Genome Organization and Evolution

1
Genome Organization and Evolution
Reading Introduction to Bioinformatics.
Arthur M. Lesk. Fourth Edition Chapter 2
2
Genes

• A gene is the basic physical and functional unit
  of heredity. 
• Genes, which are made up of DNA, act as
  instructions to make proteins
• DNA which codes for functional RNA?
• Control regions?

3
Gene organization

• A gene may occur on either strand of DNA
• Genes are continuous stretches (almost always) in
  prokaryotes
• Genes are (often) discontinuous stretches (exons)
  in eukaryotes. The intervening regions are called
  introns
• Upstream is a binding site
• Location of regulatory region is less predictable

4
The Central Dogma

• One gene, one protein
• Like most dogmas, not entirely true
• Alternative splicing permits the manufacture of
  many products from a single gene
• The protein products are sometimes called the
  proteome
• With current technology, more gene information is
  available than protein information

5
Transmission of information

• How hereditary information is stored, passed on,
  and implemented is considered a fundamental
  problem is biology.
• Three types of maps are essential
• Linkage maps of genes
• Banding patterns of chromosomes
• DNA sequences

6
Gene maps

• Gene maps help describe the spatial arrangement
  of genes on a chromosome.
• Genes are designated to a specific location on a
  chromosome known as the locus and can be used
  as molecular markers to find the distance between
  other genes on a chromosome.
• Maps provide researchers with the opportunity to
  predict the inheritance patterns of specific
  traits

7
Chromosome banding pattern maps

• Chromosomes are identified by the banding
  patterns revealed by different staining
  techniques.

8
DNA sequence

• Physically a sequence of nucleotides in the
  molecule,
• Computationally a string of characters A, T, G,
  and C
• Genes are regions of the sequence, in many cases
  interrupted by noncoding regions

9
High-resolution maps

• Variable number tandem repeats (VNTRs
  minisatellites), 10-100 bp, are a sort of genetic
  fingerprint
• Short tandem repeat polymorphisms (STRPs
  microsatellites), 2-5 bp, are another kind of
  marker
• A contig is a series of overlapping DNA clones of
  known order along a chromosome from an organism
• A sequence tagged site (STS), 200-600 bp, is a
  known unique location in the genome

10
Identifying genes

• Open Reading Frames (ORF) is a region of DNA that
  begins with an initiation codon and ends with a
  stop codon.
• An ORF is a potential gene
• Gene finding techniques are based on one or a
  combination of the following
• Similarity to known genes
• Properties of the DNA sequence itself (ab-initio
  approaches)

11
Prokaryote genomes

• Genetic material of the cell takes the form of a
  large single circular piece of double stranded
  DNA. Example E. coli 4,639,211 pb
• 89 coding
• 4,285 genes
• 122 structural RNA genes
• Prophage remmants
• Insertion sequence elements
• Horizontal transfers

12
Metagenome

• Genetic information of an entire environmental
  sample
• DNA is extracted directly from the environment
  using Next Generation Sequencing
• Determine the sequences directly from a sample
  without culturing individual strains
• Provide information about species that cannot be
  cloned in the traditional way

13
Eukaryotic genome

• The full genetic information in a eukaryotic cell
• Example C. elegans
• 10 chromosomes
• 19,099 genes
• Coding region 27
• Average of 5 introns/gene
• Both long and short duplications

14
Human Genome Project

• At the height of the Human Genome Project,
  sequencing factories were generating DNA
  sequences at a rate of 1000 nucleotides per
  second 24/7.
• Technical breakthroughs that allowed the Human
  Genome Project to be completed have had an
  enormous impact on all of biology..

Molecular Biology Of The Cell. Alberts et al.
491-495
15
Human Genome Project
Goals  identify all the approximate 30,000
genes in human DNA, determine the sequences of
the 3 billion chemical base pairs that make up
human DNA, store this information in
databases, improve tools for data analysis,
transfer related technologies to the private
sector, and address the ethical, legal, and
social issues (ELSI) that may arise from the
project.   Milestones 1990 Project initiated
as joint effort of U.S. Department of Energy and
the National Institutes of Health June 2000
Completion of a working draft of the entire human
genome (covers gt90 of the genome to a depth of
3-4x redundant sequence) February 2001
Analyses of the working draft are published
April 2003 HGP sequencing is completed and
Project is declared finished two years ahead of
schedule
http//doegenomes.org http//www.sanger.ac.uk/HGP/
overview.shtml
U.S. Department of Energy Genome Programs,
Genomics and Its Impact on Science and Society,
2003
16
What does the draft human genome sequence tell
us?
By the Numbers The human genome contains 3
billion chemical nucleotide bases (A, C, T, and
G).  The average gene consists of 3000 bases,
but sizes vary greatly, with the largest known
human gene being dystrophin at 2.4 million
bases.   The total number of genes is estimated
at around 30,000--much lower than previous
estimates of 80,000 to 140,000.   Almost all
(99.9) nucleotide bases are exactly the same in
all people.   The functions are unknown for over
50 of discovered genes.
http//doegenomes.org
U.S. Department of Energy Genome Programs,
Genomics and Its Impact on Science and Society,
2003
17
What does the draft human genome sequence tell us?
How It's Arranged The human genome's gene-dense
"urban centers" are predominantly composed of the
DNA building blocks G and C.   In contrast, the
gene-poor "deserts" are rich in the DNA building
blocks A and T. GC- and AT-rich regions usually
can be seen through a microscope as light and
dark bands on chromosomes.   Genes appear to be
concentrated in random areas along the genome,
with vast expanses of noncoding DNA between.  
Stretches of up to 30,000 C and G bases repeating
over and over often occur adjacent to gene-rich
areas, forming a barrier between the genes and
the "junk DNA." These CpG islands are believed to
help regulate gene activity.   Chromosome 1 has
the most genes (2968), and the Y chromosome has
the fewest (231).
http//doegenomes.org
U.S. Department of Energy Genome Programs,
Genomics and Its Impact on Science and Society,
2003
18
What does the draft human genome sequence tell
us?
The Wheat from the Chaff Less than 2 of the
genome codes for proteins.   Repeated sequences
that do not code for proteins ("junk DNA") make
up at least 50 of the human genome.  
Repetitive sequences are thought to have no
direct functions, but they shed light on
chromosome structure and dynamics. Over time,
these repeats reshape the genome by rearranging
it, creating entirely new genes, and modifying
and reshuffling existing genes.   The human
genome has a much greater portion (50) of repeat
sequences than the mustard weed (11), the worm
(7), and the fly (3).
http//doegenomes.org
U.S. Department of Energy Genome Programs,
Genomics and Its Impact on Science and Society,
2003
19
What does the draft human genome sequence tell
us?
How the Human Compares with Other Organisms
Unlike the human's seemingly random distribution
of gene-rich areas, many other organisms' genomes
are more uniform, with genes evenly spaced
throughout.   Humans have on average three times
as many kinds of proteins as the fly or worm
because of mRNA transcript "alternative splicing"
and chemical modifications to the proteins. This
process can yield different protein products from
the same gene.   Humans share most of the same
protein families with worms, flies, and plants
but the number of gene family members has
expanded in humans, especially in proteins
involved in development and immunity.   Although
humans appear to have stopped accumulating
repeated DNA over 50 million years ago, there
seems to be no such decline in rodents. This may
account for some of the fundamental differences
between hominids and rodents, although gene
estimates are similar in these species.
Scientists have proposed many theories to explain
evolutionary contrasts between humans and other
organisms, including those of life span, litter
sizes, inbreeding, and genetic drift.
http//doegenomes.org
U.S. Department of Energy Genome Programs,
Genomics and Its Impact on Science and Society,
2003
20
What does the draft human genome sequence tell
us?
Variations and Mutations Scientists have
identified about 3 million locations where
single-base DNA differences (SNPs) occur in
humans. This information promises to
revolutionize the processes of finding
chromosomal locations for disease-associated
sequences and tracing human history.   The
ratio of germline (sperm or egg cell) mutations
is 21 in males vs females. Researchers point to
several reasons for the higher mutation rate in
the male germline, including the greater number
of cell divisions required for sperm formation
than for eggs.
http//doegenomes.org
U.S. Department of Energy Genome Programs,
Genomics and Its Impact on Science and Society,
2003
21
What does the draft human genome sequence tell us?

• Led to the discovery of whole new classes of
  proteins and genes, while revealing that many
  proteins have been much more highly conserved in
  evolution than had been suspected.
• Provided new tools for determining the functions
  of proteins and of individual domains within
  proteins, revealing a host of unexpected
  relationships between them.

Molecular Biology Of The Cell. Alberts et al.
491-495
22
What does the draft human genome sequence tell us?

• By making large amounts of protein available, it
  has yielded an efficient way to mass produce
  protein hormones and vaccines
• Dissection of regulatory genes has provided an
  important tool for unraveling the complex
  regulatory networks by which eukaryotic gene
  expression is controlled.

Molecular Biology Of The Cell. Alberts et al.
491-495
23
How does the human genome stack up?
Organism Genome Size (Bases) Estimated Genes
Human (Homo sapiens) 3 billion 30,000
Laboratory mouse (M. musculus) 2.6 billion 30,000
Mustard weed (A. thaliana) 100 million 25,000
Roundworm (C. elegans) 97 million 19,000
Fruit fly (D. melanogaster) 137 million 13,000
Yeast (S. cerevisiae) 12.1 million 6,000
Bacterium (E. coli) 4.6 million 3,200
Human immunodeficiency virus (HIV) 9700 9
http//doegenomes.org
24
Future Challenges What We Still Dont Know
Gene number, exact locations, and functions
Gene regulation DNA sequence organization
Chromosomal structure and organization
Noncoding DNA types, amount, distribution,
information content, and functions
Coordination of gene expression, protein
synthesis, and post-translational events
Interaction of proteins in complex molecular
machines Predicted vs experimentally determined
gene function Evolutionary conservation among
organisms Protein conservation (structure and
function) Proteomes (total protein content and
function) in organisms Correlation of SNPs
(single-base DNA variations among individuals)
with health and disease Disease-susceptibility
prediction based on gene sequence variation
Genes involved in complex traits and multigene
diseases Complex systems biology including
microbial consortia useful for environmental
restoration Developmental genetics, genomics
U.S. Department of Energy Genome Programs,
Genomics and Its Impact on Science and Society,
2003
25
Evolution of genomes

• Adaptation of species is coterminous with
  adaptation of genomes
• Where do genes come from? (Answer from other
  genes)
• Homologs and paralogs
• Lateral transfer
• Molecular species each have their own family tree
• Genes are widely shared

26
Close relatives

• Yeast, fly, worm and human share at least 1308
  groups of proteins
• Unique to vertebrates immune proteins (for
  example)
• Unique molecules are adapted from ancient
  molecules of different purpose but similar design
• Most new proteins come from domain rearrangement
• Most new species come from control region
  variation