Reading material
Textbooks
Table of Contents from:
Epigenetics by Allis, Jenuwein and Reinberg. 2007 CSH press
This book is on reserve in the library.
Sweatt, J. David, MJ Meaney, EJ Nestler, and S Akbarian (2013) Epigenetic Regulation in the Nervous System. Basic Mechanisms and Clinical Impact, Academic Press <-- Available electronically from the library.
Handbook of Epigenetics. The New Molecular and Medical Genetics. 2011. Elsevier Trygve Tollefsbol editor. <--- This book is on reserve in the library.
This one is NOT part of a reading assignment.
Here is a chapter for those of you who need a refresher course on some molecular techniques. At least look at the pictures. Basic Tools of Recombinant DNA.pdf. This is chapter 4 from Recombinant DNA Genes and Genomes - a short course by Watson, Myers, Caudy and Witkowski. 3rd edition. It provides an easy to digest refresher on a variety of molecular techniques. Use it as a resource if necessary.
Reading material before Exam 1.
Chapter 2 A brief history of epigenetics in Epigenetics by Allis, Jenuwein and Reinberg CSHL Press 2007 Ch2BriefHistoryEpigenetics.pdf
Chapter 1 from Sweatt, J. David, MJ Meaney, EJ Nestler, and S Akbarian (2013) Epigenetic Regulation in the Nervous System. Basic Mechanisms and Clinical Impact, Academic Press Ch 1 Overview.pdf <-- Entire book is available on the UT library website.
Chapter 3 Overview and Concepts in the book Epigenetics by Allis, Jenuwein and Reinberg CSHL Press 2007 Ch3 Overview Concepts.pdf
Review article: Heintzman, ND, Ren, B (2007) The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cell Mol Life Sci, 64:386–400. Heintzman & Ren 2007.pdf <---- In this paper TAF1=TAFII150 and TAF2=TAFII250.
Ch 13 Chromatin structure and transcription Weaver emb.pdf
Reference material. Scan and plan on referring to it throughout the semester as needed.
Section I: Molecular Mechanisms of Epigenetics. From Handbook of Epigenetics. 2011. Chapters 2 and 3.
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Material for group of six student presentations.
Student groups give powerpoint presentations on these topics.
The chapters below will serve as guidelines. You will need to use some of the references to understand the techniques.
If you are doing chapter 8 please scan chapter 9 to avoid redundancy and vice versa.
Each group consists of 3 people. Each person must speak for 10 minutes - NO MORE!!!
DNA methylation assays About 30 minutes
Starting point -> Chapter 8 Analysis of Gene-specific DNA methylation. From Handbook of Epigenetics. 2011. Chapter 8 Tollefsbol.pdf
For your presentation, please organize the talks according to the underlying principle.
I do not expect everyone to memorize each acronym but to understand how things are done. Then emphasize the most common techniques used in 2013. Group all of the uncommon ones together and mention the most interesting ones. Try to identify which techniques will be in heavy use in the future.
Give real examples in which something interesting was found.
This is the presentation from the 2011 class. Use it to help you get started. A fine presentation but they did not distinguish between common and rarely used approaches because I did not tell them to.
Methylation Assay Presentation from 2011.
Here is the presentation from Epigenetics 2012. This group also had slightly different directions than you do.
Gene_Specific_Group_Presentation.pptx
Genome-wide DNA methylation assays About 30 minutes
Starting point -> Chapter 9 Methods for assessing genome-wide DNA methylation. From Handbook of Epigenetics. 2011. Chapter 9 Tollefsbol.pdf
For your presentation, please organize the talks according to the underlying principle.
I do not expect everyone to memorize each acronym but to understand how things are done. Then emphasize the most common techniques used in 2013. Group all of the uncommon ones together and mention the most interesting ones. Try to identify which techniques will be in heavy use in the future.
Give real examples in which something interesting was found.
This is the presentation from the 2011 class. Use it to help you get started. A fine presentation but they did not distinguish between common and rarely used approaches because I did not tell them to.
Genomewide methylation assays.pdf from 2011.
Here is the presentation from Epigenetics 2012.
Genome-Wide DNA Methylation Talk SP12.pptx
Use these help sheets while reading the chapter.
HELP SHEET 1 FOR THE PRESENTERS.
HELP Sheet 2 for the presenters.
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Reading material after Exam 1 and before Exam 2.
Epigenetics by Allis (on reserve in the life science library): Chapter 4 Epigenetics in Saccharomyces cerevisiae.pdf
Alternative chapter to Chapter 4 is: Cold Spring Harb Perspect Biol-2013-Grunstein-.pdf
Chapter 8 RNAi and Heterochromatin.pdf in Epigenetics by Allis (on reserve in the life science library): Chapter 8 RNAi and Heterochromatin.pdf
I noticed that some of my slides directly correlate to pages from Chapter 6 of Allis. Therefore, here is this chapter in case you want to look at the Allis’s explanation. Chapter 6 Schizosaccharomyces pombe y Neurospora crassa.pdf
Next poster assignment be made today. Poster assignment
Heintzman, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature, 459:108–112.
Heintzman, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet, 39:311–318.
Topic Stress.
Background but not assigned. Fill in gaps if you need to.
Champagne, FA, Francis, DD, Mar, A, Meaney, MJ (2003) Variations in maternal care in the rat as a mediating influence for the effects of environment on development. Physiol Behav, 79:359–371.
Meaney, MJ, Szyf, M (2005) Maternal care as a model for experience-dependent chromatin plasticity? Trends Neurosci, 28:456–463.
Reading assignment
Chapter 18 DNA Methylation in mammals.pdf from Allis.
Chapter 24 Transgenerational Epigenetics.pdf from The Handbook of Epigenetics. 2011
Xchromosome inactivation, etc.
Reading assignment. Chapter 17 Dosage Compensation in mammals.pdf
Poster papers
Poster Session 1
Dang, W, Steffen, KK, Perry, R, Dorsey, JA, Johnson, FB, Shilatifard, A, Kaeberlein, M, Kennedy, BK, Berger, SL (2009) Histone H4 lysine 16 acetylation regulates cellular lifespan. Nature, 459:802–807.
Miele, A, Bystricky, K, Dekker, J (2009) Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS Genet, 5:e1000478.
Poster Session 2
Verdel, A, Jia, S, Gerber, S, Sugiyama, T, Gygi, S, Grewal, SI, Moazed, D (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science, 303:672–676.
Volpe, TA, Kidner, C, Hall, IM, Teng, G, Grewal, SI, Martienssen, RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297:1833–1837.
Poster Session 3 <-- X chromosome inactivation and regulation by related mechanisms.
Silva, J. et al. (2003) Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. Dev Cell, 4, 481-495.
Rinn, J.L. et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129, 1311-1323.
Poster Session 4 Topic Stress. <-- I may change these papers.
Weaver, IC, D'Alessio, AC, Brown, SE, Hellstrom, IC, Dymov, S, Sharma, S, Szyf, M, Meaney, MJ (2007) The transcription factor nerve growth factor-inducible protein a mediates epigenetic programming: altering epigenetic marks by immediate-early genes. J Neurosci, 27:1756–1768. Weaver et al nerve growth factor 2007.pdf
Weaver, IC, Cervoni, N, Champagne, FA, D’Alessio, AC, Sharma, S, Seckl, JR, Dymov, S, Szyf, M, Meaney, MJ (2004) Epigenetic programming by maternal behavior. Nat Neurosci, 7:847–854. Weaver Epigenetics 2004.pdf
