Course Description


Syllabus 2014.pdf


Dr. Nigel Atkinson

Office Pat 228

Office hours Wed 1 pm.


This course will focus on a field that is sometimes called Epigenetics. I say sometimes because the recent reincarnation of this field is rapidly evolving. In addition, there are older incarnations of this field that have different expectations and different definitions. Many groups are avoiding the confusion by avoiding the term epigenetics and only using terms like DNA methylation, histone modification, chromosome remodeling,  e.t.c. In this course we will consider as epigenetic modifications to chromatin that alter gene expression. These modifications may be covalent changes to DNA or histones or even non-coding RNA.


















What will we do in this course?

1.    Lecture and Poster Session Format

I will lecture on a topic a bit.

You will read papers on the topic.

You will almost always work in small groups.

At first you will study the papers in class and out of class.

You will present a papers in a classroom poster session.

2.    Poster sessions

I believe that students most easily learn stuff when you they are called upon to present it. However, I think that powerpoint presentations allow people to present stuff that they do not understand.

Based on my own experience, I think that talking about science is the best way to learn science.* For this reason, I am going to divide you into small groups of about 4 people. You will study a paper with your group. Some studying of papers will be done in class. Why? I want to eaves drop and help you when problems arise.

Then you will construct a poster. We will have a poster session and each person will present the poster for 15 minutes. Sounds impossible but it is only occasionally impossible. I have done this in classes for about 15 years and it can work.

During the poster session students who are not giving a poster are part of the audience. You should listen to the poster presentations. You should ask questions. Why? You will be asked questions about them on the exams. I promise you that the easiest way to learn the material is to have the poster presenters teach it to you.

  1. *This does not rule out some memorization. To talk about science you have to have some details in memory.

3.   Class project

Undergraduates must choose ONE of the two possible projects.

GRADUATE STUDENTS must do two projects.

Group project - write an authoritative Wikipedia page on a topic of your choice.

You will form a group of 3 to 4 people. You will all work on the same Wikipedia page.

You must choose a topic that has not been covered in depth in Wikipedia. I expect it to be authoritative, up to date, interesting, and referenced. You may not use other Wikipedia articles in your reference section although you may link to them in the text. You should try to include summary figures. This is a project and should involve writing, editing, polishing and a deep study of the literature on the topic. I expect it to be about 5 to 10 pages when printed not including references.

Here are examples from the 2012 class.

Cancer epigenetics  <-- Group work

Epigenetics in Learning and Memory <-- Group work

Epigenetics in stem cell differentiation <-- Group work

Epigenetics of autism <-- Group work

Epigenetics of cocaine addiction <-- Group work

Ube3a-ATS <-- Work of a single individual

Individual Grant proposal

Some of you may have experimental ideas that you would like to develop. If so then this project is for you.

You may choose to write a grant proposal instead of working on a group project. If you decide to do this you must commit to it since it will be hard to add you to a Wikipedia group later on.

Undergraduates: The grant proposal should be no more than 10 pages of double spaced text - not including the reference list at the end. You will only propose ONE experiment. You may do two if you wish but you only have to do  one.

Graduate Students: 12 pages not including the references.

You will propose TWO experiments. You can do three but you only have to do two.

You will turn in a 1 page summary first. I will comment on it and then the final grant proposal will be due late in the course.

Group project - Use Encode, Modencode, or the Epigenome Browswer to ask an answer a real scientific question.

Write a paper on it.

You can use one of the epigenomics websites to perform a class project. I will provide you with a data set for analysis if you wish. You may also have other sources of data for analysis.

4.   The Encode/Modencode/Human Epigenome Browser Questions

The US government is really big on making epigenetic data universally available. Many people believe that this data can be reanalyzed in new ways that the people who collected the data never foresaw. Much of this analysis has and will involve statistics and programming but some of it involves simple visualization of data. This is all very new and in the big picture we really don’t know what can be accomplished using these databases.

You are going to study one of these three genome browsers. I will ask you questions and give you projects that as a group you will answer. Your final answers for everything will be done on the wiki site.

5.  Wiki lecture notes

This may be the weirdest thing about this course. This grew out of the idea that originally there was not a comprehensive text for an epigenetics couse. Allis is great but dated, Tollefsbol is newer, good in places, horrible in others, and has a nasty tendency to contradict itself. Originally, I was going to lecture, have you study papers, and write your own text book as a group. Well, this was far to ambitious, but a reasonable compromise that I came up with was the Wiki lecture notes.

A wiki is a document that a group of people can all write together. You are most familiar with it as Wikipedia - the encyclopedia written by the masses. You are going to write a set of lecture notes using the software that runs Wikipedia. Some of you will write notes, some will clarify, some will organize.

Anything that you can type or draw you can put in there. You cannot put figures downloaded from the net or copied from a textbook in it. You cannot copy and paste my figures into it. I won’t allow it.

What is your motivation for doing this?

Motivation 1 - you can take the final version of the wiki notes with you to the exams. No other notes are allowed.

One thing that you may be worrying about is that a subset of the class might do most of the work on the notes and students who do not contribute might make use of the material. Don’t worry about it. In the past when I have done this the students who contribute end up with a set of notes that they can rapidly access during an exam. If you have not worked on the notes then they become less useful to you.

Each Lecture we will have ONE raw note taker. I expect them to try to do a good job.

The raw note taker will post their notes (typed, scanned, text messaged, whatever) to the Raw Notes section of the Wiki Notes.

Everyone should update and modify the wiki Lecture Notes to make them the best set of notes possible.

I will let you examine notes made by the previous class.

Motivation 2 - You will become familiar with the easy-to-use wikimedia software. This will make it easier when you write your Wikipedia article.

6.   This wiki stuff sounds like we need to communicate with each other. Yes. The Wiki software has ways to do this. You are probably adept at a variety of tools that are useful for this purpose.

Here is a link to the class mailing list.

  1. 7.   Other small amounts of homework will be given. This homework is not usually very time consuming.

Even though the homework seems insignificant, in the past, some students who were borderline with respect to a grade failed to get the higher grade because they skipped the homework.

8.  Much of your grade is dependent on group work how do I avoid problems?

You may be thinking that either:

  1. 1)Eek! my grade will be partially determined by the performance of my peers. What if they don’t pull their weight? Will I have to do all of the work?

  2. 2)Yay! my grade will be partially determined by the performance of my peers. What if I don’t  pull my weight? Can I get them to do all of the work?

I avoid this problem because:

  1. 1)I am not a dummy. I can usually tell when people are not trying.

  2. 2)The poster presentation requires that you actually know stuff. You are alone.

  3. 3)I give out a peer evaluation forms on a regular basis. If someone is coasting I will find out. You will find out too because I send you your evaluation.

  4. 4)Poster groups are disbanded and reformed with each set of papers.

  5. 5)I can see each and every edit to the Wiki site. Therefore, I will know if one member of a group project is doing all of the work.


This book is on reserve in the library.

Textbook: Epigenetics by Allis, Jenuwein and Reinberg. 2007 CSH press.

Reading material from the literature will also be required.

This book is on reserve in the library.

Textbook: Handbook of Epigenetics. The New Molecular and Medical Genetics. 2011. Elsevier Trygve Tollefsbol editor.

Molecular Biology. Weaver 4th edition.

How will your grade be determined?

Students will have two written exams and various projects.

Students will participate in presentations of scientific papers. There will be 5 poster presentations per semester and a number of lecture type presentations.

  1. 1.Exam 1 - classical exam
    We will cover more material than will be covered on this first exam. Multiple choice and short answer.

    100 point classical multiple choice exam. The purpose will be to make sure that you learn some basic concepts early in the course so that we can have reasonable discussions later. It will cover the nuts and bolts of transcription, transcription regulation and the control of chromatin structure. The purpose really is to have you learn the starting material so that you can appreciate the later material.

    This exam is open wiki.

  1. 2.Second exam - Multiple choice and short answer. This exam is open wiki. The topic of this exam is the various scientific papers that we have been studying.

  1. 3.Wikipedia article, Class Project, or Grant proposal.
    The grant will be 10 (undergrad) or 12 (grad) pages of text DOUBLE SPACED. I will give you a  guide and two examples.

Final grade

The sum of the following divided by 875 and multiplied by 100

Exam 1 (100 points)

Exam 2 (100 points)

Class Project (200 points)

Participation grade (400 points)

Encode/ModEncode/Epigenetic Browser Homework (50 points)

Other Homework grade (25 points)

I will let you know how you are doing as we move through the semester.

Grading scale

I use a 100 point scale for all of my grading. Your final grade will be on a 100 point scale.

The numeric grade to letter grade conversion is:

A = 90-100
B = 80-89.99
C = 70-79.99
D = 60-69.99
F = 50-59.99

Exam schedule is in the Syllabus and on the Exam page which will may include additional information.

The other important stuff that I need to say follows.


Academic Calendar that includes all information about dropping, etc.:


Academic accommodations for students with disabilities:

The University of Texas at Austin provides, upon request, appropriate academic accommodations for qualified students with disabilities. For more information, contact the Office of the Dean of Students at 471-6259, 471-4641 TTY.

Please advise me about any needed accommodations at least two weeks prior to a major examination.

Academic accommodations for religious Holy Days:

As per University policy, accommodations will be made for religious holy days. A student must make the instructor aware of a needed religious-related absence at least fourteen days prior to the class absence or on the first class day for holy days that fall within the first two weeks of the semester.

Any changes to University policy will take precedence over those listed here.

Scholastic Honesty

We have been requested by our Dean to inform all students, in writing, that cheating is against University rules and will not be tolerated.   Any student caught cheating will be reported to the Dean's office and we will make all efforts to see that those students will receive the maximum penalty permitted under University regulations including flogging.