functionalgenomics

BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Possible Protein Functions
• • • • Structural component Enzyme Hormone Regulator
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
S
A F E
P
G B
A C
D
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
From DNA Sequences to Functions
• • • • Expression profiles (transcriptome) Protein profiles (proteomics) Protein-protein interactions Computational analyses and modeling
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Current and Potential Applications
• • • • Molecular medicine Microbial genomics Risk assessment Bioarchaeology, anthropology, evolution, and human migration • DNA forensics (identification) • Agriculture, livestock breeding, and bioprocessing
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Impacts of Human Genome Project
• Led to two major technological breakthroughs: – high-throughput DNA sequencing, and – powerful computational tools for sequence analysis • Switch to data-intensive mode of research • Broad scope and scale • From one-gene-at-a-time (reductionist) approach to whole-genome approach • Can keep track of all the components at once i.e. profiling
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Re-Defining “Functions”
• Molecular function – the function of a protein is defined by its action on substrates to form products • Contextual (Cellular) function – the context of a protein interacting with other proteins
enzymatic reaction
Metabomics
Metabolite
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Gen Transcript Prote Metab Gen Prote
genes Sequence of a transcripts ~ ome = complete set of proteins metabolites genome proteome
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Functional Genomics, Gene Chips and Proteomics
Further Readings: Nature 405: 819-846 “Functional Genomics” by S.P. Hunt and F.J. Liversey, Ch. 2-7, 10 “Differential Display Methods and Protocols” by P. Liang and A.B. Pardee, Ch. 1-5 “The Yeast Two-Hybrid System” by P.L. Bartel and S. Fields, Ch. 2 and 7 Acknowledgements: Dr. KK Wong (Baylor College of Medicine) Dr. HC Leung (Singapore Genome Institute)
Different Approaches to Identify Functions
• Purify the gene product (or express the gene product in a heterologous system) and then perform biochemical studies (e.g. enzymatic activities; reaction kinetics; interactions of molecules) • Perform computational analysis of the gene product (e.g. searching for homologue (orthologues and paralogues) or conserved functional domains; prediction of 3-D structure based on physical parameters) • Study the physiological effects of the gene product or the compound formed by the action of the gene product (e.g. exogenous application of purified target compounds to cell cultures, tissues, or whole organism
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Genomics
DNA (Gene)
transcription
Transcriptomics
RNA
translation
Functional Genomics Proteomics
Protein
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
What have already been achieved?
• Completed sequences of more than 20 prokaryotic genomes (e.g. E. coli, Methanococcus jannaschii, Mycobacterium tuberculosis, etc.) • Yeast, worm, fruit fly • Human • Arabidopsis thaliana and rice
~ omics = Analysis of theБайду номын сангаас
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Structural versus Functional Genomics
• Structural genomics: – Construction of high resolution genetic, physical and transcript maps of an organism • Functional genomics: – Development and application of global experimental approaches to assess gene function by making use of the information and reagents provided by structural genomics
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
Expression Profiling (Transcriptome)
• mRNA makes protein • Determining gene expression pattern will help understanding the biological activities and roles of its encoded protein • Multi-gene patterns of expression give hint to common regulatory mechanisms • Genes with similar expression behavior are likely to be related functionally – “guilt-byassociation”
BIO4320 Lecture Materials, Prepared by Dr. Hon-Ming Lam
To Identify and Isolate Differentially Expressed Genes
• • • • • • • • Differential hybridization Differential display RAP (RNA Arbitrarity Primed)-PCR Subtraction library SSH (Suppression subtractive hybridization) RDA (Representational difference analysis) SAGE (Serial Analysis of Gene Expression) DNA microarray (membranes) and DNA chip (glass slides)