Download Functional Genomics

Chapter 1. Genomics: Toward A Genome-Level Understanding of the
Structure, Functions, and Evolution of Biological Systems
CBBL
- Young-sik Sohn-
Introduction

Understanding the physiology and behavior of an organism
Determination of an entire genome sequence
↓
Elucidate the functions of these sequences
↓
Providing meaning to the nucleotide sequence data
Bioinformatics/Functional Genomics
Definitions and Classification

Genomics
 described a new scientific discipline concerned with
mapping, sequencing, and analyzing genomes
 genome-level understanding of the molecular basis of the
structure and functions
 using whole-genome sequence information and highthroughput genomic technologies
Concept and classification of genomics
Challenges of Studying Functional Genomics

Defining gene function
 Substantial portions of ORFs are functionally unknown
 Relationships of genes to enzymes are not only one to one

Identifying and characterizing the molecular machines of life
 Many protein machines appear to be highly conserved

Delineating gene regulatory networks
 Coordinated behavior of genetic regulatory networks
determines the physiological properties of a living cell
Challenges of Studying Functional Genomics

System-level understanding of biological systems
beyond individual cells
 Relationship between biodiversity and functional properties
of ecosystems is important

Computational challenges
 Using computer model to know biological cellular functions

Multidisciplinary collaborations
 Collaborations among investigators with different research
capabilities are needed to meet these challenges
Scope and General Approaches

Structural genomics
function of a protein ≈ three-dimensional structure
∴ understanding folded structure
↓
biochemical functions or role in a pathway
Scope and General Approaches

Transcriptomics
 Comprehensive analysis of transciptomes is of great value
for studying gene function and regulation
① correlation of gene expression and function
② connection between gene expression and physiological
states
③ gene expressed together may function together
④ importance of transcriptonal regulation
⑤ technological advances
Scope and General Approaches

Proteomics
 It can be classified into three main categories
① protein identification and analysis
② proteome-wide differential display of proteins under
various growth conditions
③ protein-protein interactions
Scope and General Approaches

Metabolomics
 Two major approaches to understand gene functionality via
metabolic analysis
① identify the biochemical reactions catalyzed by enzymes
encoded by genes of unknown function
② functional analysis by
coresponses
Importance of Microbial Functional Genomics
to the Study of Eukaryotes

Functional analysis of microbial genomes
Crucial to understanding gene functions and regulatory
networks in microorganisms themselves
↓
Defining networks in higher organisms
∵ ① many genes involved in essential life processes are
conserved among microorganisms
② Mitochondria and chloroplasts are important
components of eukaryotic life processes
③ Many microorganisms have formed intimate
relationships with higher eukaryotes
Summary

The goal is to use genome sequence information and
related genomic technologies to link sequences with
functions and phenotypes and to understand how
biological systems at different levels function in nature

Microbial genome is not only important to understanding
microorganisms themselves but also very important to
higher organisms
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