserving effect of X inactivation.
In the X chromosomes of humans and
mice, there are five blocks of gene loci that have
the same sequences, although they are in different
regions and in part oriented in different
directions;
Sequence homologies of the X and the Y chromosomes of man
During the evolution of vertebrates, the X and
the Y chromosomeswere derived froman autosome.
While the Y chromosome has become
considerably smaller, the X chromosome has for
the most part retained the gene loci of originally
autosomal character. In five regions (I–V), the X
chromosome and Y chromosome of man contain
sequence homologies. The homologous
sequences on the extreme distal ends of both
chromosomes (I and II) correspond to a pseudoautosomal
region. In region I, homologous pairing
and crossing-over occur regularly during
meiosis.
the Y chromosomeswere derived froman autosome.
While the Y chromosome has become
considerably smaller, the X chromosome has for
the most part retained the gene loci of originally
autosomal character. In five regions (I–V), the X
chromosome and Y chromosome of man contain
sequence homologies. The homologous
sequences on the extreme distal ends of both
chromosomes (I and II) correspond to a pseudoautosomal
region. In region I, homologous pairing
and crossing-over occur regularly during
meiosis.
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