The Chromatin, Epigenetics & Gene Expression course is designed for students, postdocs, and principal investigators who have recently ventured into the exciting area of gene regulation. Emphasis will be placed on exposing students to a broad array of methodologies to study gene regulation, chromatin structure and dynamics, including both state-of-the-art and well-developed methods.
Students will perform widely used techniques such as:
- Chromatin immunoprecipitation (ChIP)
- ChIP coupled with sequencing (ChIP-seq)
- Chromatin accessibiliy assays (ATAC-seq)
- RNA expression analysis (RT-qPCR, RNA-seq)
- Electrophoretic Mobility Shift Assay (EMSA)
- Chromatin Biochemistry
Students will perform ChIP-seq and ATAC-seq and apply a basic pipeline to analyze their genomic results.
Students will learn about state-of-the-art genetic perturbation strategies. They will perform two of these methods to reduce or eliminate the expression of a gene of interest: RNA interference(RNAi), rapidly inducible degrons (dTAG), and CRISPR-Cas9 targeted disruption. Further, students will compare how each method affects gene expression and function.
Students will learn how to assemble recombinant chromatin with modified histones and test specificity of epigenetic “reader” proteins and enzymes that modify chromatin. Quantitative methods will be used to analyze activity and selectivity for specific substrates.
This course will also provide the basic concepts behind different methods to analyze the chromatin architecture of the genome. Moreover, we will discuss the computational methods required to analyze data concerning three-dimensional chromatin architecture.
Experience with basic recombinant DNA and molecular biology techniques is a prerequisite for admission to this course. Lectures by the instructors will cover the current state of the gene expression and epigenetics fields, theoretical aspects of the methodology, and broader issues regarding strategies for investigating the regulation of gene expression in eukaryotes. Emphasis will be placed on advantages and limitations of specific techniques, and data interpretation. Each evening, an invited speaker who is an expert in the field will present their work and interact with students. The students are encouraged and expected to actively participate in these discussions, and to take advantage of the many opportunities to network and receive input on their projects and future plans.
Prior Year Invited Speakers:
Karen Adelman, Harvard Medical School, Boston, MA
Ioannis Aifantis, HHMI/NYU School of Medicine, New York, NY
Kate Alexander, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY;
Effie Apostolou, Weill Cornell Medicine, New York, NY
Hector Franco, Univ of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico;
Melissa Harrison, University of Wisconsin Madison, Madison, WI
Erica Larschan, Brown University, Needham, MA
Michael Levine, Princeton University, Princeton, CA
Kristen Lynch, University of Pennsylvania, Philadelphia, PA
Geeta Narlikar, University of California, San Francisco, San Francisco, CA
Robert Roeder, The Rockefeller University, New York, NY
Ali Shilatifard, Northwestern University, Chicago, IL
Lori Sussel, Barbara Davis Center for Childhood Diabetes and the University of Colorado, Aurora, CO
Dylan Taatjes, CU Boulder, Boulder, United States
Seychelle Vos, Massachusetts Institute of Technology, Cambridge, MA