The Chromatin, Epigenetics and 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) coupled with sequencing (ChIP-seq), reporter assays of enhancer activity, and RNA analysis. They will apply a basic pipeline to analyze sequencing results and will discuss current informatics strategies. Students will isolate transcription factor complexes and assess their activity in functional assays, and will knock-down specific factors using RNAi and evaluate the effects on gene expression.
This course will provide the basic concepts behind different methods to analyze the chromatin architecture of the genome. Students will perform Chromosome Conformation Capture (3C) experiments, together with other approaches aimed to interrogate the 3D organization of genomes. Moreover, we will discuss the computational methods required to analyze these data.
Students will learn how to assemble recombinant chromatin and use biophysical methods such as FRET to assay the activity of chromatin remodeling enzymes. They will also learn principles of enzyme kinetics and will apply these to quantify the remodeling reactions.
Given the broad biological roles for DNA-binding transcription factors, and emerging roles of non-coding RNAs in transcription regulation, Electrophoretic Mobility Shift Assays (EMSAs) are again becoming widely used for assessing transcription factor binding to regulatory DNA or RNA elements. Students will learn how to perform and interpret EMSA experiments, using both microscale thermophoresis and gel-based methods.
Experience with basic recombinant DNA techniques is a prerequisite for admission to this course. Lectures by the instructors will cover the current state of the gene expression field, 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.