The Human Genome.

Download Report

Transcript The Human Genome.

Marek Vácha
Human Genome – Internal Universe
 After many centuries of investigations we
have built up an approximate
understanding of at least the more
accesible parts of our external Universe
 ...however, there is also a largely
unexplored Universe within us
 about 1011 neurons
 and somewhere in the region of 1015
Three Stage Approach
Whole-genom shotgun approach
Celera Genomics
Public Consortium and Celera
Public Consortium x Celera Genomics
Francis Collins
Craig Venter
Genome Gallery
Genome Gallery
Number of Genes
 Mycoplasma genitalium – 480 genes
 probably 265 – 350 genes only are really
Number of Chromosomes
 Myrmecia pilosula 1 pair of chromosomes
 fern Ophioglossum reticulatum 630 pairs
of chromosomes
Human Genome Project
 officialy beagan in 1990
 the project involved 20 large sequencing
centers in six countries plus a host of
other labs working on small projects
 largely completed in 2003
 the sequence of each chromosome was
carefully analyzed and described in series
of papers, the last of which covered
chromosome 1 and was published in 2006
Nuclear Genome and Mitochondrial Genome
Human Genome
Human Genome
 Dna sequences that code for proteins or give
rise to tRNA or rRNA compose a mere 1,5 %
of the human genome
 If we include introns and regulatory
sequences associated with genes, the total
amount of DNA that is gene-related - coding
and non-coding - constitutes about 25 % of
the human genome
 put another way, only about 6 % (1,5 % out
of 25 %) of the lenght of the average gene is
represented in the final gene product
 Unique noncoding
 pseudogenes
 gene fragments
 small noncoding RNA
 the genes that
produce small
noncoding RNAs are
a tiny percentage of
the genome,
distributed between
the 20 % introns and
the 15 % unique
noncoding DNA
Dispersed repeats
(Jobling, M.A., et al. (2004) Human Evolutionary Genetics. New York, Garland
Number of
Copies in the
% of
850 000
6 000 – 8 000 pb
1 500 000
100 – 300 pb
450 000
6 000 – 11 000 pb
Copy DNA of
300 000
2 000 – 3 000 pb
Transposon movement
Retrotransposon movement
 Transposable elements and related
sequences make up 25% - 50 % of most
mammalian genomes and even higher
percentages in amphibians and many
 the very large size of some plant genomes
is accounted for not by extra genes, but by
extra transposable elements
 sequences like these make up 85 % of the
corn genome!
Human Genome
nuclear genome
mitochondril genome 16,6 kb
Human Genome
coding DNA
50 Mb (cca 1,5%)
regulatory sequences 100Mb (3%)
noncoding repetitive 50%
number of genes
cca 22 000
nuclear genome
cca 22 000
37 genes
Number and
Sequence Lenght
Chromosome 21 is
bigger than 22
9,10,11 are also
named in the wrong
Dates of 2010
 Fritillaria assyriaca 124 billion bp
 Polychaos dubia (single-celled amoeba)
670 billion bp
 There is a wide range of genome sizes
within the groups of protists, insects,
aphibians, and plants
 and less of a range within mammals and
Genomes of Bacteria and Archea
 genomes are „compact“
 genomes are correllated to metabolic diversity
 Mycoplasma genitalium – lives inside of
eucaryotic cells
 genome 580 000 bp., 517 genes
 Streptomyces coelicolor – soil bactery with
extremely complicated metabolical pathways
 genome 8,7 mil. bp., 7 846 genes
Genomes of Bacteria and Archea
 large genetic diversity between species
 cca 15 % - 30 % of genes are unique to a
 lateral gene transfer
 Thermatoga maritima – lives in hot springs up to
80 Celsia with many Archea
 up to 25 % of its genes closely related to genes of
Archea !
 transferes are realized by viruses, plasmids and
Genomes of Bacteria and Archea
 virulence genes among patogenic bacterias
often arise by lateral gene transfer
Genomes of Eucarya
 genes are generally orders of magnitude
 exons are only few percent of the genome
 majority of the genome are „repeated
Year 2001
 approximately 50 organisms entirely or
nearly entirely sequenced
 10 archea
 E.coli
 Saccharomyces cerevisiae
 C. elegans
 Arabidopsis thaliana
Year 2010
 1 200 genomes entirely sequenced
 1 000 of bacteria
 80 archeal genomes
 124 eucaryotic species
 1980: one lab 1000bp a day
 2000: one lab 1000bp per second, 24 hours
a day, seven days a week
 first human genome: 13 years and cost $ 100
 James Watson´s genome: four months
(2007) for about $ 1 million
 2010: 3 humans, each $ 4 400
 2011: one day, $ 1000, cca 1000 persons
 all exons: $ 600
Craig Venter´s Genome
 3 millions SNPs
 14 779 changes in protein coding regions
 20% never seen before
 2020 change in protein sequence
(nonsynonymous aminoacid substitutions)
 12% predicted to disrupt function of proteins
 11% in disease-causing genes
2010: Homo Neanderthalensis
 Between 1% and
4% of the
Eurasian human
genome seems to
come from
Svante Paabo (pictured here with a
Neanderthal skull) led the research effort
Sekvenování genomu neandertálce
2010: Homo Neanderthalensis
 The Neandertal Genome Project
What does it mean to be a human?
Why we act as we act?
 Nature (Genes)
 Nurture (Environment)
 Developmental Noise
 Freedom
James Watson
 ” We used to think that our fate was in our
stars. Now we know, in large part, that our
fate is in our genes.“
Francis Crick
 The development of biology is going to destroy to
some extent our traditional grounds for ethical
beliefs, and it is not easy to see what to put in their
A Man: a Periodic Table of Genes?
 „All matter can be reduced
to a periodic table of
elements, but at a higher
level, every living thing can
be reduced to a periodic
table of genes.“
(Strachan, T., Read, A.P., (2004) Human Molecular Genetics. 3rd ed.
Garland Publishing, New Yourk, p. 208)
 James Watson: ”We used to think
that our fate was in our stars. Now
we know, in large part, that our
fate is in our genes.“
 Walter Gilbert: „When we have the
complete sequence of the human
genome, we will know what it is to
be a human“
 E.O.Wilson:Ethics, as we
understand it, is an illusion fobbed
on us by our genes to get us to
 The search for the Holy Grail of who we
are, has now reached its culminating
phase; the ultimate goal is the acquisition
of all the details of our genome... that will
transform our capacity to predict what we
will become.
 Walter Gilbert
Le Fanu, J., (2009) Why us? How Science Rediscovered the Mystery of Ourselves. Pantheon Books, New
E.O. Wilson
( On Human Nature)
 „The question is no longer whether human
social behavior is genetically determined. It
is to what extent. The accumulated
evidence for a large hereditary component
is more detailed and compelling than most
persons, including even geneticists, realize.
I will go further, it is decisive.“
 The psychologist Thomas Bouchard has
said, "For almost every behavioral trait so
far investigated, from reaction time to
religiosity, an important fraction of the
variation among people turns out to be
associated with genetic variation. This fact
need no longer be subject to debate;
rather it is time instead to consider its
Robert Weinberg
 So what are you going to do if you begin
to find on a chip of a child's DNA that this
kid is likely to be very good in language,
probably is going to have poor math skills,
will be a rather anxious and obsessive
person, will have difficulty associating with
his or her peers, and is likely to come
down with heart disease at the age of 45?
How is that going to affect your
relationship to that person, that child?
Salvador Luria:
“‘Will the Nazi program to eradicate Jewish or
otherwise ‘inferior’ genes by mass murder be
transformed into a kinder, gentler program to
‘perfect’ human individuals by ‘correcting’ their
genomes in conformity perhaps to an ideal
‘white, Judeo-Christian, economically successful’
Ethical Questions
 knowledge gained from the HGP may lead to
the construction of a „standard“ human
 if this occurs, one must ask what variation society
would view as permissible before an individual´s
genome was labelled substandart or abnormal?
Ethical Issues
 knowledge gained from the HGP may lead to
the construction of a „standard“ human
 if this occurs, one must ask what variation society
would view as permissible before an individual´s
genome was labelled substandart or abnormal?
Human Genome Diversity Project
 this project would map DNA from
approximately 25 individuals representing
500 of the world´s 5000 or so different
ethnic groups
 concerns about discriminations of some
Human Genome Diversity Project
 first proposed in 1991 by a group of human
geneticist, led by Luca Cavalli-Sforza and
Allan Wilson
 project was launched in September 1993
 the primary goals of the founders were to
advance research into human history and
evolution, but they foresaw other possible
uses – in medicine, population genetics,
anthropology, and other fields
 …what they did not foresee was the ethical –
and political – storm ahead the Project
(Jobling, M.A., Hurles, M.E., Tyler-Smith, C., (2004) Human Evolutionary Genetics. Garland
Publisher, New York, p. 275)
Human Genome Diversity Project
 the HGDP continues to exist but, probably
at least in part because of the political
controversy attached to it, has never
received substantial funding – and has
never come close to achieving its goals
 this project would map DNA from
approximately 25 individuals representing
500 of the world´s 5000 or so different
ethnic groups, a total of 12 500 individuals
Human Genome Diversity Project
 RAFI (Rural Advancement Foundation
International) had begun excoriate project as
„bio-pirate“ interested in
stealing valuable genes from indigenous people
underhanded commercial goals
planning to undermine indigenous culture
overthrow indigenous land rights
to help US produce ethnically targeted biological
 to clone armies of indigenous warrior slaves
(Jobling, M.A., Hurles, M.E., Tyler-Smith, C., (2004) Human Evolutionary Genetics. Garland
Publisher, New York, p. 275)
Human Genome Diversity Project
 Whenever genetics is used to look at nationalities or
ethnicities, its methods, and its history, raise concerns
about how the data might be used, or abused, to
support racist or nationalistic views. When the groups
involved have been oppressed, they may well fear
commercial exploitation or worse harms, up to
 And, given history of Australian aboriginal people or
Native American Nations, their reluctance to participate
is not, and must not be treated as, unreasonable.
 Sometimes, in spite of researcher´s best effort,
indigenous people will say no. One key to ethical
human population genetics research is learning to
accept that answer.
(Jobling, M.A., Hurles, M.E., Tyler-Smith, C., (2004) Human Evolutionary Genetics. Garland Publisher, New York, p.
The Ethics of Genome Sequence Publications
 as soon as the first sequences were
published it became apparent that they could
only be used if available in computer
readable form
 1980s
 the European Molecular Biology Laboratory
 the National Institute of Health (NIH)
 Japanese National Institute of Genetics
 these organizations later joined into an effective
international collaboration to share data
The Ethics of Genome Sequence Publications
 2003:
 this community database (EMBL-
 contains over 40 billion bp of sequence
 from over 100 000 different organism
 All three databases implemented a policy
that was both courageous and
foresighted: to make all of their data freely
available to all (whether they be
companies, academics or „John Smith“)
The Ethics of Genome Sequence Publications
 By the late 1980s most reputable scientific
journals were demanding deposition of
sequence data in this database as a precondition for the publication of a scientific paper.
 This immediately gave rise to a conflict:
commercial companies (and some academics)
saw their DNA sequence data as a intelectual
property that might be turned into money. They
were often reluctant to make their data freely
available, since this might both compromise
patent protection and reduce value of their
Bermuda Agreement 1996
 = all data from the Human Genome
Project will be deposited in the public
sequence databanks
 each sequencing center will release its
own data every day
Bermuda Agreement 1996
 1998: Celera Genomics
 „Discovery can´t wait!“
 Public consortium had no access to
Celera´sequence data
 Celera had free access to Public
consortium data
Human Genome: Invention or Discovery?
 Human Genome is a discovery, freely
available to all – like calendar
 or Einstein theory of Relativity
 or Double Helix of DNA
 Human Genome is a invention
 like a bulb
 or steam engine
 can patent invention, but not
Human Genome: Discovery
 Human Genome is a discovery
 sequence data of human genome – or any
other organism –are fundamental to
 they are as fundamental as the periodic table
is to chemistry and as Euclid´s axioms are to
 data belong to all of us,
 they are not commodities to be sold in the
market place like apples and oranges!
Human Genome: Discovery
 there is also pragmatic reason: databases
are most useful if, within a given scientific
domain, they are not fragmented
 much of modern genomics would simply
be impossible if the universe of sequence
data were split between hundreds of
different databases
 by allowing publication without sequence data
deposition in the community sequence
databse Science has encouraged
fragmentation of the universe sequence data
Patenting of Human Genes
 genetics research should
be a cooperative search
for new knowledge,
rather the self-interested
pursuit of profits
 once patenting comes to
the fore, researchers
may become
increasingly reluctant to
share information,
thereby diminishing its
transfer between
 In the US it costs a woman between
$3,000 and $4,000 to be tested for familial
breast cancer because a corporation owns
the patent for the two genes involved.
Patenting of Human Genes
(Richards, J.E., Hawley, R.S., (2005) The Human Genome. Burlington,
Elsevier Academic Press)
 the gene can be patented if there is an idea
regarding some use that could be made of
that gene for a particular purpose, such as
screening people to find out if they are at risk
for a particular disease
Ethical Issues: Racism is dead
 1,5 milions bp – difference between mother
and her daughter
 2,25 milions bp - difference between
grandmother and granddaughter
 3 milions bp - difference between two
random chosen people on Earth
 Lewotine (1972) used 17 loci (blood groups, serum proteins,
red blood cell enzymes) for which variation had been
detected by immunological or electrophoretic methods and
had allele frequency data available for several populations
 the populations were classified into seven „races“ termed
Black Africans,
South Asian Aborigines,
Oceanins and
Australian Aborigines,
 based on morphological, linguistic, historical and cultural
 the overwhelming conclusion was that most
variation lies within population, and that „races“
had no genetic reality,a conclusion reinforced by
subsequent analyses using independent
population samples and DNA markers
 Lewontine concluded:
 Human racial classification is of no social value and is
positively destructive of social and human relations.
Since such racial classifications is now seen to be of
virtually no genetic or taxonomic significance either, no
justification can be offered for its continuance.
(Jobling, M.A., Hurles, M.E., Tyler-Smith, C., (2004) Human Evolutionary Genetics. Garland Publisher,
New York, p. 277)
„Race“ is not a biological concept
 modern population genetics makes the
concept of „race“ in the human context
biologically meaningless, although socially
 polish jews are more similar to polish nonjews than to jews in f.e. Sapin
Humans show little genetic variation
compared with other species
Genetická variabilita (%)
Out of Africa a multiregionální
Dvě teorie vzniku moderního člověka
(multiregionální model a „out of Africa“)
Chimp Genome and Human
What makes us "human"?
Ethical Issues: The Chimpanzee Genome
Are there any differences between chimps and humans?
 The chimpanzee genome is 98.77%
identical to the human genome. On average,
a typical human protein-coding gene differs
from its chimpanzee ortholog by only two
amino acid substitutions; nearly one third of
human genes have exactly the same protein
translation as their chimpanzee orthologs. A
major difference between the two genomes is
human chromosome 2, which is the product
of a fusion between chimpanzee
chromosomes 12 and 13.
Human and Chimpanzee chromosomes
Human and Chimpanzee chromosomes
 chromosomes 12 and 13 in
a human ancestor fused
end to end to form human
chromosome 2
 The centromere from
ancestral chromosome 12
remained functional on
human chromosome 2.
while the one from ancestral
chromosome 13 did not
 Among the 3 billion base pairs in the DNA
of both humans and chimpanzees,
researchers found differences in 40 million
 When measured by changes in their
genetic codes, humans and chimpanzees
are about 10 times more different than are
individual humans from each other.
Evolution at Two Levels in Humans and Chimpanzees
 The organismal differences between chimpanzees
and humans would ... result chiefly from genetic
changes an a few regulatory systems, while amino
acid substitutions in general would rarely be a key
factor in major adaptive shifts. (Mary-Claire King
and Alan Wilson)
 That is to say, the allelic substitutions of the
genes that encode protein sequences - which
seem to be pretty much the same for chimps
and humans - are not what is importatnt. The
important difference are where, when, and
how much the genes are activated
cit. v Gilbert, S.F., Epel, D., (2009) Ecological Developmental Biology. Sinauer Associates, Inc. Sunderland, MA.
USA, p. 325
 We cannot see in this why we are so
different from chimpanzees. Part of the
secret is hidden in there /in the genome/,
but we don´t understand it yet.
 Svante Paabo
Le Fanu, J., (2009) Why us? How Science Rediscovered the Mystery of Ourselves. Pantheon Books, New
 Why is there not the slightes hint in the
Human Genome of those unique attributes
of the upright stance and massively
expanded brain that so distinguish us from
our primate cousins?
Le Fanu, J., (2009) Why us? How Science Rediscovered the Mystery of Ourselves. Pantheon Books, New
 1997
„There is no gene for
the human spirit“
… but is it true?
Creationism is dead
 51% sequences we share with yeasts
 57% sequences we share Brassica
 98,6% sequences we share wit Pan
Creationism is
Collins, F., (2006) The
Language of God. Free
Press, New York, p. 128)
"Little People with Wings"
 The diverse subtlety of form, shape and colour
that distinguishes snowdrop from tulips, flies
from frogs and humans, is nowhere to be found.
 There is not the slighest hint in the composition
of the genes of fly or man to account for why the
fly should have six legs, a pair of wings and a
brain the size of a full stop, and we should have
two arms, two legs and that prodigious brain.
Le Fanu, J., (2009) Why us? How Science Rediscovered the Mystery of Ourselves. Pantheon Books, New York.
 We have moved, in the wake of Genome
project, from assuming that we knew the
principle, if not the details, of that greatest
marvels, the genetic basis of the infinite
variety of life, to recognisisng that we not
only don´t understand the principles, we
have no conception of what they might be.
Le Fanu, J., (2009) Why us? How Science Rediscovered the Mystery of Ourselves. Pantheon Books, New
Convention for the Protection of Human Rights and Dignity of the Human Being with regard to the Application of Biology and
Convention on Human Rights and Biomedicine
OVIEDO, 1997
 Chapter IV – Human genome
 Article 11 – Non-discrimination
 Any form of discrimination against a person on
grounds of his or her genetic heritage is
The Genetic Information Nondiscrimination Act
passed the American Senate in 2003
 Act will prevent insurers and employers
from discriminating based on genetic
information. This means that an insurance
company cannot deny you insurance or
charge you more because you have a
particular genotype, and that an employer
cannot fire you or pay you less because
you have a particular genotype.
Next Lecture
 Do genes influence human behaviour?
 ...coming soon!