Use full for UG and PG students for understanding the branches of genomics.

1. Functional Genomics, Pharmaco
Genomics & Metagenomics
Submitted BY;
Sangeeta V. Jadav
Reg.No.-2010117051
GPB

2. INTRODUCTION
• Genomics - It is the study of genomes.
• The field of genomics comprises of two main areas:
• 1.Structural genomics
• 2. Functional genomics
• Structural genomics - deals with genome
structures with a focus on the study of genome mapping and
assembly as well as genome annotation and comparison.
Functional genomics:
• Determining the role of genes through gene disruption
(knockouts, under expression and over expression)

4. Functional genomics
Branch of genomics that determines biological
functions of genes and their products.
Functional genomics (transcriptomics and
proteomics) is a global, systematic and
comprehensive approach for identification and
description of the processes and pathways
involved in the normal and abnormal state of
genes.

5. Goals of functional genomics
• It is estimated that approximately 30% of the
open reading frames in a fully sequenced
organism have unknown function at the
biochemical level and are unrelated to any
known gene. This is why recently the interest
of researchers has shifted from genome
mapping and sequencing to determination of
genome function by using the functional
genomics approach.

6. Example:
• A single gene can give rise to multiple gene
products. RNA can be alternatively spliced or
edited to form mature mRNA. Besides,
proteins are regulated by additional
mechanisms such as posttranslational
modifications, compartmentalization and
proteolysis. Finally, biological function is
determined by the complexity of these
processes.

7. Techniques of functional genomics:
• At the DNA level(Genetic interaction mapping, the
ENCODE project)
1) Genetic interaction mapping
 Systematic pair wise deletion of genes or inhibition of
gene expression can be used to identify genes with
related function, even if they do not interact physically.
2) The ENCODE project:
 The ENCODE (Encyclopaedia of DNA elements)
project is an in-depth analysis of the human genome
whose goal is to identify all the functional elements of
genomic DNA, in both coding and noncoding regions.

8. 1. Differential display
2. Expressed sequence tags
3. Serial analysis of gene expression
4. DNA microarrays
GENE EXPRESSION PROFILING AT
THE TRANSCRIPT LEVEL:

9. • Microarrays measure the amount of mRNA in a sample
that corresponds to a given gene or probe DNA sequence.
• Probe sequences are immobilized on a solid surface and
allowed to hybridize with fluorescently labelled “target”
mRNA.
• The intensity of fluorescence of a spot is proportional to
the amount of target sequence that has hybridized to that
spot, and therefore to the abundance of that mRNA
sequence in the sample.
• Microarrays allow for identification of candidate genes
involved in a given process based on variation between
transcript levels for different conditions and shared
expression patterns with genes of known function.
1) Microarray

11. • SAGE (serial analysis of gene expression) is an
alternate method of gene expression analysis
based on RNA sequencing rather than
hybridization.
• SAGE relies on the sequencing of 10–17 base
pair tags which are unique to each gene.
• These tags are produced from poly-A mRNA and
ligated end-to-end before sequencing.
• SAGE gives an unbiased measurement of the
number of transcripts per cell, since it does not
depend on prior knowledge of what transcripts to
study (as microarrays do).
2) SAGE

12. RNA sequencing has taken over microarray and SAGE
technology in recent years and has become the most
efficient way to study transcription and gene
expression. This is typically done by next-generation
sequencing.
A subset of sequenced RNAs are small RNAs, a class
of non-coding RNA molecules that are key regulators
of transcriptional and post-transcriptional gene
silencing, or RNA silencing. Next generation
sequencing is the gold standard tool for non-coding
RNA discovery, profiling and expression analysis.
• Proteome analysis (Protein microarray, 2D-PAGE)
3) RNA sequencing

13. • Gene function can be investigated by
systematically “knocking out” genes
one by one. This is done by
either deletion or disruption of function
(such as by insertional mutagenesis)
and the resulting organisms are
screened for phenotypes that provide
clues to the function of the disrupted
gene.
Loss-of-function techniques

14. RNAi
• RNA interference (RNAi) methods can be used to
transiently silence or knock down gene expression
using ~20 base-pair double-stranded RNA typically
delivered by transfection of synthetic ~20-mer short-
interfering RNA molecules (siRNAs) or by virally
encoded short-hairpin RNAs (shRNAs). RNAi screens,
typically performed in cell culture-based assays or
experimental organisms (such as C. elegans) can be
used to systematically disrupt nearly every gene in a
genome or subsets of genes (sub-genomes); possible
functions of disrupted genes can be assigned based on
observed phenotypes.

15. Application of functional genomics
• Sequencing of crop –plant genomes
• Genetic discovery for useful traits
• Genome wide regulatory networks to improve
trait.
• Evolutionary study
• Phylogenetic relationship
• Fine mapping
• Disease diagnosis
• Gene expression study

16. Importance of functional genomics in
crop improvement
• Knowing the exact sequence and location of all
the genes of a given organism is only the first step
towards understanding how all the parts of
biological system work together. In this respect
functional genomics is the key approach to
transforming quantity to quality in to crop
improvement.
• Functional genomics is a general approach toward
understanding how the genes of an organism work
together by assigning new functions to unknown
gene.

17. Case Study

19. Pharmacogenomics:
From DNA to Drug Treatment

20. “It is more important to know
what sort of person has a disease
than to know what sort of
disease a person has.”
-Hippocrates
(460 BC – 370 BC)

21. • Pharmacogenomics
– The science of how genes affect the way people people
respond to drugs
– How genes affect…
…the way our body processes drugs (pharmacokinetics)
…the interaction of drugs with receptors (pharmacodynamics)
…the treatment efficacy and adverse side effects
• Pharmacogenetics
– A subset of ‘pharmacogenomics’
– The study of how inherited variation affects drug response
and metabolism

22. Pharmacogenomic Studies
• Pharmacogenomic studies are rapidly elucidating the inherited nature of
these differences in drug disposition and effects, thereby enhancing drug
discovery and providing a stronger scientific basis for optimizing drug
therapy on the basis of each patient’s genetic constitution.
• It is well recognized that different patients respond in different ways to the
same medication.
• Genetics can account for 20 to 95 percent of variability in drug disposition
and effects.
• Numerous examples of cases in which inter individual differences in drug
response are due to sequence variants in genes encoding drug-metabolizing
enzymes, drug transporters, or drug targets
• Unlike other factors influencing drug response, inherited determinants
generally remain stable throughout a person’s lifetime.

23. Goals of Pharmacogenomics
• Personalized Medicine :There is an emerging
goal among ‘translational scientists’ to make
medical practice more personalized
• Pharmacogenetics is
an important step
towards that goal
• The effects of this
movement are seen in
many aspects of society

25. Why is this a good approach?
• Drugs can be dangerous
– Many people have severe adverse reactions to drugs
– Many people respond to drugs at different doses
– Many drug treatments are horribly unpleasant, painful
• Drugs are expensive (to take and to make)
– Ineffective drugs are a waste of money to take
– Drug development needs to account for response variability

27. WHAT IS METAGENOMICS??
• Metagenomics (also Environmental Genomics, Ecogenomics
or Community Genomics) is the genomic analysis of microbial
communities.
• The term is derived from statistical concept of “meta” analysis
(the process of statistically combining separate analysis) and
genomics (study of whole genome of an organism essentially in
the context of uncultured microbes).
• Metagenomics is the study of genetic material of organisms that
are difficult to culture in laboratory and are recovered directly
from environmental samples.
• Take a sample off of the environment  Isolate and amplify
DNA/mRNA  Sequence it.

28. WHAT IS METAGENOMICS??
• Microbes are present in every biological niche even humans body carry
ten times more bacterial cells and 100 times more bacterial genes than
its own cells and genes.
• 16S rRNA studies have confirmed that less than 1% of microorganisms
in nature can be cultivated by conventional techniques (Torsvik et al.
1990).
• The collective genomes of microbes indigenous to a certain habitat
especially of extreme climates such as hot geysers, salt lakes or high
altitudes are now often referred to as the metagenome (Handelsman, et
al. 1998).
• Metagenomics is employed as a means of systematically investigating,
classifying and manipulating the entire genetic material isolated from
a particular environmental sample.

29. The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert
M. Goodman, Sean F. Brady, and others, and first appeared in publication in 1998.

30. Why iS iT revolutionary?
Classical microbiology
1 colony 1 analysis 1 bacterial identification
20 colonies 20 analyses 20 bacterial identifications
Time consuming
Laborious
expensive
• If you want to identify one
colony, you need to isolate
and send this colony for
sequencing
• If you want to identify
more colonies, you have
to repeat operations for
each single colony

31. Why is it revolutionary?
Bacterial diversity profile
METAGENOMICS
Over 5.000 identifications
amongst the most
important populations
1 analysis
• If you want to identify
all the members of
community : You need
to send single sample
for sequencing

32. AIMS OF A METAGENOMICS
1. Examining phylogenetic diversity using 16S rRNA and
other phylogenetically informative genes-diversity patterns
of microorganisms can be used for monitoring and
predicting environmental conditions and changes.
2. Examining genes/operons for desirable enzyme
candidates (e.g., cellulases, chitinases, lipases, antibiotics
and other natural products). These may be exploited for
industrial or medical applications.
3. Examining variation or diversity within genes of key
enzymes. This may help in identifying or designing optimal
catalysts.
4. Examining secretory, regulatory and signal transduction
mechanisms associated with samples or genes of interest.

33. AIMS OF A METAGENOMICS
5. Examining transporter systems
6. Examining bacteriophage or plasmid sequences. These
potentially influence diversity and structure of microbial
communities.
7. Examining potential lateral gene transfer events.
8. Examining genes/operons for nutrient gathering, auto-
inducers (for community sensing), central intermediary
metabolism, etc. These may provide insights into syntrophic
interactions or reveal basis for the success of organisms in
their environment.

34. Metagenomic
Analysis
Sequence based
analysis
Function driven
analysis

35. Sequence-driven analysis
• The diversity of biological species in metagenome is measured usually
through sequence-driven analysis.
• Studies based on the extraction of total community DNA from
environmental samples followed by polymerase chain reaction (PCR),
cloning, ARDRA (amplified ribosomal DNA restriction analysis) is a
DNA fingerprinting technique based on restriction enzyme digestion and
agarose gel electrophoresis of PCR amplified 16s rRNA gene using
primers for conserved region.
• Recovery and analysis of 16S rRNA genes directly from environmental
DNA provide a means of investigating microbial populations in any
habitat, eliminating dependence on isolation of pure cultures.

36. Sequence-driven analysis

37. Function driven analysis
• Functional metagenomics involves screening metagenomic
libraries for a particular phenotype, e.g. salt tolerance,
antibiotic production or enzyme activity, and then identifying
the phylogenetic origin of the cloned DNA.
• In function driven approach, metagenomic libraries are
screened for expressed traits and once identified the clones
are characterized by biochemical and sequence analysis.
• Screening by heterologous gene expression is a powerful yet
challenging approach to metagenome analysis.

38. Functional analysis

39. FLOW-DIAGRAM OF A METAGENOME PROJECT
Binning is the process of
grouping reads or contigs
and assigning them to
operational taxonomic units.
Binning methods can be
based on either
compositional features or
alignment (similarity), or
both.

40. T H
Y
A N K
O U