Scribd
Upload
12 views20 pages

1.1 - Introduction To Omics

Uploaded by

sana javaid
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPT, PDF, TXT or read online on Scribd
12 views20 pages

1.1 - Introduction To Omics

Uploaded by

sana javaid
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPT, PDF, TXT or read online on Scribd
You are on page 1/ 20

Using ‘Omic Technologies

to Investigate Gene
Function
Genomics, ‘Omics & Technology
• Molecular biology: major scientific discipline for
past ~50 years
• Genomics = “analysis of genomes”: became
important science during 1990’s
• Analyses of various other biological molecules have
developed into their own scientific disciplines; e.g.
Metabolomics = “analysis of metabolites”, etc.
• Transcriptomics/Proteomics: developed during past
10-15 years
• Bioinformatics: has developed as major branch of
science - enables efficient analysis of data from
“omics” experiments
Genomics & Technology
• Significance of “omics” coincides with dramatic
improvements in different technologies:
molecular biology: increased range of
approaches for purification and manipulation of
proteins and nucleic acids
computers: required for gathering and analysis
of data
internet: allows data to be shared, quickly and
easily
• All developments have increased speed and cost-
effectiveness - available to much wider audience
Transcriptomes
• Genome: all of hereditary information encoded in
the DNA (or RNA)
• Transcriptome: set of all mRNAs ("transcripts”)
produced from a genome
• Term can be applied to:
complete set of transcripts for a given organism
specific subset of transcripts present in a
particular cell type or under specific growth
conditions
• Transcriptome varies because it reflects genes that
are actively expressed at any given time
DNA Microarrays Show
Differences in Gene Expression
• Microarray chips contain fragments from genes in
the group to be analyzed
– Full genome of bacteria or yeast, or protein
families from larger genomes
• mRNA or cDNA from different samples are
differentially tagged
• Analysis on the same chip shows differences
Transcriptomics
• Transcriptomics uses high-
throughput techniques based
on DNA microarrays
• For further details about
microarrays see Lucchini et
al., Microbiology, 147, 1403-
1414 (2001)

Nelson & Cox, “Lehninger, Principles of


Biochemistry”, 4th edn, 2004, p. 328
Transcriptomics

Nelson & Cox, “Lehninger, Principles of


Biochemistry”, 4th edn, 2004, p. 328
Transcriptomics

Nelson & Cox, “Lehninger, Principles of


Biochemistry”, 4th edn, 2004, p. 328
Transcriptomics

Nelson & Cox, “Lehninger, Principles of


Biochemistry”, 4th edn, 2004, p. 328
Transcriptomics

Nelson & Cox, “Lehninger, Principles of


Biochemistry”, 4th edn, 2004, p. 328
Transcriptomics

Nelson & Cox, “Lehninger, Principles of


Biochemistry”, 4th edn, 2004, p. 328
Transcriptomics
•Experiments performed
under different
conditions
•Determines effect of
conditions on
expression
•Produces huge amount
of data
•Lots of repeats required
- expensive
Nelson & Cox, “Lehninger, Principles of
Biochemistry”, 4th edn, 2004, p. 328
Polymerase Chain Reaction (PCR)
• Used to amplify DNA in the test tube
– Can amplify regions of interest (genes) within DNA
– Can amplify complete circular plasmids
• Mix together
– Target DNA
– Primers (oligonucleotides complementary to target)
– Nucleotides: dATP, dCTP, dGTP, dTTP
– Thermostable DNA polymerase
• Place the mixture into thermocycler
– Melt DNA at ~95°C
– Cool to ~ 50–60°C, primers anneal to target
– Polymerase extends primers in 5’3’ direction
– After a round of elongation is done, repeat steps
General Steps of PCR
General Steps of PCR
•Repeat steps 1–3 many times:
DNA Microarrays: Applications

DNA microarrays allow simultaneous screening of


many thousands of genes: high-throughput screening
•Genome-wide genotyping
– Which genes are present in this individual?
•Tissue-specific gene expression
– Which genes are used to make proteins?
•Mutational analysis
– Which genes have been mutated?
Adaptations to PCR
• Reverse Transcriptase PCR (RT-PCR)
– Used to amplify RNA sequences
– First step uses reverse transcriptase to convert
RNA to DNA
• Quantitative PCR (Q-PCR)
– Used to show quantitative differences in gene
levels
qPCR
Proteomes
• Proteome: set of all proteins produced under a given
set of conditions
• Term can be applied to:
complete set of proteins for a given organism
specific subset of proteins present in a particular
cell type or under specific growth conditions
• Proteome varies because it reflects genes that are
actively expressed at any given time
• Proteomics analyses many samples using 2D-
electrophoresis and mass spectrometry
• High-throughput, but less than transcriptomics
Gel Electrophoresis
• Electrophoresis separates molecules by size
• Resolution is limited

Berg, Tymoczko & Stryer, “Biochemistry”,


6th edn, 2006, p. 71

You might also like