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The Human Genome
The International Human Genome Consortium
Initial sequencing and analysis of the
human genome
Nature, 409, February 15, 860-921 (2001)
Venter et al. (Celera)
The Sequence of the Human Genome
Science, 291, February 16, 1304-1351 (2001)
HC LEE
January 8, 2002
Computational Biology Lab
National Central University
1984 to 1986 – first proposed at US DOE meetings
1988 – endorsed by US National Research Council
- creation of genetic, physical and sequence maps of
the human genome
- parallel efforts in key model organisms: bacteria, yeast,
worms, flies and mice;
- develop of supporting technology
- ethical, legal and social issues (ELSI)
1990 – Human Genome Project (NHGRI)
Later – UK, France, Japan, Germany, China
Time-line large scale genomic analysis
1995 – First complete bacterial genomes
Completed sequences
2002 – About 35 bacterial genomes;
0.5-5 Mb; hundreds to 2000 genes
1996 April – Yeast (Saccharomyces cerevisiae)
12 Mb, 5,500 genes
1998 Dec. -Worm (Caenorhabditis elegans)
97 Mb, 19,000 genes
2000 March - Fly (Drosophila melanogaster)
137 Mb, 13,500 genes
2000 Dec. - Mustard (Arabidopsis thaliana)
125 Mb, 25,498 genes
2000 June – Human (Homo sapiens) 1st rough draft
2001 Feb 15/16 – Human, “working draft”
3000 Mb, 35,000~40,000 genes
Nature, 409, February 15, 860-921 (2001)
IHGCS paper
Science, 291, February 16, 1304-1351 (2001)
Celera paper
Sequencing
BAC:
Bacterial Artificial
Chromosome clone
Contig: joined
overlapping collection
of sequences or clones.
C-value paradox: Genome size does
C-value
paradox
not correlate
well with
organismal
complexity.
Human Homo sapiens 3000 Mb
Yeast S. cerevisiae 12 Mb
Amoeba dubia 600,000 Mb
Genomes can contain a large quantity
of repetitive sequence, far in excess of
that devoted to protein-coding genes
Global properties
• Pericentromeric and subtelomeric regions of
chromosomes filled with large recent transposable
elements
• Marked decline in the overall activity of
transposable elements or transposons
• Male mutation rate about twice female
– most mutation occurs in males
• Recombination rates much higher in distal regions
of chromosomes and on shorter chromosome arms
– > one crossover per chromosome arm in each
meiosis
Important features of Human proteome
• 30,000–40,000 protein-coding genes
• Proteome (full set of proteins) more
complex than those of invertebrates.
– pre-existing components arranged into a
richer architectures.
• Hundreds of genes seem to come from
horizontal transfer from bacteria
• Dozens of genes seem to come from
transposable elements.
Human proteome is complex
• Gene codes proteins (also RNAs)
• Number of genes does not reflect
complexity of organism
Org’nism
no. genes no. proteins
Worm
Fly
Human
20,000
13,500
~40,000
~20,000
>>20,000
>>100,000
The Human Genome
Human genome content
Total length 3000 Mb
~ 40,000 genes (coding seq)
Gene sequences < 5%
Exons ~ 1.5% (coding)
Introns ~ 3.5% (noncoding)
Intergenic regions (junk) > 95%
Repeats > 50%
Gene codes proteins (also RNAs)
(transcription & translation)
Procaryotes (single cell):
one gene, one protein
Eucaryote (multicell):
gene = intron + exon;
one gene, many proteins
Fig 35a
Size distributions of exons in Human, Worm
and Fly. Human have shorter exons.
Fig 35c
Size distributions
of intons in
Human, Worm
and Fly.
Human have
longer introns.
Fig 35b
Gene recognition
• Coding region and non-coding region have
different sequence profiles
– coding region is “protected” from mutation and
is less random
• Gene recognition by sequence alignment
• Gene prediction by Hidden Markov Model
trained by set of known genes
• Many genes are homologs – similar in
vastly different organisms
Gene recog’n difficult for Human
• Easy for procaryotes (single cell) – one
gene, one protein
• More difficult for eukaryotes (multicell) –
one gene, many proteins
• Very difficult for Human – short exons
separated by non-coding long introns
Genes predicted in Human Genome
Int’l Consortium
Celera
known genes 14,882
novel genes
16,896
17,764
21,350
Total
39,114
31,778
Two predictions disagree
John B. Hogenesch, et al
Cell, Vol. 106, 413–415
August 24, 2001
“…predicted transcripts
collectively contain partial
matches to nearly all know
genes, but the novel genes
predicted by both groups
are largely non-overlapping
Global properties with
evolutionary implications
• Long-range variation in GC content not
random
• CpG islands protected by genes
• Genetic and physical distance nonlinear
• > 50% genome composed of repeats
GC-rich and GC-poor regions have different biological
properties, such as gene density, composition of
repeat sequences, correspondence with cytogenetic
bands and recombination rate.
Standard
deviation
15 times
wider than
random
distrib’n
GC content is correlated with coding regions
GC content in introns (exons) vs
introns (exons) length.
Fig 14 CpG islands
CpG islands and genes are correlated.
CpG dinucleotides are methylated; methyl-CpG steadily
mutate to TpG. Hence CpG is greatly under-represented
in human DNA. Except in CpG islands near genes.
Recombination rate vs
Physical position from
centromere of genes. Rate
higher in distal regions.
Fig 15 recomb rate (distal)
Recombination rate
higher on shorter
chromosome arms
Fig 16 recomb rate (short arm)
The genome
mutates and copies itself
• 50%, probably much more, of genome
composed of repeats
– Many traces of repeats obliterated by mutation
– Lower organisms may have longer genomes
• Five types of repeats
– transposable elements; processed pseudogenes;
simple k-mer repeats; segmental duplications (10300 kb); (large) blocks of tandemly repeated
sequences
Interspersed repeats: fixed transposable
elements copied to non-homologous regions.
Fig 17 transposables
Total 45%
Classes of transposable elements. LINE, long interspersed
element. SINE short interspersed element.
Genes are sometimes protected from repeats
Fig 21
Two regions of about 1 Mb on chromosomes 2 and 22. Red bars,
interspersed repeats; blue bars, exons of known genes. Note the
deficit of repeats in the HoxD cluster, which contains a collection
of genes with complex, interrelated regulation.
Simple sequence (k-mers) repeats: SSR
Tab 14 SSR content
Fig 32b
Mosaic patterns of duplications. For each region top horizon line:
segment of sequence (100–500 kb) with interchromosomal (red)
and intrachromosomal (blue) duplications displayed. Lower lines
with a distinct colours: separate sequence duplication. y axis:
per cent nucleotide identity.
b. An ancestral region from Xq28 that has contributed various
'genic' segments to pericentromeric regions.
Fig 30
Fig 32a
An active pericentromeric
region on chromosome 21.
Fig 32c
c. A pericentromeric region from chromosome 11.
Fig 32d
d. A subtelomeric region from chromosome 7p.
Fig 33
Finished HG has 1.5% interchromosomal 2% intrachromosomal
segmental duplications. The duplications are 10–50 kb long
and highly homologous. Structure in similarity may indicate
that interchromosomal duplications occurred in a punctuated
manner.
Human Proteome
• Number of human genes (~40,000) only twice that
of worm or fly
• Many more transcripts (combination of exons in
one gene)
• Many more proteins, perhaps >> 100,000
• Most proteins are still homologs of non-human
proteins
• Homologs (from a common ancestor gene)
– orthologs – derived through speciation
– paralogs: derived through duplication
Completed eukaryotic proteomes
Human
Fly
Worm
Identified genes 32,000 13,338 18,266
Annotated
domain families 1,262 1,035 1,014
Distinct domain
architectures 1,695
1,036 1,018
Yeast Mustard weed
6,144
25,706
861
1,010
310
-
Functional categories of eukaryote proteomes
Distribution of homologues of predicted human proteins
Fig 38 distribution of homologs
Simplified cladogram
(relationship tree)
of the 'many-to-many'
relationships of
classical nuclear
receptors. Triangles
indicate expansion
within one lineage;
bars represent single
members. Numbers in
parentheses indicate
the number of
paralogues in each
group.
Fig 42 domain accretion
Domain accretion in chromatin proteins in various lineages before the
animal divergence, in the apparent coelomate lineage and the vertebrate
lineage are shown using schematic representations of domain architectures (not to scale). Asterisks, mobile domains that have participated in
theaccretion. Species in which a domain architecture has been identified
are indicated (Y, yeast; W, worm; F, fly; V, vertebrate).
Fig 45 domain expansion
Lineage-specific expansions of domains and
architectures of transcription factors
Conserved segments
in human and mouse
genome
Colour code:
Mouse genome
Applications to medicine and
biology
• Disease genes
– human genomic sequence in public databases
allows rapid identification of disease genes in
silico
• Drug targets
– pharmaceutical industry has depended upon a
limited set of drug targets to develop new
therapies
– now can find new target in silico
• Basic biology
– basic physiology, cell biology…
The next steps
• Finishing the human sequence
• Developing the IGI (integrated gene index)
and IPI (protein)
• Large-scale identification of regulatory
regions
• Sequencing of additional large genomes
– mouse, super-rice, pig, fish…
• Completing the catalogue of human variation
– Single nucleotide polymorphism
– nasal and throat cancer…
• From sequence to function