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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

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the human genome
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

slide3

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
completed sequences
Completed sequences

1995 – First complete bacterial genomes

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

ihgcs paper
IHGCS paper

Nature, 409, February 15, 860-921 (2001)

celera paper
Celera paper

Science, 291, February 16, 1304-1351 (2001)

sequencing
Sequencing

BAC:

Bacterial Artificial

Chromosome clone

Contig: joined

overlapping collection

of sequences or clones.

c value paradox
C-value paradox
  • C-value paradox: Genome size does
  • 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
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
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
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 20,000 ~20,000

Fly 13,500 >>20,000

Human ~40,000 >>100,000

human genome content
Human genome content
  • The Human Genome
  • 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
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
Fig 35a

Size distributions of exons in Human, Worm and Fly. Human have shorter exons.

fig 35c
Fig 35c

Size distributions

of intons in

Human, Worm

and Fly.

Human have

longer introns.

gene recognition
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
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
Genes predicted in Human Genome

Int’l Consortium Celera

known genes 14,882 17,764

novel genes 16,896 21,350

Total 31,778 39,114

two predictions disagree
Two predictions disagree

“…predicted transcripts

collectively contain partial

matches to nearly all known

genes, but the novel genes

predicted by both groups

are largely non-overlapping.”

John B. Hogenesch, et al

Cell, Vol. 106, 413–415

August 24, 2001

global properties with evolutionary implications
Global properties with evolutionary implications
  • Long-range variation in GC content not random
  • CpG islands protected by genes
  • Genetic and physical distance non-linear
  • > 50% genome composed of repeats
standard deviation 15 times wider than random distrib n
Standard deviation 15 times wider than random distrib’n

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.

slide25

GC content in introns (exons) vs

introns (exons) length.

fig 14 cpg islands
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.

fig 15 recomb rate distal
Fig 15 recomb rate (distal)

Recombination rate vs

Physical position from

centromere of genes. Rate

higher in distal regions.

fig 16 recomb rate short arm
Fig 16 recomb rate (short arm)

Recombination rate

higher on shorter

chromosome arms

the genome mutates and copies itself
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 (10-300 kb); (large) blocks of tandemly repeated sequences
fig 17 transposables
Fig 17 transposables

Interspersed repeats: fixed transposable

elements copied to non-homologous regions.

Total 45%

Classes of transposable elements. LINE, long interspersed

element. SINE short interspersed element.

fig 21
Fig 21

Genes are sometimes protected from repeats

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.

tab 14 ssr content
Tab 14 SSR content

Simple sequence (k-mers) repeats: SSR

fig 32b
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 32a
Fig 32a

An active pericentromeric

region on chromosome 21.

fig 32c
Fig 32c

c. A pericentromeric region from chromosome 11.

fig 32d
Fig 32d

d. A subtelomeric region from chromosome 7p.

fig 33
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
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
Completed eukaryotic proteomes

Human Fly Worm Yeast Mustard weed

Identified genes 32,000 13,338 18,266 6,144 25,706

Annotated

domain families 1,262 1,035 1,014 861 1,010

Distinct domain

architectures 1,695 1,036 1,018 310 -

fig 38 distribution of homologs
Fig 38 distribution of homologs

Distribution of homologues of predicted human proteins

slide43

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
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 architec-

tures (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
Fig 45 domain expansion

Lineage-specific expansions of domains and

architectures of transcription factors

slide46

Conserved segments

in human and mouse

genome

Colour code:

Mouse genome

applications to medicine and biology
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
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