01:694:413 Chromatin and Epigenomics

Prerequisites

01:447:384 or 01:694:408 or 01:146:478

Course Syllabus:

Fall 2024 (subject to change)

Lesson Plan

1. Introduction [SG]
2. Nucleosome I [SG]
3. Nucleosome II [SG]
4. ATP-dependent nucleosome remodeling [SG]
5. Histone modification I [SG]
6. Histone modification II and histone variants [SG]
7. DNA methylation [SG]
8. Chromatin and cancer [SG] 
9. Review [SG]
10. Guest lecture by Dr. Simone Sidoli, “Proteomics for chromatin biology”
11. Techniques in Epigenomics [MZ]
12. Maintenance of epigenetic marks. [MZ]
13. Genome architecture [MZ]
14. Genomic programming and Imprinting [MZ]
15. Polycomb mechanisms [MZ]
16. Guest lecture by Dr. Marc Gartenberg (RWJMS), 
17. Dosage compensation [MZ]
18. Constitutive Heterochromatin [MZ]
19. RNAi as a heterochromatin signal [MZ]
20. Guest lecture by Dr. Mike Hampsey (RWJMS)
21. Guest lecture by Dr. Kevin Monahan (MBB)
22. Nuclear RNAi in C. elegans [SG]
23. piRNA [MZ]

Course Satisfies Learning Goals

• Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.
• Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
• Students demonstrate the ability to communicate their research and findings orally through seminar and poster presentations and through written research papers.

Exams, Assignments, and Grading Policy

60% Exams (20% each)- Each exam will cover one of the sections, as well as the corresponding guest lecture. The format of the exams may vary between instructors. 

10% Participation- In lectures as well as other student presentations)

30% Student Presentation- Each group (2 students) will be assigned a research article at the beginning of the course. Both members of the team must participate in reading, analyzing and digesting the paper. They (as a team) will submit their written answers to a set of questions (see below) one month before the presentation.

Each group will make an appointment with a faculty member to rehearse their presentation 2 weeks before the scheduled presentation date.  At this meeting, the students will present written answers to a set of questions described below. The faculty member will provide feedback for the students to revise their presentation. The quality of the team preparation for this meeting, and how well the students incorporate faculty feedback into their presentation will become part of the grade for the student presentation section.

Each classroom presentation will consist of 20 minutes to present slides. The two team members will generally alternate in presenting the material. Additional 10 minutes after the presentation will be reserved for questions from the instructors and the other students. We encourage you to rehearse the final presentation to ensure a good time management.

Presentations should introduce the problem the paper is trying to address, give a brief overview of the techniques used (unless they are very common, like RT-PCR or Southern blotting), a rundown of the major results and conclusions, and present a critique of the paper’s strong and weak points. Do not attempt to discuss every single experiment but focus on the major issues. Remember that you only have 10 minutes each to present the paper, so be brief and to the point. The slides or transparencies should be free of superfluous clutter and clear enough to stand on their own. In order to fully understand the paper and the problem the students should be prepared to read and analyze the most important previous literature that the paper refers to. Questions from the audience and instructors may also refer to issues that the paper doesn’t cover directly but are pertinent to their conclusions, especially if they have been covered in class.

Questions (written answers are due three weeks one month before the presentation and should usually involve 4-5 pages):

Introduction:

• What are the main questions that the paper is trying to answer?
• What information is necessary to understand the main question addressed by the paper?
• What system is used by the study? Why?
• What are the specific discoveries made by the study? What is the most important finding?
• What is the significance to the field?

Methods:

• What techniques are used to address the questions?
• What are the advantages of the techniques?
• Can you think of an alternative technique?

Results:

• How do you describe the results that support the major conclusion? (For example: what do the bands in each lane of a gel represent? What are the controls? What are the axes of graphs?)
• Do you have any alternative interpretations?

Discussion:

• Do the experiments support the stated goals and conclusions?
• What models do the authors propose based on the finding?
• What are the new questions raised by the finding? 
• Are there any medical implications? 

Course Materials

All course materials will be posted on the Canvas site

Course Closed?  

If 694:413 is closed please contact This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.

Faculty

Co-Coordinator: This email address is being protected from spambots. You need JavaScript enabled to view it.
                          Phone: 445-0824
                          Office: Nelson A123
                          Office hours: By Appointment

Co-Coordinator: This email address is being protected from spambots. You need JavaScript enabled to view it.
                           Phone: 445-1497
                          Office: Nelson A133
                          Office hours: By Appointment

** All information is subject to change at the discretion of the course coordinator.