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Limitations of genome projects
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107 3.109
What do proteins do for a living?
(A) Identifying genes from the sequence
(B) Gene expression profiling
(C) Genome activity studies
Genomes2 by TA Brown; chapter 7
Post-genomics
(A) Hunting genes from the sequence
2 broad approaches
1) Ab initio method (computational)
2) Experimental method
Ab initio method (computational) Scanning ORFs (open reading frames) –
initiation or termination codons Codon bias found in specific species Exon-intron boundaries Upstream control sequences – e.g
conserved motifs in transcription factor binding regions
CpG islands
Homology searches
Ab initio method (computational)…..
Software for automated annotation of genes like GENSCAN, Genie, GENEBUILDER etc are being used. These scan for special features like
1) Scanning ORFs (open reading frames) – initiation or termination codons
5’- ATGACGCATGATCGAGGAT –3’
3’ – TACTGCGTACTAGCTCCTA –5’
AACTAA
ATG
CCTCTA
TCC
Ab initio method (computational)… Codon bias found in specific species
Not all codons used at same frequency e.g.human leucine mainly coded by CTG and rarely by TTA or CTA
Exon-intron boundaries (splice sites)5’-AG GTAAGT-3’ hit and miss affair
Upstream control sequences – e.g conserved motifs in transcription factor
binding regions CpG islands
experimental method
Experimental evaluation based on the use of transcribed RNA to locate exons and entire genes from DNA fragment.
experimental method 2 main strategies Hybridisation approaches – Northern
Blots, cDNA capture / cDNA select, Zoo blots
Transcript mapping: RT-PCR, exon trapping etc In this method, known DNA databases are searched to find out whether the test sequence is similar to any other known genes, suggesting an evolutionary relationship.
Northern Blot Zoo Blot
Fig 7.4: Genomes 2 Fig 7.5: Genomes 2
RT-PCR Exon trapping
Fig 7.: Genomes 2 Fig 7.8: Genomes 2
(B) Gene expression profiling
• COMPUTATIONAL APPROACH
Homology searches for either
- Orthologous genes (homologues in
different organisms with common
ancestor)
- Paralogous genes (genes in the same
organism, e.g. multigene families)
(B) Gene expression profiling…..
• EXPERIMENTAL APPROACH
gene inactivation methods (knockouts,
RNAi, site-directed mutagenesis,
transposon tagging, genetic
footprinting etc)
Gene overexpression methods (knock-
ins, transgenics, reporter genes etc)
(C) Genome activity studies
Gene expression needs to be complemented by
Transcriptome analysis
Proteome analysis
The transcriptome
mRNA
Pre-r RNA Pre-t RNA sn RNA
sno RNA
sc RNA
t RNA tm RNA etc
hn RNA
Non-coding RNA(96%)
coding RNA(4%)
Total RNA
r RNA
All organisms eukaryotes bacteria
The transcriptome
complete collection of transcribed elements of the genome
transcriptome maps will provide clues on
Regions of transcription • Transcription factor binding sites • Sites of chromatin modification • Sites of DNA methylation • Chromosomal origins of replication
The transcriptome
Analysis can be done by either
SAGE (serial analysis of gene expression) technology
Microarray technology
SAGEShortcut to doing cDNA library screeningSAGE tags identify • mRNAs derived from known genes • anonymous mRNAs, also known as expressed
sequence tags (ESTs) • mRNAs derived from currently unidentified genes
Advantages• Analyzes all transcripts (Transcriptome) without prior
selection of known genes • Provides quantitative data on both known and
unknown genes • Ideally suited for determining changes on gene
expression as consequence of an experimental treatment (e.g. carcinogen, hormone)
SAGE
Microarrays – allows comparisons
Microarrays….
Proteomics
Proteomics
Nature (2003) March 13: Insight articles from pg 194
Proteomics
Proteome projects - co-ordinated by the HUPO (Human Protein Organisation)
Involve protein biochemistry on a high-throughput scale
Problems limited and variable sample material, sample degradation, abundance, post-translational modifications, huge tissue, developmental and temporal
specificity as well as disease and drug influences.
Nature (2003) March 13: Insight articles from pgs 191-197.
Approaches in proteomics
Nature (2003) March 13: Insight articles from pgs 191-197.
High throughput approach
1)Mass- spectrometry
based
2)Array based
3)Structural
proteomics
4)Informatics
5)Clinical proteomics
High throughput approaches in proteomics
1) Mass spectrometry-based proteomics: relies on the discovery of protein ionisation techniques.
used for protein identification and
quantification, profiling, protein interactions and modifications.
Nature (2003) March 13: Insight articles from pgs 191-197
Mass spectrometry (MS)
Nature (2003) March 13: Insight articles from pgs 191-197
Principle of MS
Nature (2003) March 13: Insight articles from pgs 191-197.
oion source, omass analyser that measures mass-to-charge ratio (m/z)odetector that registers the number of ions at each m/z value
Electrospray ionisation (ESI)matrix-assisted laser desortion/ionisation (MALDI)
MALDI-MS - simple peptide mixtures whereas
ESI-MS - for complex samples.
Principle of MALDI-TOF
Fig 7.24 Genomes 2 by TA Brown pg 210
Matrix assisted laser desorption/ionisation – time of flight
2) Array-based proteomics
Nature (2003) March 13: Insight articles from pgs 191-197.
Based on the cloning and amplification of identified ORFs into homologous (ideally used for bacterial and yeast proteins) or sometimes heterologous systems (insect cells which result in post-translational
modifications similar to mammalian cells). A fusion tag (short peptide or protein
domain that is linked to each protein member e.g. GST) is incorporated into the plasmid construct.
Array based proteomics….
Nature (2003) March 13: Insight articles from pgs 191-197.
a. Protein expression and purification b. Protein activity: Analysis can be done using
biochemical genomics or functional protein microarrays. c. Protein interaction analysis two-hybrid analysis (yeast 2-hybrid), FRET (Fluorescence resonance energy transfer), phage display etc d. Protein localisation: immunolocalisation of epitope-tagged products. E.g the use of GFP or luciferase tags
3) Structural proteomics !
Nature (2003) March 13: Insight articles from pgs 191-197.
a. Protein expression and purification b. Protein activity: Analysis can be done using
biochemical genomics or functional protein microarrays. c. Protein interaction analysis two-hybrid analysis (yeast 2-hybrid), FRET (Fluorescence resonance energy transfer), phage display etc d. Protein localisation: immunolocalisation of epitope-tagged products. E.g the use of GFP or luciferase tags
PROTEIN INTERACTION MAPS FOR MODEL ORGANISMS
Nature Reviews Molecular Cell Biology 2; 55-63 (2001); doi:10.1038/35048107
Challenges for the future – ‘physiome’
Nature Reviews Molecular Cell Biology 4; 237-243 (2003)
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