Lecture 3 Early Embryogenesis and Cell Fate How is blastopore formed? What organ will blastopores become? The results of gastrulation: three germ layers and archenteron and blastopore Tissues and organs from each germ layer Procedure of neurulation and the functions and origins of each part including notochord Epithelial cells and mesenchymal cells Fate mapping: how to make a fate map? Vital dye staining experiment Fluorescent dye experiment Genetic labeling experiment Lecture 4 Genomic Equivalence Germ plasm theory by August Weismann What is genomic equivalence? Evidence for genomic equivalence Rouxs experiment Cell transplant and cell removal experiment in frog embryo Drieschs experiment Hans Spemanns experiment Nuclear transfer technique and animal cloning Briggs and Kings frog cloning using blastula cell nucleus Gurdons Xenopus cloning using intestinal cell nucleus Ian Wilmuts sheep cloning using breast cell nucleus Jaenischs mouse cloning using lymphocyte nucleus The article, Nuclear Transfer Bringing in the clones Every somatic cell has the same DNA (genome), then, how do they differentiate into different types of cells? Lecture 5 Genes and Transcriptional Regulation What is the gene? What is the genome? Where are the genes written? (Which molecule has genes on it?) How do genes work? What is the function of genes? What is gene expression? What determines the identity and function of a protein? What determines the structure (shape) of a protein? What determines the amino acid sequence of a protein? Overview of gene expression mRNA transcription Protein translation What is proteome? Different types of cells have different proteome. How different types of cells have different set of proteins although they have the same genome? What are the housekeeping genes? Overview of gene expression regulation The structure of genes: Transcription initiation site, 5 UTR, exons, and introns, 3 UTR Regulatory elements on DNA: promoters and enhancers Transcriptional regulation The switch on DNA for transcription regulation: enhancers and promoter Promoter, TATA box, general transcription factors, and RNA polymerase II Enhancers and specific transcription factors The structure of transcription factors How do enhancers and specific transcription initiate transcription? Chromatin structure and transcription regulation Nucleosomes, histone octamer and chromatin structure Histone acetylation and histone methylation Histone structure modifying enzymes: histone methyltransferase, histone demethylase, histone acetyltransferase, and histone deacetylase Heterochromatin vs. euchromatin Steps of the initiation of transcription Enhancer modularity How can one gene be transcribed in multiple types of cells? One gene can have multiple enhancers How can multiple genes be transcribed in one type of cell? A cell has a variety of specific transcription factors that bind to different enhancers of different genes. Multiple genes can have the same enhancers for the same speci.

1. Lecture 3 Early Embryogenesis and Cell Fate
How is blastopore formed? What organ will blastopores become?
The results of gastrulation: three germ layers and archenteron and blastopore
Tissues and organs from each germ layer
Procedure of neurulation and the functions and origins of each part including notochord Epithelial
cells and mesenchymal cells
Fate mapping: how to make a fate map?
Vital dye staining experiment
Fluorescent dye experiment
Genetic labeling experiment
Lecture 4 Genomic Equivalence
Germ plasm theory by August Weismann
What is genomic equivalence?
Evidence for genomic equivalence
Rouxs experiment
Cell transplant and cell removal experiment in frog embryo
Drieschs experiment
Hans Spemanns experiment
Nuclear transfer technique and animal cloning
Briggs and Kings frog cloning using blastula cell nucleus
Gurdons Xenopus cloning using intestinal cell nucleus
Ian Wilmuts sheep cloning using breast cell nucleus
Jaenischs mouse cloning using lymphocyte nucleus
The article, Nuclear Transfer Bringing in the clones
Every somatic cell has the same DNA (genome), then, how do they differentiate into different
types of cells?
Lecture 5 Genes and Transcriptional Regulation
What is the gene?
What is the genome?
Where are the genes written? (Which molecule has genes on it?)
How do genes work? What is the function of genes?
What is gene expression?
What determines the identity and function of a protein?
What determines the structure (shape) of a protein?
What determines the amino acid sequence of a protein?
Overview of gene expression
mRNA transcription
Protein translation
What is proteome?
Different types of cells have different proteome.
How different types of cells have different set of proteins although they have the same genome?
What are the housekeeping genes?

2. Overview of gene expression regulation
The structure of genes: Transcription initiation site, 5 UTR, exons, and introns, 3 UTR
Regulatory elements on DNA: promoters and enhancers
Transcriptional regulation
The switch on DNA for transcription regulation: enhancers and promoter
Promoter, TATA box, general transcription factors, and RNA polymerase II
Enhancers and specific transcription factors
The structure of transcription factors
How do enhancers and specific transcription initiate transcription?
Chromatin structure and transcription regulation
Nucleosomes, histone octamer and chromatin structure
Histone acetylation and histone methylation
Histone structure modifying enzymes: histone methyltransferase, histone demethylase, histone
acetyltransferase, and histone deacetylase
Heterochromatin vs. euchromatin
Steps of the initiation of transcription
Enhancer modularity
How can one gene be transcribed in multiple types of cells?
One gene can have multiple enhancers
How can multiple genes be transcribed in one type of cell?
A cell has a variety of specific transcription factors that bind to different enhancers of different
genes.
Multiple genes can have the same enhancers for the same specific transcription factor.
Silencers: NRSE and NRSF
Lecture 6 - Epigenetics
1. DNA methylation regulates gene transcription.
What is DNA methylation? What is the function of DNA methylation?
Which part of DNA is methylated?
Study three examples how DNA methylation silences gene expression.
Methylation of promoter and the example of -globin and -globin expression
Methylation of enhancer
How MeCP2 works
2. How DNA methylation is inherited by the daughter DNA from the parental DNA? CpG
methylation
Dnmt3 & Dnmt1
3. X chromosome inactivation
Everything
4. Genomic imprinting
Everything
5. Further thinking
Why are cloned animals often sick and die early?
Why are identical twins not exactly identical when they grow older?

3. Lecture 7 Post-Transcriptional Regulations
1. Alternative splicing
What is splicing? How does splicing happen?
What is alternative splicing?
What are the consequences of alternative splicing?
Study everything that we discussed about DSCAM protein.
Study three examples of mis-regulation of splicing.
2. RNA stability and gene expression regulation
Two ways that can regulate the level of a certain molecule: synthesis and degradation.
Cells can regulate the stability of the mRNA of a certain gene. Increased stability means less
degradation.
What happens when the mRNAs of a gene are stabilized?
Higher stability less degradation prolonged life span the steady state level increase Study the
experiment about the effect of prolactin on casein mRNA stability thoroughly. 3. Control of gene
expression at translational level
What is the Futile cycle mutant? What is wrong in that mutant?
What is the phenotype of the Futile cycle mutant embryo?
How can the Futile cycle mutant embryo make blastula even in the absence of zygotic DNA?
What does it mean?
Study how the translation of maternal mRNAs in egg is blocked and resumed.
Study the regulation of Caudal translation by Bicoid in Drosophila oocytes.