Description: The aim of the course is to provide an introduction to chromatin dynamics, particularly the structural and biochemical modifications of chromatin that underlie epigenetic states and their effects on gene expression and development. The importance of epigenetic states is perhaps the major discovery of molecular biology in the past ten years. They are critical to understanding the control of gene expression in development, the programming and reprogramming that takes place in the differentiation of pluripotent stem cells and they provide an accounting for many of the genomic malfunctions that result in human disease. An acquaintance with the concepts of what has come to be known as Epigenomics is essential for a Molecular Biology major.
Please go to the 694:413 site on Sakai to download the current lectures. Lecture notes will no longer be posted on this site.
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| # |
Day |
Date |
Topic |
Instructor |
| 1 |
Th |
9/6 |
Chromatin/Introduction: DNA packaging. Chromatin structure. Nucleosome structure. 10 nm fiber and higher order folding of nucleosome arrays, metaphase chromosomes and interphase; polytene chromosomes as a model. Euchromatin, heterochromatin and repetitive DNA. Chromatin modifications: positioning, remodeling, covalent modifications, histone variants, DNA methylation. Histone modifications. DNA replication and histone deposition |
VP |
| 2 |
M |
9/10 |
Transcriptional machinery and regulatory elements. Promoters, enhancers; promoter factors; enhancer factors; relationship to chromatin structure. PIC assembly, initiation, elongation, pausing, termination and polyadenylation. Transcription factories. |
DD |
| 3 |
Th |
9/13 |
Chromatin, Epigenetics, Epigenomics. The epigenetic code and its contribution to the 'readout' of the genome during development. Goals and purpose of modern epigenomics. The nucleosome as building block of chromatin. Chromosome architecture, chromatin, and epigenetics. Synteny, gene clustering, gene co-regulation. |
TK |
| 4 |
M |
9/17 |
Nucleosome structure. Posttranslational modifications of histones within the nucleosome. Histone modification and their role in transcription. Structural impact on the nucleosome. Signaling through modifications. Other modes of changing chromatin structure. Combinatorial chromatin remodeling. Generation and function of chromatin domains. |
TK |
| 5 |
Th |
9/20 |
Complexes modifying histones: Acetyltransferases, Kinases, Methyltransferases, Ubiquitinases, and others. Chromatin modifications in transcription, cross-histone effects. Transcription through the nucleosome. |
TK |
| 6 |
M |
9/24 |
Quiz 1
Histone variants. Variants of H3, H2A, and others. Their function in chromosome architecture, transcription, and genome integrity control. |
TK |
| 7 |
Th |
9/27 |
The histone code hypothesis. Epigenetic marks. Bromodomains. Chromodomains, Tudor, PHD, MBT and other chromatin-interacting domains. Recruitment of chromatin modifiers. Scaffolding and stabilization of chromatin structure. The nature of epigenetic memory. Methods for studying chromatin complexes. Biochemical purifications; Antibody-based purifications. Epitope tagging; In vitro Assays; Detection of of modifications. Mass spectroscopic methods. |
TK |
| 8 |
M |
10/1 |
Repressive chromatin marks Polycomb complexes. Heterochromatin complexes. Repressive methylation marks H3. Polycomb Response Elements and their properties. Homeotic genes, chromatin states, their maintenance and role during development |
VP |
| 9 |
Th |
10/4 |
Detection of proteins and histone modifications Chromatin immunoprecipitation. Detection of chromatin marks and proteins. Genome browsers. ChIP/chip, genomic tiling arrays. Computational methods, sliding windows, peak-finding, false discovery rates. Parallel sequencing methods. |
VP |
| 10 |
M |
10/8 |
Polycomb target genes Genomic programming. Pluripotent cells and differentiation. Mechanisms of repression. Pairing-dependent effects. Trans-interactions. Nuclear architecture. Chromosome domains. |
VP |
| 11 |
Th |
10/11 |
Quiz 2
ATP-dependent chromatin remodeling. Nucleosomes positioning. Sequence-dependence |
TK |
| |
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10/11 |
Take Home Exam Handed Out |
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| 12 |
M |
10/15 |
Small RNAs and chromatin Antisense and double stranded RNA. Dicer, Argonaute and RDRP. Post-transcriptional interference. Co-suppression. Transcriptional interference and recruitment of histone modifications, DNA methylation. RNAi-dependent gene silencing. Heterochromatic silencing models and mechanisms |
Guest Lecture
Dr. Hristo Houbaviy
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| 13 |
Th |
10/18 |
DNA methylation DNA methylating and methyl-DNA-binding factors. Maintenance versus de novo methylation. Semiconservative replication and maintenance of methylation. Layers of repressive modifications; Relationship to histone modification and to RNAi. |
TK |
| |
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10/22 |
Take Home Exam Due |
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| 14 |
M |
10/22 |
Chromatin insulators Enhancer-promoter interaction. Blocking elements. Scs, gypsy and directional blocking. Enhancer capture, topological hindrance, supercoil models. Double insulator effects. Insulator proteins. Loop domains, nuclear architecture and anchored loop models. |
VP |
| 15 |
Th |
10/25 |
Genetic imprinting Parent of origin-dependent expression. Parental conflict model. Beckwith-Wiedeman syndrome example. Prader-Willi/Angelman syndrome. DNA methylation marks and germ line erasure. Insulator-based mechanisms. 3C conformation capture methods and applications to imprinted genes. Imprinted non-coding RNAs. |
VP |
| 16 |
M |
10/29 |
Dosage compensation X chromosome dosage and three compensation strategies. XX down regulation and chromatin machinery. X hyperactivation and MSL chromatin machinery. X inactivation, chromosome counting, Xist and Tsix RNAs, Polycomb mechanisms, macroH2A, DNA methylation. |
VP |
| 17 |
Th |
11/1 |
Guest Lecture - |
Dr. Marc Gartenberg |
| 18 |
M |
11/5 |
Chromatin and Disease. Part I. Human genetic disorders caused by underlying defects in chromosome/chromatin structure; chromatin modifications; disorders of chromatin-mediated repression; defects in DNA methylation disorders; disorders of chromatin activation; disorders of chromosome abnormalities (deletions & duplications); chromatin-modifying enzyme defects. |
DD |
| 19 |
Th |
11/8 |
Chromatin Diseases. Part II. Epigenetic determinants of cancer. DNA methylation and chromatin alterations in human tumors; chromatin remodeling/modifying enzymes as targets for anti-cancer therapy. |
DD |
| 20 |
M |
11/12 |
Genomic methods I. Determining changes in gene dosage and genetic variations. CGH arrays and SNP mapping. "454"sequencing. Application of the methods for identifying disease-causing genes; applications in diagnosis of human diseases |
DD |
| 21 |
Th |
11/15 |
Genomic methods II Assessing genome-wide changes in gene expression; DNA microarrays, principles and applications. Data analysis and validation; interpretation of microarray data; applications in determining regulatory circuitry; applications in biomarker identification and diagnostics; “customized medicine”? |
DD |
| 22 |
M |
11/19 |
Genomic methods III. Model organisms Model organisms RNAi-based screens; genetic screens and yeast two-hybrid applications. Limitations of cell-based assays; whole-organism screens; validation and data interpretation. Regulatory circuitries and the interactome. |
DD |
| |
Th |
11/22 |
No Class - Thanksgiving Break |
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| 23 |
M |
11/26 |
Modeling whole-genome circuits The Systems Biology approach; simple integrated circuits; complex integrated circuits; genes forming switches and making choices; understanding cancer by circuitry? Can entire organisms be modeled by the systems approach? |
DD |
| 24 |
Th |
11/29 |
Student presentations. |
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| 24 |
M |
12/3 |
Student presentations. |
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| 25 |
Th |
12/6 |
Student presentations. |
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| 29 |
M |
12/10 |
Final Exam |
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| Grading |
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Take-Home Exam 25% |
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4 or 5 Quizzes 25% |
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Participation 15% |
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Final Exam 35% |
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