Download Looking within human genome

Looking Within Human
Genome
King abdulaziz university
Dr. Nisreen R Tashkandy
GENOMICS ; THE PIG PICTURE
GENOMICS
• Is concerned with sequencing genomes of all
different types of organisms
Shotgun sequences
• A type of rapid DNA sequencing
• Make it possible to sequence the entire
genomes in a reasonable amount of time
How ?
• Genomic DNA is cut into large fragments about
150,000,000 base pairs (150MB) long.
• Insert large fragments into a vector called a
bacterial artificial chromosome
• Clone it into bacteria to replicate
• Mapping for large fragments to determine their
relative order to each other
• Each large fragment is broken up into smaller
fragments then sequence
• Computer lines up the overlapping sequencies
Human genome
• The average gene size is about 3.000 base pairs
• The number of genes on each chromosome varies
from 2,968 genes on chromosome 1 to just 231
genes on the Y chromosome.
• At least 50% of the human genome consists of
small repeating sequences that do not code for
sequencing.
• Genes are randomly clustered together on
chromosomes and separated from other clusters of
genes by noncoding DNA in between
• The areas of DNA that contains genes contain
lots of G-C base pairs, whereas the regions of
noncoding DNA contain lots of A-T base pairs.
• Less than 2% of the genome contains the code
for proteins and RNA molecules.
• The other 98% of the genome consists of various
types of DNA and DNA whose function isnt yet
known.
• The known functions of noncoding DNA
include:
• Regulatory sequences that control how DNA is
used like promoters and origins of replication.
• Sequences that are involved in the structuring of
DNA within the cell such as those that determine
nucleosome positioning
• Small repeated sequences, Junk DNA, not know
function
Comparative genomics
• The greater the similarities between two
genomes the closer the relationship between the
species.
• Database of genomic data are searched for
sequences for known genes to see whether the
known sequence is found in the genome of
another organism
• Comparison of closely related species such as
Chimpanzess and human
Which sequences show the effects of
natural selections?
• Matching up the DNA sequences of related
organisms like human and mice
• Then comparing the rates of mutation in different
areas of the genome
• Secientist then can identify areas of DNA that
have undergone natural selection.
Remember
• All life on earth is very similar.
• Your DNA sequence shows that close relationship
between you and your earthly neighbours.
• 99% between humans
• 96% identical to Chimpanzees
• 40% to mice
Main observations in genome size
differences
• Certain plants have acquired multiple sets of
chromosomes during their evolution
• Organisms that have many sets of chromosomes
are Polyploid.
• Polyploid organisms can have very large genomes.
• Human have lots of repetitive sequences in their
genomes which range from150 to 300 base pair
called Alu
• Alu occurs more than 1.1 million times in human
Functional Genomics
• The functions of DNA sequences.
• Relationship between genes and interactions
between gene products. (RNAs & proteins)
How much variation within a genome
• SNPs single nucleotide Polymorphisms we use
it to compare or detriment how much variation
exists within a genome of a species.
When and where does gene expression
occur?
• By comparing cells of different species or at
different developmental stages to each other in
order to determine patterns of gene expression
between species and during development.
How do genes and the products of
different genes interact with each
other?
• Relationships between genes are suggested when
the same genes occur in a number of related
species
• Or when genes occur together in the same part of
the genome.
• So gene products are proposed when they are
produced at the same time in the cell.
Open reading frames
• Genes are encoded within open reading frames
• Sections of DNA that begin with code for a start
codon and end with the code for a stop codon.
• Prokaryotic genes: very easy to locate. Because
the sequence of promoters are well known and
no introns
Eukaryotic open reading frame
• Are harder to identify
• Less than 2% of the human genome is actually
made of genes. Contain Introns
• That’s make it very difficult like looking or
hunting for a needle in a haystack
Pharmacogenomics
• Combines traditional pharmacology and genomics
with the goal of TAILORING drug therapies more
precisely to suit particular disease or an individual
genome
Which genes and proteins are
associated with this disease
• Identify Genes and proteins that cause a
particular disease
• Develop very specific drugs that target those
genes and proteins
• Drugs that very specific will cause far fewer
side effect than some of the medicine in use
today that effect normal proteins as well as
disease causing protiens
What drug is the best treatment for a
person with a particular genotype?
• Adverse reactions to certain drugs.
• If adverse reactions are common in people
with a particular genotype.
• THEN its possible to use this genotype to
predict how they will react to a drug
• In another words: doctors can start the right
treatment from the beginning based on the
GENOTYPE
GENOTYOE SCREENING
• Some disease have a genetic basis
• While others diseases are more likely to affect
some people than others.
• SO IN SHORT:
• Allows identification of any genetic diseases that
a person inherited
• Prediction risk factors
• People can make lifestyle choices to minimize
their risk for disease.
References
• Molecular & Cell Biology for DUMMIES
• Rene Fester Kratz 2009