융합구조게놈학

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자연과학 >생물ㆍ화학ㆍ환경 >생물학
강의학기

2012년 2학기

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Omics approach has profoundly affected all aspects of Life Sciences including genetics, medical genetics, genomics, and proteomics. This course will cover three areas of the Life Sciences that gained whole new perspectives by the approach and raises new questions to current dogmas: Omics of whole genomes, whole proteomes, and structural proteomics.

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Introduction

차시별 강의

1.	Introduction	What we need to learn How to learn Topics
1.	Introduction	What we need to learn How to learn Topics
2.	Universe Earth Life on Earth	I. A brief “history” of Universe--Contnued II. A brief “history” of the solar system
2.	Universe Earth Life on Earth	III. A brief “history” of the earth IV. A brief “history” of life on earth
3.	Whole Genomes	1. Genes and Genomes 2. Interrupted Genes: Gene structure of Eukaryotes
3.	Whole Genomes	3. Diversity of genes Some DNA Sequences Code for More Than One Protein 4. Genome Content 4.1. Genic and non-genic regions 4.2. Synteny 4.3. Genome of Organelles
4.	Human Genome; A New Landscape	Before ENCODE--Summary, continued Scale of ENCODE Project After ENCODE--Summary ENCODE abbreviations
4.	Human Genome; A New Landscape	Functional genomic elements Experimental tools Networks of looping interactions. General features of the DHS landscape. Chromatin accessibility and DNA methylation patterns. Genetic variation in regulatory DNA linked to mutation rate.
5.	Human Whole Genome	Human Evolution (past, present, future) Variations of Human Genomes (as of ~2008) We need to know Genome variations among Major Variations
5.	Human Whole Genome	Human Genetic Variations Known mechanisms that cause the variations by DNA restructuring Genomics provides a platform for investigation of biological phenomena in a comprehensive, unbiased, hypothesis-free manner.
6.	Human Genome Features	Genome Anatomy and Physiology 1. Protein-coding genes 2. Conserved non-coding elements (CNEs) 3. CNEs and species evolution 4. Transposones as drivers of evolutionary innovation 5. Small non-coding RNAs (ncRNAs) 6. Ubiquitous transcription 7. Large intergenic non-coding RNAs (lincRNAs) 8. Epigenomic map 9. Three-dimensional structure of the genome
6.	Human Genome Features	Genomic Variations 1. Linkage disequilibrium, HapMap and SNPs. 2. Copy number polymorphisms (CNPs) 3. Mapping structural variations of whole genome 4. Mapping structural variations on a chromosome
6.	Human Genome Features	Medicine 1. Mendelian and chromosomal disorder 2. Common Diseases and Traits 3. Cancer Clinical Genomics Human Diversity and History 5. SNP, haplotype, CNV variations across populations 5-1. SNP, haplotype, CNV variations across populations
7.	The Cancer Genome-1: Cancer Landscape	Cancer as an evolutionary process Mutations in a cancer genome Acquisition of somatic mutations in cancer genomes Driver and passenger mutations Landscape of cancer genome Cancer genome sequencing in future
7.	The Cancer Genome-1: Cancer Landscape	Cancer as an evolutionary process Mutations in a cancer genome Acquisition of somatic mutations in cancer genomes Driver and passenger mutations Landscape of cancer genome Cancer genome sequencing in future
8.	The Cancer Genome-2: Cancer Evolution	Dynamic Evolution of Cancer Genome - Interplay of somatic mutation, adaptation of clones to their - environment and natural selection - High heterogeneity of cancer genomes - Forces that act on nascent cancer clones as they evolve - Mutational processes that generate genetic variation
8.	The Cancer Genome-2: Cancer Evolution	- The heterogeneous cancer genome _ Heterogeneity of The mutatinal landscape - Heterogeneity within an individual cancer - Cellular ground state and cancer evolution - The role of genomic crises in tumorigenesis - The role of mutation rate in cancer evolution
9.	Father’s age and disease risk of his children	Mutations generate sequence diversity and provide a substrate for selection. The rate of de novo mutations is therefore of major importance to evolution. Genome-wide mutation rates by sequencing the entire genomes of 78 Icelandic parent–offspring trios at high coverage. With an average father’s age of 29.7, the average de novo mutation rate is 12 x 10-9 per nucleotide per generation.
9.	Father’s age and disease risk of his children	Most notably, the diversity in mutation rate of single nucleotide polymorphisms is dominated by the age of the father at conception of the child. The effect is an increase of about two mutations per year. An exponential model estimates paternal mutations doubling every 16.5 years. These observations shed light on the importance of the father’s age on the risk of diseases such as schizophrenia and autism.
10.	Creation of a New Life Form	“Creation of a bacterial cell controlled by a chemically synthesized genome” DG Gibson et al., July 2, 2010, Science, Vol. 329, 52-56 1995; Mycoplama genitalium genome sequenced, one of the smallest genomes. Rapid decrease in the cost of chemical synthesis of short DNA fragments. Basic science of joining DNA fragments into a larger piece by in vitro enzymatic methods and in vivo recombination methods in yeast.
10.	Creation of a New Life Form	“Creation of a bacterial cell controlled by a chemically synthesized genome” DG Gibson et al., July 2, 2010, Science, Vol. 329, 52-56 1995; Mycoplama genitalium genome sequenced, one of the smallest genomes. Rapid decrease in the cost of chemical synthesis of short DNA fragments. Basic science of joining DNA fragments into a larger piece by in vitro enzymatic methods and in vivo recombination methods in yeast.
11.	Process of Discovery: DNA Structure	“Obsession,” Vision Audacity of young minds Fallacy of some “common wisdoms” or “textbook facts” First few “great ideas” are often wrong Checking with “experts” with cautions “Out-of-box” thinking “Crystallizing” or “gelling” of many important facts by the new discovery Big discovery  Happiness (“Aha”)
11.	Process of Discovery: DNA Structure	“Obsession,” Vision Audacity of young minds Fallacy of some “common wisdoms” or “textbook facts” First few “great ideas” are often wrong Checking with “experts” with cautions “Out-of-box” thinking “Crystallizing” or “gelling” of many important facts by the new discovery Big discovery  Happiness (“Aha”)