Computational Biology

1. 3/24/2023
©Bud Mishra, 2001
L2-1
Computational Biology
Lecture #2: Genome
Organization
Bud Mishra
Professor of Computer Science and
Mathematics
9 ¦ 24 ¦ 2001


2. 3/24/2023
©Bud Mishra, 2001
L2-2
Active Areas of
Research(1)
• Human Genome Project: (Completed?)
– Read 3 billion base pairs in 46 human
chromosomes
– Deemed “substantially completed on June 27,
2000.”
• Polymorphisms and Haplotyping
– SNPs (Single Nucleotide Polymorphisms): Catalog
the single base pair variations occurring about 1 in
800 base pairs of human genome over the entire
populations
– RFLP-Map: Restriction Fragment Length
Polymorphisms

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L2-3
Active Areas of
Research(2)
• Transcription Maps:
– Identify all (about 30,000 (?)) the genes in the
human genome.
– Particularly interesting are the ones involved in
cancer…About 100 oncogenes and 1000 tumor
suppressor genes
• Linkage Analysis:
– Relate genes (or polymorphic markers) to
phenotypes (externally observable traits) by
analyzing genomes of a family (kinship) or over a
population.

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©Bud Mishra, 2001
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Active Areas of
Research(3)
• Functional Genomics:
– Understand how an interactive network of
genes affect a chain of metabolic pathways
to ultimately determine the phenotypes
• Comparative Genomics:
– Relate genes within and across species to
understand their evolutionary
relationship…Phylogeny.

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©Bud Mishra, 2001
L2-5
Active Areas of
Research(4)
• Cell Informatics:
– Interaction between proteins (membrane
and soluble ones) to determine the
dynamics of a cell.
– Interaction among a heterogeneous
population of cells.
• Rational Drug Design:
– Design of drugs and delivery systems to
modify the dynamics of the cells.

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©Bud Mishra, 2001
L2-6
Introduction to Biology
• Genome:
– Hereditary information of an organism is encoded
in its DNA and enclosed in a cell (unless it is a
virus). All the information contained in the DNA of
a single organism is its genome.
• DNA molecule can be thought of as a very long
sequence of nucleotides or bases:
S = {A, T, C, G}

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Complementarity
• DNA is a double-stranded polymer and should be thought of as
a pair of sequences over S. However, there is a relation of
complementarity between the two sequences:
– A , T, C , G
– That is if there is an A (respectively, T, C, G) on one
sequence at a particular position then the other sequence
must have a T (respectively, A, G, C) at the same position.
• We will measure the sequence length (or the DNA length) in
terms of base pairs (bp): for instance, human (H. sapiens) DNA
is 3.3 £ 109 bp measuring about 6 ft of DNA polymer completely
stretched out!

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©Bud Mishra, 2001
L2-8
The Central Dogma
• The intermediate molecule carrying the information out of the nucleus
of an eukaryotic cell is RNA, a single stranded polymer.
• RNA also controls the translation process in which amino acids are
created making up the proteins.
• The central dogma(due to Francis Crick in 1958) states that these
information flows are all unidirectional:
“The central dogma states that once `information' has passed into
protein it cannot get out again. The transfer of information from
nucleic acid to nucleic acid, or from nucleic acid to protein, may be
possible, but transfer from protein to protein, or from protein to
nucleic acid is impossible. Information means here the precise
determination of sequence, either of bases in the nucleic acid or of
amino acid residues in the protein.”

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©Bud Mishra, 2001
L2-9
Interrupted Genes:
• An open reading frame (containing a
gene) consists of
– INTRONS: Intervening sequences a
Noncoding regions
– EXONS: Protein coding regions
• Introns are abundant in eukaryotes and
certain animal viruses.

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©Bud Mishra, 2001
L2-10
Interrupted Genes:
Intron1 Intron2
Intron3
Exon1 Exon2
Transcription
Splicing
DNA
RNA
Primary transcript
mRNA

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©Bud Mishra, 2001
L2-11
Interrupted Genes:
• Introns can occur between individual
codons or within a single codon
Nucleu
s
Cell
hnRNA
(heterogeneous nuclear
RNA)
Mixture of primary
transcripts with varying
numbers of introns spliced.
mRNA

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©Bud Mishra, 2001
L2-12
Some Genes…
Gene Product Organism Exon
Length
#Intron Intron
Length
Adenoshine deaminase Human 1500 11 30,000
Apolipoprotein B Human 14,000 28 29,000
Erythropoietin Human 582 4 1562
Thyroglobulin Human 8500 = 40 100,000
a-interferon Human 600 0 0
Fibroin Silk Worm 18,000 1 970
Phaseolin French 1263 5 515

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©Bud Mishra, 2001
L2-13
Regulation of Gene
Expressions
• Motifs (short DNA sequences) that regulate transcription
– Promoter
– Terminator
• Motifs that modulate transcription
– Repressor
– Activator
– Antiterminator
Promoter
Gene
Transcription
al
Initiation
Transcription
al
Termination
Terminator
10-35bp

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Promoters
• pol I (RNA polymerase I)
– Transcribes ribosomal RNA genes 100 » 1000 bp
in front of the gene
• pol II (RNA polymerase II)
– Transcribes genes encoding polypeptides
– Complex and variable regulatory regions
• pol I (RNA polymerase I)
– Transcribes transfer RNA and other small RNAs
– Both up and down stream

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©Bud Mishra, 2001
L2-15
Motifs
• Each motif is a binding site for a specific protein
• Transcription Factor:
– Transcription factors (specific to a cell/environmental
conditions) bind to regulatory regions and facilitate
• Assembly of RNA polymerase into a transcriptional complex
• Activation of a transcriptional complex.
• Termination Factor:
– Assembly of proteins for termination and modification of the
end of the RNA
• Epigenetic Changes
– Methylation of the cytosine in the 5’ region
– Structural changes in cromatin

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L2-16
Organization of Genetic Information
• Bacterial Genome:
– Genes are closely spaced along the DNA.
– The sequences of genes may overlap.
– Related genes (encoding enzymes whose
functions are part of the same pathway or
whose activities are related) are linked as a
single transcription unit.

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©Bud Mishra, 2001
L2-17
Organization of Genetic Information
• Eukaryotic Genome:
– Genes are separated by long stretches of
noncoding DNA sequences.
– Multiple genes in a single transcription unit
is extremely rare.
– Multiple chromosomes – Linear
– Chloroplasts and mitochondria – Circular
– Genes appearing on the same
chromosome are syntenic.

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©Bud Mishra, 2001
L2-18
Location of Some Genes on
Human Chromosome.
Genes chromosome
a-globin cluster 16
b-globin cluster 11
Immunoglobulin
k (light chain) 2
l (light chain) 22
Heavy Chain 14
Pseudogenes 9,32,15,18
Growth Hormone 17
Thymidine kinase 17
Genes chromosome
Insulin 11
Galactokinase 11
Viral oncogene
C-sis 22
C-mos 8
C-Ha-Ras-1 11
C-myb 6
Interferons
a & b luster 9
g 12

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©Bud Mishra, 2001
L2-19
Eukaryotic Genome
• Multiple copies of the same gene
– Solve “supply problem”
– There are several hundred robosomal RNA genes
I mammals
• Pseudogenes
– Nonfunctional copies of genes…(Deletions or
alterations in the DNA sequence)
– Number of pseudo genes for a particular gene
varies greatly…Different from one organism to
another.

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©Bud Mishra, 2001
L2-20
Genes in Eukaryotes
• A gene may appear exactly once
• It may be part of a family of repeated sequence .
Members of a family may be clustered or dispersed.
• Members of a gene family may be related and
functional (expressed at different times in
development, or in different cells) or may be pseudo
genes.
• Chromosomal Morphology:
– Nucleolar organizers (genes for ribosomal RNA)
– Telomeric and Centromeric regions (Tandemly repeated
sequences)

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©Bud Mishra, 2001
L2-21
The Rearrangement of DNA
Sequences
• Reshuffling of genes between homologous
chromosomes via reciprocal crossing-over
during both meiosis and mitosis.
• Gene synteny and linkages are usually
preserved.
• Most rearrangements are random.
• Some rearrangements are normal processes
altering gene expressions in an orderly and
programmed manner.

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©Bud Mishra, 2001
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Chromosomal Aberrations
• Breakage
• Translocation (Among non-homologous
chromosomes.)
• Formation of acentric and dicentric chromosomes.
• Gene Conversions
• Amplification an deletions
• Point mutations
• Jumping genes a Transposition of DNA segments
• Programmed rearrangements a E.g., antibody
responses.

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©Bud Mishra, 2001
L2-23
Repeat Structure
• Copy Number: 2 » 106
• Direct Repeats “head-to-tail”
– Tandem repeats or separated by other sequences
• Inverted Repeats “head-to-head”
– Stem-and-loop structure
– Hairpin structure
• Reverse Palindrome
• True Palindrome

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©Bud Mishra, 2001
L2-24
Repeat Structure
• Tandem Direct
Repeats
• Inverted Repeats
• Reverse Palindrome
• True Palindrome
5’-AAGAG AAGAG AAGAG-3’
5’-GTCCAGNL NCTGGAC-3’
CAGGTCNL NGACCTG
G C
A T
C G
C G
T A
G C
Stem-and-loop structure
Associated with inverted
repeats
5’-GAATTC-3’
CTTAAG
5’-GTCAATGA AGTAACTG-3’

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©Bud Mishra, 2001
L2-25
Repeats within the
Genome
• Gene Family
– Genes and its cognate pseudogenes
• Satellite: Repeats made of noncoding
units
– Minisatellites: Tandem repeats…Mostly in
centromeric regions
– Satellite repeat units vary in length freom 2
base pairs to several thousands.

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©Bud Mishra, 2001
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Interspersed Repeats
• SINES: Short Interspersed Repeats
– Each repeat unit is of length 100 – 500 bps
– Processed pseudogenes derived from
class III genes
– Example: Alu repeats…dimeric head-to-tail
repeats of 130 bp
• LINES: Long Interspersed Repeats
– Each unit is of length > 6 Kb.

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©Bud Mishra, 2001
L2-27
A Genome Grammar
• Consists of
– A stochastic grammar specifying target DNA
sequence together with
– A description of polymorphisms and
– A description of the sampling strategy for
experiments
• h specificationi ! h DNA-Seg i
h Poly-Seg i*
h Sample-Seg i+

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©Bud Mishra, 2001
L2-28
Stochastic Grammar
• h DNA-Seg i !
“.dna” h DNA-Spec i
• h Poly-Seg i !
“.poly” h Weight i+ h Poly-Spec i
• h Sample-Seg i !
“.sample” h Sample-spec i

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©Bud Mishra, 2001
L2-29
DNA Sequence
• .dna
A = 150 Ã sequence of length 150—
Pr(A) = Pr(T) = Pr(C) = Pr(G) = ¼
B = A A m(.30) Ã A followed by a mutated
copy of A---Pr(Mutation) = .30
C » 3-7 p(.2, .3, .3) Ã A string of length 3 to 7,
Pr(A) =.2, Pr(T) = .3, Pr(C)=.3, Pr(G) = .2
---C = Constant String
D = C m(0.03) n(10,30) Ã m = mutation rate,
n = copy number
• S = 30,000,000
B m(.05, .10) p(.1,.1,.01) n(10)
D !(500)

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©Bud Mishra, 2001
L2-30
Polymorphisms
• Modify the ancestral sequence by a series of
– S Point mutation (SNPs)
– D Deletions
– X Translocations
• .poly .8 .8
S 0.00012T
D 1-1 .00012
D 2-2 .00006
D 3-3 .00002
D 500-1000 .00005
X 1000-2000 .0005
.poly .4
S .001
D 1-2 .0005
Two haplotypes of .8 each and
one haplotype of weight .4

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©Bud Mishra, 2001
L2-31
Sampling
• .sample
48,000 Ã Number of Samples
400 600 .5 Ã Read Lengths
.01 .02 Ã Sequence Read Errors
.33 .33 Ã Failure of Read
.3 1800 2200 .005 Ã Clone size
• .sample
12,000
400 600 .5
.01 .03
.33 .33
.4 9000 11000 .015

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©Bud Mishra, 2001
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Experiment
• First sample generate 48,000 end reads from
inserts of average length 2 Kbp.
– Sample proportions: 40% from haplotype H1, 40%
from H2 and 20% from H3
• Second sample generates 12,000 end reads
from inserts of average length 10 Kbp.
– Sample proportions: 40% from haplotype H1, 40%
from H2 and 20% from H3