What is genomics?

Study of genomes

What is the genome?

Entire genetic compliment of an organism

How many types of genomes are there in this world?

Prokaryotic genomesEukaryotic Genomes

Nuclear GenomesMitochondrial genomesCholoroplast genomes

• https://www.ted.com/talks/richard_resnick_welcome_to_the_genomic_revolution

What can genome sequence tell us?

• Everything about the organism's life• Its developmental program• Disease resistance or susceptibility• History• Where you are going?

How will we change in this century because of the Genomics?

• Biotechnology: more products• GMOs: More food-More problems?, food safety• Individualized medicine• Gene therapy• Immortality? Disease free life?• crop improvement • improve and develop agricultural practices• harness natural energy,• clean up our environment

LOOKING AT A GENOME

• key question is how many genes it contains• four levels 1. Genome2. Transcriptome - set of all RNA molecules3. Proteome - entire set of proteins expressed by a

genome4. Proteins

SOME QUICK FACTS ABOUT GENOMES

• Individual genomes show extensive variation.• Not all genes are essential.

In yeast and fly, deletions of <50% of the genes have detectable effects.

QUICK FACTS cont…

• A substantial part of most eukaryotic nuclear genomes is made up of Repetitive DNA.

– Repetitive DNA: individual sequence elements that are repeated many times over, either in tandem arrays or interspersed throughout the genome.

– Single copy DNA: which includes most genes, and is made up of sequences that are not repeated elsewhere.

Genes and Proteins & the role of Introns

• Introns: non-coding sections of precursor mRNA (pre-mRNA)

• Exons: coding sections that remain in the mRNA sequence

INTRONS AND EXONS

INTRONS AND EXONS

• Introns produce a major selection advantage and consequently are characteristic of higher, more developed organisms

• The relationship of introns to cancer and their use as tumor markers is also being explored.

• Are genes uniformly distributed in chromosomes?

– Some chromosomes are relatively poor in genes, and have >25% of their sequences as “deserts” – regions longer than 500 kb where there are no genes.

How is human genome organized?

• About 3% coding and rest of it junk (repetitive DNA).

• Nuclear and mitochondrial• You are 99.99% similar to your neighbor

Why human genome?

• We want to know about ourselves• How do we develop?• How do we struggle, survive and die?• Where are we going and where we came

from?• How similar are we to apes, trees, and yeast?

HUMAN GENOME PROJECT

• a 13 year effort, which is coordinated by the

–Department of Energy (DOE) and–National Institutes of Health (NIH).

HUMAN GENOME PROJECTGoals

• Identify the approximate genes in human DNA.• Determine the sequences of 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.• Address the ethical, legal and social issues (ELSI),

that may arise from the project.

• http://www.hhmi.org/biointeractive/sanger-method-dna-sequencing

• http://www.hhmi.org/biointeractive/shotgun-sequencing

A CLOSER LOOK AT THE HUMAN GENOME

• The human genome contains 3164.7 million nucleotide bases ( approx. 3 billion A,C,T and G).

• The average gene is made up of 3000 bases, but sizes of genes vary greatly.

• The total number of genes is estimated at around 30000.

• Almost all (99.9%) nucleotide bases are exactly the same in all the people.

A CLOSER LOOK AT THE HUMAN GENOME

• Less than 2 % of the genome codes for protein.

A CLOSER LOOK AT THE HUMAN GENOME

• Repeated sequences that do not code for proteins (“junk DNA”) make up at least 50% of the genome.

• Repetitive sequences fall into five classes:1. Transposons2. Processed pseudogenes3. Simple sequence repeats4. Segmental duplications5. Tandem repeats form blocks of one type of sequence

A CLOSER LOOK AT THE HUMAN GENOME

A CLOSER LOOK AT THE HUMAN GENOME

• The sequence of human genome emphasizes the importance of transposons.

• Most of the transposons in the human genome are nonfunctional; very few are currently active.

• They have played an active role in shaping the genome.

A CLOSER LOOK AT THE HUMAN GENOME

• Some present genes originated as transposons, and evolved into their present condition after losing the ability to transpose.

• Almost 50 genes appear to have originated like this.

A CLOSER LOOK AT THE HUMAN GENOME

• The human genome’s gene-dense “urban centres” are predominantly composed of C and G bases.

• The gene-poor “deserts” are rich in A and T bases.

• Genes appear to be concentrated in random areas along the genome, with vast expanses of non-coding DNA in between.

A CLOSER LOOK AT THE HUMAN GENOME

• Stretches of up to 30000 G and C bases repeating over and over occur adjacent to gene-rich areas, forming a barrier between the genes and the “junk” DNA.

SEQUENCING THE GENOMES OF OTHER ORGANISMS

• The sequence of many organisms have been carried out and is still being carried out at a rapid pace.

• There are many medical, genetic and commercial reasons for sequencing the genomes of various organisms.

• As of September 2007 the complete sequence was known of,

– 1879 viruses,– 577 bacterial species, and– roughly 23 eukaryotic species (of which about

half are fungi).

– Wooly Mammoth(?)

GENERAL GENOMIC COMPARISONSOrganism Genome Size

(Bases)Estimated Genes

Human (Homo sapiens) 3 billion 30,000

Laboratory mouse (M. musculus)

2.6 billion 30,000

Thale cress (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

GENOMES AND EVOLUTION

• Comparisons of different genomes show a steady increase in gene number as additional genes are added to make eukaryotes, make multicellular organisms, make animals, and make vertebrates.

• Most of the genes that are unique to vertebrates are concerned with the immune or nervous system.